Calcium in PDB 6vfp: Crystal Structure of Human Protocadherin 1 EC1-EC4
Protein crystallography data
The structure of Crystal Structure of Human Protocadherin 1 EC1-EC4, PDB code: 6vfp
was solved by
J.Brasch,
O.J.Harrison,
L.Shapiro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.87 /
3.20
|
|
Space group
|
P 61 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
148.595,
148.595,
149.846,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
22.2 /
26.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin 1 EC1-EC4
(pdb code 6vfp). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Human Protocadherin 1 EC1-EC4, PDB code: 6vfp:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 1 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca505
b:0.3
occ:1.00
|
OE1
|
A:GLU61
|
2.3
|
0.7
|
1.0
|
|
OD2
|
A:ASP106
|
2.3
|
98.3
|
1.0
|
|
OD1
|
A:ASP59
|
2.4
|
0.6
|
1.0
|
|
OE1
|
A:GLU9
|
2.4
|
0.7
|
1.0
|
|
OE2
|
A:GLU10
|
2.4
|
0.5
|
1.0
|
|
O
|
A:HOH606
|
2.4
|
0.2
|
1.0
|
|
CG
|
A:ASP59
|
3.0
|
0.1
|
1.0
|
|
HG3
|
A:GLU10
|
3.0
|
0.8
|
1.0
|
|
HG2
|
A:GLU10
|
3.1
|
0.8
|
1.0
|
|
CD
|
A:GLU10
|
3.2
|
0.2
|
1.0
|
|
CG
|
A:GLU10
|
3.3
|
0.5
|
1.0
|
|
CD
|
A:GLU9
|
3.3
|
0.7
|
1.0
|
|
CG
|
A:ASP106
|
3.4
|
0.9
|
1.0
|
|
CD
|
A:GLU61
|
3.4
|
0.0
|
1.0
|
|
H
|
A:GLU61
|
3.4
|
0.6
|
1.0
|
|
OD2
|
A:ASP59
|
3.4
|
0.0
|
1.0
|
|
HA
|
A:ASP59
|
3.5
|
0.9
|
1.0
|
|
HB2
|
A:GLU61
|
3.6
|
0.8
|
1.0
|
|
OE2
|
A:GLU9
|
3.7
|
0.3
|
1.0
|
|
H
|
A:ARG60
|
3.7
|
0.4
|
1.0
|
|
OD1
|
A:ASP106
|
3.8
|
0.5
|
1.0
|
|
CB
|
A:ASP59
|
4.0
|
0.6
|
1.0
|
|
OE2
|
A:GLU61
|
4.0
|
0.9
|
1.0
|
|
CA
|
A:ASP59
|
4.1
|
0.8
|
1.0
|
|
N
|
A:ARG60
|
4.2
|
0.8
|
1.0
|
|
HB2
|
A:ASP59
|
4.2
|
0.1
|
1.0
|
|
HB2
|
A:GLU9
|
4.2
|
0.9
|
1.0
|
|
N
|
A:GLU61
|
4.3
|
0.7
|
1.0
|
|
CB
|
A:GLU61
|
4.3
|
0.2
|
1.0
|
|
CG
|
A:GLU61
|
4.4
|
0.7
|
1.0
|
|
OE1
|
A:GLU10
|
4.4
|
0.6
|
1.0
|
|
CG
|
A:GLU9
|
4.5
|
0.6
|
1.0
|
|
C
|
A:ASP59
|
4.5
|
0.4
|
1.0
|
|
OD1
|
A:ASN107
|
4.5
|
0.9
|
1.0
|
|
HG3
|
A:GLU9
|
4.5
|
0.6
|
1.0
|
|
HG2
|
A:GLU61
|
4.6
|
0.2
|
1.0
|
|
CB
|
A:ASP106
|
4.6
|
0.5
|
1.0
|
|
CA
|
A:CA509
|
4.6
|
0.0
|
1.0
|
|
HB2
|
A:ASP106
|
4.7
|
0.0
|
1.0
|
|
O
|
A:HOH605
|
4.7
|
94.8
|
1.0
|
|
HB3
|
A:ARG60
|
4.7
|
0.2
|
1.0
|
|
CB
|
A:GLU10
|
4.8
|
0.6
|
1.0
|
|
HB3
|
A:ASP59
|
4.8
|
0.1
|
1.0
|
|
HD11
|
A:ILE104
|
4.9
|
0.7
|
1.0
|
|
H
|
A:GLY62
|
4.9
|
0.5
|
1.0
|
|
CB
|
A:GLU9
|
4.9
|
0.2
|
1.0
|
|
HB3
|
A:ASP106
|
4.9
|
0.0
|
1.0
|
|
CA
|
A:GLU61
|
5.0
|
0.7
|
1.0
|
|
Calcium binding site 2 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 2 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca506
b:0.9
occ:1.00
|
OD2
|
A:ASP218
|
2.2
|
95.0
|
1.0
|
|
OE1
|
A:GLU184
|
2.3
|
96.7
|
1.0
|
|
OD1
|
A:ASP182
|
2.3
|
0.5
|
1.0
|
|
OE1
|
A:GLU122
|
2.4
|
0.6
|
1.0
|
|
O
|
A:HOH607
|
2.4
|
98.7
|
1.0
|
|
O
|
A:HOH603
|
2.4
|
0.8
|
1.0
|
|
CG
|
A:ASP218
|
3.2
|
0.7
|
1.0
|
|
HA
|
A:ASP182
|
3.3
|
0.7
|
1.0
|
|
CD
|
A:GLU122
|
3.3
|
0.8
|
1.0
|
|
CG
|
A:ASP182
|
3.4
|
0.6
|
1.0
|
|
H
|
A:GLU184
|
3.4
|
0.4
|
1.0
|
|
CD
|
A:GLU184
|
3.4
|
96.5
|
1.0
|
|
OD1
|
A:ASP218
|
3.5
|
0.9
|
1.0
|
|
H
|
A:ARG183
|
3.6
|
1.0
|
1.0
|
|
HB2
|
A:GLU184
|
3.6
|
0.2
|
1.0
|
|
HD21
|
A:ASN219
|
3.7
|
0.6
|
1.0
|
|
OE2
|
A:GLU122
|
3.8
|
0.9
|
1.0
|
|
CA
|
A:ASP182
|
4.0
|
0.6
|
1.0
|
|
HD22
|
A:ASN219
|
4.0
|
0.6
|
1.0
|
|
N
|
A:ARG183
|
4.0
|
87.5
|
1.0
|
|
CB
|
A:ASP182
|
4.1
|
0.8
|
1.0
|
|
HB2
|
A:ASP182
|
4.1
|
0.3
|
1.0
|
|
OE2
|
A:GLU184
|
4.1
|
0.6
|
1.0
|
|
CA
|
A:CA510
|
4.2
|
96.5
|
1.0
|
|
ND2
|
A:ASN219
|
4.2
|
0.2
|
1.0
|
|
N
|
A:GLU184
|
4.2
|
0.3
|
1.0
|
|
OD2
|
A:ASP182
|
4.3
|
1.0
|
1.0
|
|
HD21
|
A:ASN123
|
4.3
|
0.2
|
1.0
|
|
C
|
A:ASP182
|
4.3
|
0.7
|
1.0
|
|
OD1
|
A:ASN123
|
4.3
|
0.2
|
1.0
|
|
HB2
|
A:GLU122
|
4.4
|
0.5
|
1.0
|
|
HG3
|
A:GLU122
|
4.4
|
0.7
|
1.0
|
|
CB
|
A:GLU184
|
4.4
|
0.2
|
1.0
|
|
CG
|
A:GLU122
|
4.4
|
0.1
|
1.0
|
|
CG
|
A:GLU184
|
4.4
|
0.6
|
1.0
|
|
CB
|
A:ASP218
|
4.5
|
0.8
|
1.0
|
|
HB2
|
A:ASP218
|
4.6
|
0.6
|
1.0
|
|
HB3
|
A:ARG183
|
4.7
|
0.9
|
1.0
|
|
HG2
|
A:GLU184
|
4.7
|
0.1
|
1.0
|
|
HB3
|
A:ASP218
|
4.8
|
0.6
|
1.0
|
|
HG1
|
A:THR216
|
4.8
|
0.0
|
1.0
|
|
ND2
|
A:ASN123
|
4.9
|
0.2
|
1.0
|
|
CB
|
A:GLU122
|
4.9
|
0.7
|
1.0
|
|
HB3
|
A:ASP182
|
5.0
|
0.3
|
1.0
|
|
CA
|
A:GLU184
|
5.0
|
0.4
|
1.0
|
|
CG
|
A:ASN123
|
5.0
|
0.8
|
1.0
|
|
Calcium binding site 3 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 3 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca507
b:88.9
occ:1.00
|
OD2
|
A:ASP139
|
2.3
|
0.1
|
1.0
|
|
OD2
|
A:ASP137
|
2.3
|
0.2
|
1.0
|
|
O
|
A:ASN107
|
2.4
|
87.3
|
1.0
|
|
O
|
A:ASN143
|
2.4
|
98.4
|
1.0
|
|
OD1
|
A:ASN105
|
2.4
|
0.7
|
1.0
|
|
OD2
|
A:ASP197
|
2.4
|
82.9
|
1.0
|
|
OD1
|
A:ASP137
|
2.5
|
0.6
|
1.0
|
|
CG
|
A:ASP137
|
2.7
|
0.0
|
1.0
|
|
HB2
|
A:ASP139
|
3.2
|
0.8
|
1.0
|
|
HD3
|
A:PRO109
|
3.3
|
0.0
|
1.0
|
|
HB3
|
A:ASP197
|
3.3
|
0.0
|
1.0
|
|
CG
|
A:ASP139
|
3.4
|
0.1
|
1.0
|
|
CG
|
A:ASP197
|
3.4
|
92.0
|
1.0
|
|
HB2
|
A:ASP197
|
3.5
|
0.0
|
1.0
|
|
CG
|
A:ASN105
|
3.6
|
93.6
|
1.0
|
|
C
|
A:ASN107
|
3.6
|
0.1
|
1.0
|
|
C
|
A:ASN143
|
3.6
|
0.2
|
1.0
|
|
CB
|
A:ASP197
|
3.6
|
0.3
|
1.0
|
|
CB
|
A:ASP139
|
3.8
|
0.3
|
1.0
|
|
H
|
A:ASN107
|
3.8
|
0.3
|
1.0
|
|
HB3
|
A:ASN143
|
3.8
|
0.2
|
1.0
|
|
HA2
|
A:GLY144
|
3.8
|
0.8
|
1.0
|
|
HD21
|
A:ASN105
|
3.9
|
0.7
|
1.0
|
|
HA
|
A:THR108
|
4.1
|
0.4
|
1.0
|
|
HB2
|
A:ARG203
|
4.1
|
0.6
|
1.0
|
|
HB2
|
A:ASN107
|
4.1
|
0.6
|
1.0
|
|
HA
|
A:ASN105
|
4.2
|
0.7
|
1.0
|
|
ND2
|
A:ASN105
|
4.2
|
0.4
|
1.0
|
|
HD2
|
A:ARG203
|
4.2
|
0.2
|
1.0
|
|
H
|
A:ASP139
|
4.2
|
0.9
|
1.0
|
|
CB
|
A:ASP137
|
4.2
|
1.0
|
1.0
|
|
HB3
|
A:ASP139
|
4.2
|
0.8
|
1.0
|
|
CD
|
A:PRO109
|
4.3
|
0.0
|
1.0
|
|
HA
|
A:ASN143
|
4.4
|
0.8
|
1.0
|
|
HG3
|
A:ARG203
|
4.4
|
0.6
|
1.0
|
|
N
|
A:ASN107
|
4.5
|
0.9
|
1.0
|
|
CA
|
A:ASN107
|
4.5
|
0.9
|
1.0
|
|
OD1
|
A:ASP139
|
4.5
|
0.5
|
1.0
|
|
CA
|
A:ASN143
|
4.5
|
0.2
|
1.0
|
|
HB3
|
A:ASP137
|
4.5
|
0.4
|
1.0
|
|
OD1
|
A:ASP197
|
4.5
|
90.8
|
1.0
|
|
N
|
A:GLY144
|
4.5
|
1.0
|
1.0
|
|
N
|
A:THR108
|
4.5
|
0.8
|
1.0
|
|
CA
|
A:GLY144
|
4.6
|
0.2
|
1.0
|
|
CB
|
A:ASN143
|
4.6
|
0.0
|
1.0
|
|
HB2
|
A:ASP137
|
4.6
|
0.4
|
1.0
|
|
CA
|
A:THR108
|
4.7
|
0.8
|
1.0
|
|
N
|
A:PRO109
|
4.7
|
98.5
|
1.0
|
|
CB
|
A:ASN107
|
4.7
|
98.0
|
1.0
|
|
CB
|
A:ASN105
|
4.7
|
0.3
|
1.0
|
|
HD2
|
A:PRO109
|
4.8
|
0.0
|
1.0
|
|
CA
|
A:ASN105
|
4.8
|
93.1
|
1.0
|
|
C
|
A:THR108
|
4.8
|
0.6
|
1.0
|
|
HB3
|
A:ASN107
|
4.9
|
0.6
|
1.0
|
|
HG3
|
A:PRO109
|
4.9
|
0.5
|
1.0
|
|
N
|
A:ASP139
|
4.9
|
96.6
|
1.0
|
|
HB3
|
A:PRO109
|
4.9
|
0.2
|
1.0
|
|
CB
|
A:ARG203
|
5.0
|
0.8
|
1.0
|
|
HA
|
A:ASP137
|
5.0
|
0.1
|
1.0
|
|
CA
|
A:ASP139
|
5.0
|
95.7
|
1.0
|
|
HB2
|
A:ASN143
|
5.0
|
0.2
|
1.0
|
|
CG
|
A:ARG203
|
5.0
|
90.5
|
1.0
|
|
Calcium binding site 4 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 4 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca508
b:0.8
occ:1.00
|
OD2
|
A:ASP423
|
2.3
|
1.0
|
1.0
|
|
OD1
|
A:ASP364
|
2.3
|
0.6
|
1.0
|
|
O
|
A:ASN326
|
2.4
|
0.8
|
1.0
|
|
OD2
|
A:ASP364
|
2.4
|
0.3
|
1.0
|
|
OD1
|
A:ASN324
|
2.4
|
0.2
|
1.0
|
|
OD2
|
A:ASP366
|
2.4
|
0.8
|
1.0
|
|
O
|
A:ASN370
|
2.4
|
0.4
|
1.0
|
|
CG
|
A:ASP364
|
2.6
|
0.3
|
1.0
|
|
CG
|
A:ASP423
|
3.4
|
0.4
|
1.0
|
|
CG
|
A:ASP366
|
3.5
|
0.5
|
1.0
|
|
CG
|
A:ASN324
|
3.6
|
1.0
|
1.0
|
|
C
|
A:ASN326
|
3.6
|
0.1
|
1.0
|
|
C
|
A:ASN370
|
3.6
|
0.3
|
1.0
|
|
HB3
|
A:ASP423
|
3.7
|
0.9
|
1.0
|
|
HA
|
A:ALA327
|
3.7
|
0.5
|
1.0
|
|
HB3
|
A:ASN370
|
3.7
|
0.7
|
1.0
|
|
HD3
|
A:PRO328
|
3.8
|
0.7
|
1.0
|
|
CB
|
A:ASP366
|
3.8
|
0.6
|
1.0
|
|
HB2
|
A:ASP423
|
3.9
|
0.9
|
1.0
|
|
H
|
A:ASN326
|
3.9
|
0.6
|
1.0
|
|
HD21
|
A:ASN324
|
3.9
|
0.1
|
1.0
|
|
CB
|
A:ASP423
|
3.9
|
0.4
|
1.0
|
|
HD22
|
A:LEU429
|
4.0
|
0.7
|
1.0
|
|
H
|
A:ASP366
|
4.0
|
0.2
|
1.0
|
|
HA
|
A:ALA371
|
4.0
|
0.8
|
1.0
|
|
CB
|
A:ASP364
|
4.0
|
0.8
|
1.0
|
|
HB2
|
A:LEU429
|
4.0
|
0.3
|
1.0
|
|
ND2
|
A:ASN324
|
4.2
|
0.1
|
1.0
|
|
HA
|
A:ASN324
|
4.2
|
0.5
|
1.0
|
|
HB2
|
A:ASP364
|
4.3
|
0.2
|
1.0
|
|
HA
|
A:ASN370
|
4.3
|
0.1
|
1.0
|
|
HB3
|
A:ASP364
|
4.4
|
0.2
|
1.0
|
|
CA
|
A:ALA327
|
4.4
|
93.7
|
1.0
|
|
CA
|
A:ASN370
|
4.4
|
0.6
|
1.0
|
|
HB2
|
A:ASN326
|
4.4
|
0.5
|
1.0
|
|
N
|
A:ALA327
|
4.5
|
0.1
|
1.0
|
|
OD1
|
A:ASP423
|
4.5
|
0.7
|
1.0
|
|
CB
|
A:ASN370
|
4.5
|
0.4
|
1.0
|
|
HG3
|
A:PRO328
|
4.5
|
0.4
|
1.0
|
|
N
|
A:ASN326
|
4.6
|
0.7
|
1.0
|
|
OD1
|
A:ASP366
|
4.6
|
0.5
|
1.0
|
|
CA
|
A:ASN326
|
4.6
|
0.2
|
1.0
|
|
CD
|
A:PRO328
|
4.6
|
0.4
|
1.0
|
|
N
|
A:ALA371
|
4.6
|
0.9
|
1.0
|
|
C
|
A:ALA327
|
4.6
|
0.4
|
1.0
|
|
N
|
A:PRO328
|
4.7
|
0.7
|
1.0
|
|
CB
|
A:ASN324
|
4.8
|
0.6
|
1.0
|
|
N
|
A:ASP366
|
4.8
|
1.0
|
1.0
|
|
HB2
|
A:ASN370
|
4.8
|
0.7
|
1.0
|
|
CA
|
A:ALA371
|
4.8
|
0.7
|
1.0
|
|
CA
|
A:ASN324
|
4.8
|
0.3
|
1.0
|
|
CD2
|
A:LEU429
|
4.9
|
0.1
|
1.0
|
|
CB
|
A:ASN326
|
4.9
|
0.6
|
1.0
|
|
CB
|
A:LEU429
|
4.9
|
0.4
|
1.0
|
|
CA
|
A:ASP366
|
5.0
|
100.0
|
1.0
|
|
Calcium binding site 5 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 5 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca509
b:0.0
occ:1.00
|
OD1
|
A:ASP106
|
2.3
|
0.5
|
1.0
|
|
OD1
|
A:ASP103
|
2.3
|
99.1
|
1.0
|
|
OE2
|
A:GLU61
|
2.3
|
0.9
|
1.0
|
|
OD1
|
A:ASP139
|
2.4
|
0.5
|
1.0
|
|
O
|
A:ILE104
|
2.4
|
0.9
|
1.0
|
|
OE2
|
A:GLU9
|
2.4
|
0.3
|
1.0
|
|
CD
|
A:GLU61
|
2.8
|
0.0
|
1.0
|
|
OE1
|
A:GLU61
|
2.9
|
0.7
|
1.0
|
|
H
|
A:ILE104
|
3.0
|
0.2
|
1.0
|
|
H
|
A:ASP106
|
3.1
|
0.2
|
1.0
|
|
CG
|
A:ASP139
|
3.4
|
0.1
|
1.0
|
|
CG
|
A:ASP103
|
3.4
|
0.0
|
1.0
|
|
CG
|
A:ASP106
|
3.4
|
0.9
|
1.0
|
|
HH11
|
A:ARG60
|
3.5
|
0.2
|
1.0
|
|
C
|
A:ILE104
|
3.5
|
0.8
|
1.0
|
|
HA
|
A:ASP139
|
3.5
|
0.8
|
1.0
|
|
CD
|
A:GLU9
|
3.6
|
0.7
|
1.0
|
|
HH12
|
A:ARG60
|
3.7
|
0.2
|
1.0
|
|
N
|
A:ILE104
|
3.7
|
99.3
|
1.0
|
|
NH1
|
A:ARG60
|
3.8
|
0.7
|
1.0
|
|
HG13
|
A:ILE104
|
3.9
|
0.7
|
1.0
|
|
HB3
|
A:ASP139
|
3.9
|
0.8
|
1.0
|
|
CG
|
A:GLU61
|
3.9
|
0.7
|
1.0
|
|
OD2
|
A:ASP103
|
3.9
|
0.7
|
1.0
|
|
N
|
A:ASP106
|
4.0
|
84.3
|
1.0
|
|
OD2
|
A:ASP106
|
4.0
|
98.3
|
1.0
|
|
OD1
|
A:ASN107
|
4.0
|
0.9
|
1.0
|
|
HG2
|
A:GLU61
|
4.0
|
0.2
|
1.0
|
|
CB
|
A:ASP139
|
4.0
|
0.3
|
1.0
|
|
HG3
|
A:GLU61
|
4.1
|
0.2
|
1.0
|
|
HA
|
A:ASN105
|
4.1
|
0.7
|
1.0
|
|
OE1
|
A:GLU9
|
4.1
|
0.7
|
1.0
|
|
CA
|
A:ASP139
|
4.2
|
95.7
|
1.0
|
|
CA
|
A:ILE104
|
4.3
|
0.5
|
1.0
|
|
HA
|
A:ASP103
|
4.3
|
0.4
|
1.0
|
|
OD2
|
A:ASP139
|
4.3
|
0.1
|
1.0
|
|
HB3
|
A:ARG60
|
4.4
|
0.2
|
1.0
|
|
HD3
|
A:ARG60
|
4.5
|
0.5
|
1.0
|
|
HD12
|
A:ILE104
|
4.5
|
0.7
|
1.0
|
|
N
|
A:ASN105
|
4.5
|
99.2
|
1.0
|
|
CB
|
A:ASP106
|
4.6
|
0.5
|
1.0
|
|
CB
|
A:ASP103
|
4.6
|
0.5
|
1.0
|
|
HB2
|
A:ASN107
|
4.6
|
0.6
|
1.0
|
|
CA
|
A:CA505
|
4.6
|
0.3
|
1.0
|
|
CA
|
A:ASN105
|
4.7
|
93.1
|
1.0
|
|
HD22
|
A:ASN143
|
4.7
|
0.3
|
1.0
|
|
H
|
A:ASN107
|
4.7
|
0.3
|
1.0
|
|
CG1
|
A:ILE104
|
4.7
|
0.1
|
1.0
|
|
C
|
A:ASP103
|
4.7
|
0.5
|
1.0
|
|
CA
|
A:ASP106
|
4.8
|
99.3
|
1.0
|
|
HG2
|
A:GLU9
|
4.8
|
0.6
|
1.0
|
|
CA
|
A:ASP103
|
4.8
|
0.8
|
1.0
|
|
CG
|
A:GLU9
|
4.8
|
0.6
|
1.0
|
|
H
|
A:ALA140
|
4.8
|
0.2
|
1.0
|
|
C
|
A:ASN105
|
4.9
|
84.2
|
1.0
|
|
HB3
|
A:ASP106
|
4.9
|
0.0
|
1.0
|
|
HB2
|
A:ASP103
|
4.9
|
0.4
|
1.0
|
|
CZ
|
A:ARG60
|
4.9
|
0.1
|
1.0
|
|
HB2
|
A:ASP139
|
5.0
|
0.8
|
1.0
|
|
CD1
|
A:ILE104
|
5.0
|
98.9
|
1.0
|
|
N
|
A:ASN107
|
5.0
|
0.9
|
1.0
|
|
HA
|
A:ILE104
|
5.0
|
0.2
|
1.0
|
|
N
|
A:ASP139
|
5.0
|
96.6
|
1.0
|
|
Calcium binding site 6 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 6 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca510
b:96.5
occ:1.00
|
OD1
|
A:ASP218
|
2.3
|
0.9
|
1.0
|
|
OD1
|
A:ASP215
|
2.3
|
99.2
|
1.0
|
|
OE2
|
A:GLU122
|
2.4
|
0.9
|
1.0
|
|
OE2
|
A:GLU184
|
2.4
|
0.6
|
1.0
|
|
OD1
|
A:ASP251
|
2.4
|
0.0
|
1.0
|
|
O
|
A:THR216
|
2.5
|
0.6
|
1.0
|
|
HH11
|
A:ARG183
|
2.7
|
0.4
|
1.0
|
|
CD
|
A:GLU184
|
3.0
|
96.5
|
1.0
|
|
OE1
|
A:GLU184
|
3.0
|
96.7
|
1.0
|
|
H
|
A:THR216
|
3.2
|
0.7
|
1.0
|
|
H
|
A:ASP218
|
3.3
|
0.3
|
1.0
|
|
CD
|
A:GLU122
|
3.3
|
0.8
|
1.0
|
|
CG
|
A:ASP218
|
3.4
|
0.7
|
1.0
|
|
CG
|
A:ASP251
|
3.5
|
0.7
|
1.0
|
|
HE
|
A:ARG183
|
3.5
|
0.2
|
1.0
|
|
HA
|
A:ASP251
|
3.5
|
0.9
|
1.0
|
|
NH1
|
A:ARG183
|
3.5
|
0.3
|
1.0
|
|
CG
|
A:ASP215
|
3.6
|
0.2
|
1.0
|
|
OE1
|
A:GLU122
|
3.6
|
0.6
|
1.0
|
|
HD22
|
A:ASN219
|
3.6
|
0.6
|
1.0
|
|
C
|
A:THR216
|
3.6
|
0.8
|
1.0
|
|
N
|
A:THR216
|
3.8
|
0.9
|
1.0
|
|
HG1
|
A:THR216
|
3.9
|
0.0
|
1.0
|
|
HA
|
A:ASP215
|
3.9
|
0.7
|
1.0
|
|
OD2
|
A:ASP218
|
4.0
|
95.0
|
1.0
|
|
HH12
|
A:ARG183
|
4.0
|
0.4
|
1.0
|
|
HB3
|
A:ASP251
|
4.0
|
0.3
|
1.0
|
|
HB3
|
A:ARG183
|
4.1
|
0.9
|
1.0
|
|
CB
|
A:ASP251
|
4.1
|
0.7
|
1.0
|
|
NE
|
A:ARG183
|
4.1
|
0.0
|
1.0
|
|
CA
|
A:CA506
|
4.2
|
0.9
|
1.0
|
|
N
|
A:ASP218
|
4.2
|
91.1
|
1.0
|
|
CZ
|
A:ARG183
|
4.3
|
0.4
|
1.0
|
|
CA
|
A:ASP251
|
4.3
|
0.5
|
1.0
|
|
CA
|
A:THR216
|
4.3
|
0.4
|
1.0
|
|
OD2
|
A:ASP215
|
4.3
|
0.7
|
1.0
|
|
OG1
|
A:THR216
|
4.3
|
0.2
|
1.0
|
|
ND2
|
A:ASN219
|
4.4
|
0.2
|
1.0
|
|
OD2
|
A:ASP251
|
4.4
|
0.6
|
1.0
|
|
HA
|
A:ASN217
|
4.4
|
0.6
|
1.0
|
|
CG
|
A:GLU184
|
4.5
|
0.6
|
1.0
|
|
CA
|
A:ASP215
|
4.5
|
0.4
|
1.0
|
|
C
|
A:ASP215
|
4.6
|
1.0
|
1.0
|
|
CB
|
A:ASP215
|
4.6
|
0.2
|
1.0
|
|
CB
|
A:ASP218
|
4.6
|
0.8
|
1.0
|
|
HD21
|
A:ASN219
|
4.6
|
0.6
|
1.0
|
|
H
|
A:ASN219
|
4.7
|
0.7
|
1.0
|
|
HB3
|
A:ASP218
|
4.7
|
0.6
|
1.0
|
|
HG3
|
A:GLU184
|
4.7
|
0.1
|
1.0
|
|
N
|
A:ASN217
|
4.7
|
95.2
|
1.0
|
|
HB2
|
A:ASN219
|
4.7
|
0.1
|
1.0
|
|
HG2
|
A:GLU184
|
4.7
|
0.1
|
1.0
|
|
CG
|
A:GLU122
|
4.7
|
0.1
|
1.0
|
|
H
|
A:GLN252
|
4.8
|
0.1
|
1.0
|
|
HG2
|
A:GLU122
|
4.8
|
0.7
|
1.0
|
|
HD22
|
A:ASN255
|
4.8
|
0.2
|
1.0
|
|
HB2
|
A:ASP215
|
4.8
|
0.8
|
1.0
|
|
CA
|
A:ASP218
|
4.9
|
99.5
|
1.0
|
|
H
|
A:GLU184
|
4.9
|
0.4
|
1.0
|
|
CA
|
A:ASN217
|
5.0
|
98.0
|
1.0
|
|
CB
|
A:THR216
|
5.0
|
0.9
|
1.0
|
|
Calcium binding site 7 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 7 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca511
b:0.1
occ:1.00
|
OD2
|
A:ASP249
|
2.2
|
0.7
|
1.0
|
|
O
|
A:ASN255
|
2.3
|
90.1
|
1.0
|
|
OD2
|
A:ASP304
|
2.3
|
0.4
|
1.0
|
|
OD1
|
A:ASN217
|
2.3
|
0.7
|
1.0
|
|
OD2
|
A:ASP251
|
2.4
|
0.6
|
1.0
|
|
O
|
A:ASN219
|
2.4
|
86.3
|
1.0
|
|
CG
|
A:ASP249
|
2.9
|
0.1
|
1.0
|
|
OD1
|
A:ASP249
|
3.0
|
0.7
|
1.0
|
|
HB2
|
A:ASP251
|
3.2
|
0.3
|
1.0
|
|
HB3
|
A:ASN255
|
3.3
|
0.4
|
1.0
|
|
CG
|
A:ASP251
|
3.4
|
0.7
|
1.0
|
|
CG
|
A:ASP304
|
3.4
|
92.0
|
1.0
|
|
C
|
A:ASN255
|
3.5
|
0.9
|
1.0
|
|
CG
|
A:ASN217
|
3.5
|
97.0
|
1.0
|
|
C
|
A:ASN219
|
3.6
|
96.7
|
1.0
|
|
HB3
|
A:ASP304
|
3.6
|
0.2
|
1.0
|
|
HB2
|
A:ASP304
|
3.6
|
0.2
|
1.0
|
|
CB
|
A:ASP251
|
3.8
|
0.7
|
1.0
|
|
CB
|
A:ASP304
|
3.8
|
0.2
|
1.0
|
|
HA
|
A:ALA220
|
3.8
|
92.9
|
1.0
|
|
H
|
A:ASN219
|
3.8
|
0.7
|
1.0
|
|
HD3
|
A:PRO221
|
3.9
|
0.2
|
1.0
|
|
HD21
|
A:ASN217
|
4.0
|
0.4
|
1.0
|
|
HA
|
A:ASN217
|
4.0
|
0.6
|
1.0
|
|
HA
|
A:ALA256
|
4.0
|
0.5
|
1.0
|
|
HA
|
A:ASN255
|
4.1
|
0.3
|
1.0
|
|
CB
|
A:ASP249
|
4.1
|
0.7
|
1.0
|
|
CB
|
A:ASN255
|
4.2
|
0.0
|
1.0
|
|
CA
|
A:ASN255
|
4.2
|
0.8
|
1.0
|
|
HB3
|
A:ASP251
|
4.2
|
0.3
|
1.0
|
|
ND2
|
A:ASN217
|
4.2
|
0.7
|
1.0
|
|
HB3
|
A:ASP249
|
4.3
|
1.0
|
1.0
|
|
HB2
|
A:LYS310
|
4.3
|
99.8
|
1.0
|
|
H
|
A:ASP251
|
4.3
|
0.8
|
1.0
|
|
HB2
|
A:ASP249
|
4.3
|
1.0
|
1.0
|
|
HB2
|
A:ASN219
|
4.3
|
0.1
|
1.0
|
|
HD2
|
A:LYS310
|
4.5
|
0.7
|
1.0
|
|
CA
|
A:ALA220
|
4.5
|
77.4
|
1.0
|
|
N
|
A:ALA220
|
4.5
|
0.2
|
1.0
|
|
OD1
|
A:ASP304
|
4.5
|
94.7
|
1.0
|
|
N
|
A:ASN219
|
4.5
|
0.4
|
1.0
|
|
N
|
A:ALA256
|
4.5
|
0.8
|
1.0
|
|
OD1
|
A:ASP251
|
4.5
|
0.0
|
1.0
|
|
CA
|
A:ASN219
|
4.5
|
0.8
|
1.0
|
|
HB2
|
A:ASN255
|
4.7
|
0.4
|
1.0
|
|
CB
|
A:ASN217
|
4.7
|
89.5
|
1.0
|
|
CA
|
A:ASN217
|
4.7
|
98.0
|
1.0
|
|
CA
|
A:ALA256
|
4.8
|
0.8
|
1.0
|
|
CD
|
A:PRO221
|
4.8
|
86.0
|
1.0
|
|
CB
|
A:ASN219
|
4.8
|
0.8
|
1.0
|
|
C
|
A:ALA220
|
4.8
|
74.5
|
1.0
|
|
HB3
|
A:ASN219
|
4.9
|
0.1
|
1.0
|
|
N
|
A:PRO221
|
4.9
|
77.5
|
1.0
|
|
C
|
A:ASN217
|
5.0
|
82.9
|
1.0
|
|
Calcium binding site 8 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 8 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca512
b:0.1
occ:1.00
|
O
|
A:MET323
|
2.2
|
0.7
|
1.0
|
|
OE2
|
A:GLU291
|
2.3
|
0.9
|
1.0
|
|
OD1
|
A:ASP325
|
2.3
|
0.1
|
1.0
|
|
OD1
|
A:ASP322
|
2.3
|
0.8
|
1.0
|
|
OD1
|
A:ASP366
|
2.4
|
0.5
|
1.0
|
|
OE1
|
A:GLU234
|
2.4
|
0.5
|
1.0
|
|
H
|
A:MET323
|
2.8
|
0.6
|
1.0
|
|
CD
|
A:GLU291
|
3.1
|
1.0
|
1.0
|
|
CD
|
A:GLU234
|
3.2
|
0.1
|
1.0
|
|
OE2
|
A:GLU234
|
3.2
|
0.3
|
1.0
|
|
H
|
A:ASP325
|
3.2
|
0.9
|
1.0
|
|
C
|
A:MET323
|
3.3
|
0.6
|
1.0
|
|
OE1
|
A:GLU291
|
3.4
|
0.5
|
1.0
|
|
HH11
|
A:ARG290
|
3.4
|
0.4
|
1.0
|
|
CG
|
A:ASP325
|
3.4
|
0.5
|
1.0
|
|
CG
|
A:ASP322
|
3.5
|
1.0
|
1.0
|
|
CG
|
A:ASP366
|
3.5
|
0.5
|
1.0
|
|
N
|
A:MET323
|
3.5
|
0.0
|
1.0
|
|
HA
|
A:ASP366
|
3.6
|
1.0
|
1.0
|
|
HB3
|
A:ARG290
|
3.9
|
0.9
|
1.0
|
|
HH12
|
A:ARG290
|
3.9
|
0.4
|
1.0
|
|
NH1
|
A:ARG290
|
3.9
|
0.1
|
1.0
|
|
CA
|
A:MET323
|
4.0
|
0.6
|
1.0
|
|
OD2
|
A:ASP325
|
4.0
|
0.8
|
1.0
|
|
N
|
A:ASP325
|
4.0
|
0.9
|
1.0
|
|
OD2
|
A:ASP322
|
4.1
|
0.3
|
1.0
|
|
HB2
|
A:MET323
|
4.1
|
0.1
|
1.0
|
|
HA
|
A:ASP322
|
4.1
|
0.3
|
1.0
|
|
HD3
|
A:ARG290
|
4.2
|
0.0
|
1.0
|
|
HA
|
A:ASN324
|
4.2
|
0.5
|
1.0
|
|
CB
|
A:ASP366
|
4.2
|
0.6
|
1.0
|
|
CA
|
A:CA513
|
4.3
|
0.2
|
1.0
|
|
CA
|
A:ASP366
|
4.4
|
100.0
|
1.0
|
|
N
|
A:ASN324
|
4.4
|
0.1
|
1.0
|
|
OD2
|
A:ASP366
|
4.4
|
0.8
|
1.0
|
|
CG
|
A:GLU291
|
4.5
|
0.7
|
1.0
|
|
CB
|
A:ASP325
|
4.5
|
0.9
|
1.0
|
|
C
|
A:ASP322
|
4.6
|
0.9
|
1.0
|
|
CB
|
A:MET323
|
4.6
|
0.1
|
1.0
|
|
HG3
|
A:GLU291
|
4.6
|
0.0
|
1.0
|
|
CG
|
A:GLU234
|
4.6
|
0.9
|
1.0
|
|
CB
|
A:ASP322
|
4.6
|
0.9
|
1.0
|
|
CA
|
A:ASP322
|
4.7
|
0.4
|
1.0
|
|
HB3
|
A:ASP325
|
4.7
|
0.5
|
1.0
|
|
OD1
|
A:ASN326
|
4.7
|
0.4
|
1.0
|
|
CA
|
A:ASN324
|
4.7
|
0.3
|
1.0
|
|
H
|
A:GLU291
|
4.7
|
0.8
|
1.0
|
|
CA
|
A:ASP325
|
4.7
|
0.6
|
1.0
|
|
CB
|
A:ARG290
|
4.8
|
0.6
|
1.0
|
|
HA
|
A:MET323
|
4.8
|
0.5
|
1.0
|
|
HG2
|
A:GLU291
|
4.8
|
0.0
|
1.0
|
|
H
|
A:ARG290
|
4.9
|
0.5
|
1.0
|
|
H
|
A:ASN326
|
4.9
|
0.6
|
1.0
|
|
HB2
|
A:ASN326
|
4.9
|
0.5
|
1.0
|
|
C
|
A:ASN324
|
4.9
|
0.6
|
1.0
|
|
HB3
|
A:GLU234
|
5.0
|
0.5
|
1.0
|
|
HB2
|
A:GLU234
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 9 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 9 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca513
b:0.2
occ:1.00
|
OD2
|
A:ASP325
|
2.2
|
0.8
|
1.0
|
|
OE2
|
A:GLU234
|
2.3
|
0.3
|
1.0
|
|
OE1
|
A:GLU291
|
2.3
|
0.5
|
1.0
|
|
OD1
|
A:ASP289
|
2.3
|
0.6
|
1.0
|
|
O
|
A:HOH604
|
2.3
|
0.4
|
1.0
|
|
CG
|
A:ASP289
|
2.6
|
0.3
|
1.0
|
|
OD2
|
A:ASP289
|
2.9
|
0.9
|
1.0
|
|
HA
|
A:ASP289
|
3.1
|
1.0
|
1.0
|
|
CD
|
A:GLU234
|
3.2
|
0.1
|
1.0
|
|
CG
|
A:ASP325
|
3.2
|
0.5
|
1.0
|
|
CD
|
A:GLU291
|
3.3
|
1.0
|
1.0
|
|
H
|
A:GLU291
|
3.4
|
0.8
|
1.0
|
|
OD1
|
A:ASP325
|
3.5
|
0.1
|
1.0
|
|
CB
|
A:ASP289
|
3.5
|
0.5
|
1.0
|
|
H
|
A:ARG290
|
3.5
|
0.5
|
1.0
|
|
CA
|
A:ASP289
|
3.6
|
0.3
|
1.0
|
|
HD21
|
A:ASN235
|
3.7
|
0.1
|
1.0
|
|
HB2
|
A:ASP289
|
3.7
|
0.4
|
1.0
|
|
HB2
|
A:GLU291
|
3.7
|
0.7
|
1.0
|
|
HG3
|
A:GLU234
|
3.9
|
0.9
|
1.0
|
|
OE2
|
A:GLU291
|
3.9
|
0.9
|
1.0
|
|
N
|
A:ARG290
|
3.9
|
0.4
|
1.0
|
|
OE1
|
A:GLU234
|
4.0
|
0.5
|
1.0
|
|
CG
|
A:GLU234
|
4.0
|
0.9
|
1.0
|
|
HG2
|
A:GLU234
|
4.0
|
0.9
|
1.0
|
|
C
|
A:ASP289
|
4.0
|
0.7
|
1.0
|
|
N
|
A:GLU291
|
4.2
|
0.0
|
1.0
|
|
OD1
|
A:ASN326
|
4.3
|
0.4
|
1.0
|
|
CA
|
A:CA512
|
4.3
|
0.1
|
1.0
|
|
HB3
|
A:ASP289
|
4.4
|
0.4
|
1.0
|
|
ND2
|
A:ASN235
|
4.4
|
0.9
|
1.0
|
|
CG
|
A:GLU291
|
4.4
|
0.7
|
1.0
|
|
CB
|
A:GLU291
|
4.4
|
0.6
|
1.0
|
|
CB
|
A:ASP325
|
4.6
|
0.9
|
1.0
|
|
HB2
|
A:ASP325
|
4.6
|
0.5
|
1.0
|
|
HB3
|
A:ARG290
|
4.7
|
0.9
|
1.0
|
|
OD1
|
A:ASN235
|
4.7
|
0.3
|
1.0
|
|
HH12
|
A:ARG365
|
4.8
|
0.4
|
1.0
|
|
HG2
|
A:GLU291
|
4.8
|
0.0
|
1.0
|
|
H
|
A:ASP292
|
4.8
|
0.1
|
1.0
|
|
HD22
|
A:ASN235
|
4.9
|
0.1
|
1.0
|
|
HB3
|
A:ASP325
|
5.0
|
0.5
|
1.0
|
|
CA
|
A:ARG290
|
5.0
|
1.0
|
1.0
|
|
CG
|
A:ASN235
|
5.0
|
0.6
|
1.0
|
|
CA
|
A:GLU291
|
5.0
|
0.7
|
1.0
|
|
O
|
A:ASP289
|
5.0
|
0.5
|
1.0
|
|
N
|
A:ASP289
|
5.0
|
0.8
|
1.0
|
|
Calcium binding site 10 out
of 10 in 6vfp
Go back to
Calcium Binding Sites List in 6vfp
Calcium binding site 10 out
of 10 in the Crystal Structure of Human Protocadherin 1 EC1-EC4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Human Protocadherin 1 EC1-EC4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca514
b:0.8
occ:1.00
|
OD1
|
A:ASP408
|
2.8
|
0.5
|
1.0
|
|
OD2
|
A:ASP408
|
3.1
|
0.1
|
1.0
|
|
CG
|
A:ASP408
|
3.2
|
0.5
|
1.0
|
|
HB2
|
A:ASP408
|
4.3
|
0.5
|
1.0
|
|
CB
|
A:ASP408
|
4.4
|
0.8
|
1.0
|
|
OE1
|
A:GLU410
|
4.4
|
0.6
|
1.0
|
|
CD
|
A:GLU410
|
4.5
|
0.4
|
1.0
|
|
OE2
|
A:GLU410
|
4.6
|
0.9
|
1.0
|
|
HA
|
A:ASP408
|
4.9
|
0.1
|
1.0
|
|
CG
|
A:GLU410
|
5.0
|
0.1
|
1.0
|
|
Reference:
O.J.Harrison,
J.Brasch,
P.S.Katsamba,
G.Ahlsen,
A.J.Noble,
H.Dan,
R.V.Sampogna,
C.S.Potter,
B.Carragher,
B.Honig,
L.Shapiro.
Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003
Page generated: Tue Jul 16 16:41:55 2024
|
