Calcium in PDB 6pim: Crystal Structure of Human Protocadherin-1 EC3-4
Protein crystallography data
The structure of Crystal Structure of Human Protocadherin-1 EC3-4, PDB code: 6pim
was solved by
D.Modak,
M.Sotomayor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.43 /
3.05
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.569,
125.569,
45.294,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22 /
26.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-1 EC3-4
(pdb code 6pim). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of Human Protocadherin-1 EC3-4, PDB code: 6pim:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6pim
Go back to
Calcium Binding Sites List in 6pim
Calcium binding site 1 out
of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4
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 EC3-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:47.8
occ:1.00
|
OE1
|
A:GLU291
|
1.9
|
52.1
|
1.0
|
OD1
|
A:ASP322
|
2.0
|
54.0
|
1.0
|
OE1
|
A:GLU234
|
2.2
|
57.5
|
1.0
|
OD1
|
A:ASP366
|
2.3
|
52.0
|
1.0
|
O
|
A:MET323
|
2.3
|
56.9
|
1.0
|
OD1
|
A:ASP325
|
2.5
|
54.0
|
1.0
|
CD
|
A:GLU291
|
2.7
|
54.2
|
1.0
|
OE2
|
A:GLU291
|
2.8
|
54.2
|
1.0
|
CG
|
A:ASP322
|
3.2
|
58.2
|
1.0
|
CD
|
A:GLU234
|
3.3
|
53.9
|
1.0
|
CG
|
A:ASP325
|
3.4
|
53.6
|
1.0
|
CG
|
A:ASP366
|
3.4
|
50.3
|
1.0
|
C
|
A:MET323
|
3.5
|
57.8
|
1.0
|
N
|
A:MET323
|
3.5
|
56.4
|
1.0
|
OD2
|
A:ASP325
|
3.7
|
55.3
|
1.0
|
OE2
|
A:GLU234
|
3.7
|
52.2
|
1.0
|
OD2
|
A:ASP322
|
3.8
|
57.2
|
1.0
|
CA
|
A:CA503
|
3.9
|
60.9
|
1.0
|
CB
|
A:ASP366
|
4.0
|
51.5
|
1.0
|
CA
|
A:MET323
|
4.1
|
57.6
|
1.0
|
CG
|
A:GLU291
|
4.1
|
52.7
|
1.0
|
CA
|
A:ASP366
|
4.2
|
54.1
|
1.0
|
N
|
A:ASP325
|
4.2
|
58.4
|
1.0
|
CA
|
A:ASP322
|
4.3
|
56.2
|
1.0
|
CB
|
A:ASP322
|
4.3
|
58.4
|
1.0
|
ND2
|
A:ASN326
|
4.3
|
54.2
|
1.0
|
C
|
A:ASP322
|
4.4
|
56.9
|
1.0
|
OD2
|
A:ASP366
|
4.4
|
48.3
|
1.0
|
CG
|
A:GLU234
|
4.5
|
54.4
|
1.0
|
NE
|
A:ARG290
|
4.6
|
61.8
|
1.0
|
N
|
A:ASN324
|
4.6
|
59.7
|
1.0
|
CB
|
A:ASP325
|
4.6
|
54.8
|
1.0
|
CB
|
A:MET323
|
4.7
|
56.9
|
1.0
|
CB
|
A:ARG290
|
4.9
|
54.0
|
1.0
|
CA
|
A:ASN324
|
4.9
|
61.5
|
1.0
|
CA
|
A:ASP325
|
4.9
|
57.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6pim
Go back to
Calcium Binding Sites List in 6pim
Calcium binding site 2 out
of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4
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 EC3-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:48.7
occ:1.00
|
OD2
|
A:ASP364
|
2.2
|
58.3
|
1.0
|
OD1
|
A:ASP423
|
2.3
|
58.0
|
1.0
|
O
|
A:ASN326
|
2.3
|
47.1
|
1.0
|
O
|
A:ASN370
|
2.4
|
50.0
|
1.0
|
OD2
|
A:ASP366
|
2.4
|
48.3
|
1.0
|
OD1
|
A:ASN324
|
2.5
|
64.0
|
1.0
|
OD1
|
A:ASP364
|
2.7
|
61.8
|
1.0
|
CG
|
A:ASP364
|
2.8
|
58.0
|
1.0
|
CG
|
A:ASP423
|
3.0
|
58.0
|
1.0
|
OD2
|
A:ASP423
|
3.2
|
57.8
|
1.0
|
CG
|
A:ASP366
|
3.5
|
50.3
|
1.0
|
C
|
A:ASN326
|
3.5
|
49.9
|
1.0
|
CG
|
A:ASN324
|
3.6
|
66.6
|
1.0
|
C
|
A:ASN370
|
3.6
|
53.5
|
1.0
|
CB
|
A:ASP366
|
3.8
|
51.5
|
1.0
|
ND2
|
A:ASN324
|
4.1
|
72.2
|
1.0
|
CB
|
A:ASP423
|
4.2
|
58.4
|
1.0
|
CA
|
A:ASN326
|
4.3
|
49.2
|
1.0
|
CB
|
A:ASP364
|
4.3
|
56.6
|
1.0
|
N
|
A:ASN326
|
4.3
|
50.2
|
1.0
|
CB
|
A:ASN326
|
4.4
|
49.7
|
1.0
|
CA
|
A:ASN370
|
4.4
|
57.3
|
1.0
|
CB
|
A:ASN370
|
4.4
|
58.3
|
1.0
|
N
|
A:ALA371
|
4.5
|
55.3
|
1.0
|
N
|
A:ALA327
|
4.5
|
52.1
|
1.0
|
OD1
|
A:ASP366
|
4.6
|
52.0
|
1.0
|
CD1
|
A:LEU429
|
4.6
|
59.2
|
1.0
|
CD
|
A:PRO328
|
4.7
|
53.7
|
1.0
|
CA
|
A:ALA371
|
4.7
|
55.6
|
1.0
|
CA
|
A:ASN324
|
4.7
|
61.5
|
1.0
|
CB
|
A:ASN324
|
4.8
|
64.8
|
1.0
|
CA
|
A:ALA327
|
4.8
|
53.2
|
1.0
|
N
|
A:PRO328
|
4.8
|
52.2
|
1.0
|
C
|
A:ASN324
|
5.0
|
60.6
|
1.0
|
C
|
A:ALA327
|
5.0
|
53.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6pim
Go back to
Calcium Binding Sites List in 6pim
Calcium binding site 3 out
of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4
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 EC3-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:60.9
occ:1.00
|
OD2
|
A:ASP325
|
2.0
|
55.3
|
1.0
|
OD1
|
A:ASP289
|
2.2
|
54.0
|
1.0
|
OE2
|
A:GLU234
|
2.5
|
52.2
|
1.0
|
OE1
|
A:GLU291
|
2.7
|
52.1
|
1.0
|
CG
|
A:ASP325
|
2.9
|
53.6
|
1.0
|
CG
|
A:ASP289
|
3.2
|
50.2
|
1.0
|
OD1
|
A:ASP325
|
3.2
|
54.0
|
1.0
|
CD
|
A:GLU234
|
3.3
|
53.9
|
1.0
|
OE1
|
A:GLU234
|
3.6
|
57.5
|
1.0
|
CD
|
A:GLU291
|
3.6
|
54.2
|
1.0
|
CB
|
A:GLU291
|
3.8
|
50.9
|
1.0
|
OD2
|
A:ASP289
|
3.8
|
52.9
|
1.0
|
CA
|
A:CA501
|
3.9
|
47.8
|
1.0
|
ND2
|
A:ASN326
|
3.9
|
54.2
|
1.0
|
CG
|
A:GLU291
|
4.0
|
52.7
|
1.0
|
N
|
A:GLU291
|
4.1
|
48.2
|
1.0
|
CB
|
A:ASP289
|
4.2
|
48.2
|
1.0
|
CB
|
A:ASP325
|
4.2
|
54.8
|
1.0
|
CA
|
A:ASP289
|
4.3
|
47.9
|
1.0
|
N
|
A:ARG290
|
4.3
|
51.8
|
1.0
|
C
|
A:ASP289
|
4.6
|
49.3
|
1.0
|
CA
|
A:GLU291
|
4.6
|
50.9
|
1.0
|
OD1
|
A:ASN235
|
4.7
|
61.7
|
1.0
|
CG
|
A:GLU234
|
4.7
|
54.4
|
1.0
|
OE2
|
A:GLU291
|
4.7
|
54.2
|
1.0
|
ND2
|
A:ASN235
|
4.7
|
58.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6pim
Go back to
Calcium Binding Sites List in 6pim
Calcium binding site 4 out
of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4
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 EC3-4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:83.4
occ:1.00
|
OD2
|
A:ASP304
|
2.2
|
67.6
|
1.0
|
OD2
|
A:ASP249
|
2.4
|
78.7
|
1.0
|
OD1
|
A:ASN217
|
2.4
|
72.2
|
1.0
|
O
|
A:ASN255
|
2.4
|
68.3
|
1.0
|
OD1
|
A:ASP249
|
2.5
|
85.5
|
1.0
|
O
|
A:ASN219
|
2.5
|
77.7
|
1.0
|
CG
|
A:ASP249
|
2.7
|
81.2
|
1.0
|
OD2
|
A:ASP251
|
2.7
|
86.9
|
1.0
|
CG
|
A:ASP304
|
3.4
|
68.1
|
1.0
|
CG
|
A:ASP251
|
3.4
|
86.9
|
1.0
|
CG
|
A:ASN217
|
3.5
|
73.7
|
1.0
|
C
|
A:ASN219
|
3.6
|
80.9
|
1.0
|
C
|
A:ASN255
|
3.7
|
68.0
|
1.0
|
CB
|
A:ASP251
|
3.8
|
84.2
|
1.0
|
ND2
|
A:ASN217
|
4.0
|
72.3
|
1.0
|
N
|
A:ASN219
|
4.1
|
80.4
|
1.0
|
CA
|
A:ASN219
|
4.1
|
81.9
|
1.0
|
CB
|
A:ASP249
|
4.2
|
78.7
|
1.0
|
CB
|
A:ASP304
|
4.2
|
68.3
|
1.0
|
CB
|
A:ASN219
|
4.2
|
81.3
|
1.0
|
OD1
|
A:ASP304
|
4.3
|
67.4
|
1.0
|
OD1
|
A:ASP251
|
4.3
|
89.2
|
1.0
|
CA
|
A:ASN255
|
4.5
|
70.7
|
1.0
|
CB
|
A:ASN255
|
4.5
|
74.8
|
1.0
|
N
|
A:ALA256
|
4.6
|
65.6
|
1.0
|
N
|
A:ALA220
|
4.6
|
82.4
|
1.0
|
C
|
A:ALA220
|
4.7
|
76.8
|
1.0
|
CA
|
A:ALA256
|
4.8
|
65.7
|
1.0
|
CB
|
A:ASN217
|
4.8
|
76.2
|
1.0
|
O
|
A:ALA220
|
4.8
|
79.0
|
1.0
|
CD
|
A:PRO221
|
4.9
|
72.3
|
1.0
|
N
|
A:PRO221
|
4.9
|
72.9
|
1.0
|
CA
|
A:ALA220
|
4.9
|
78.6
|
1.0
|
N
|
A:ASP218
|
4.9
|
81.5
|
1.0
|
C
|
A:ASN217
|
5.0
|
80.2
|
1.0
|
CA
|
A:ASN217
|
5.0
|
78.3
|
1.0
|
CG
|
A:LYS310
|
5.0
|
80.0
|
1.0
|
|
Reference:
D.Modak,
M.Sotomayor.
Identification of An Adhesive Interface For the Non-Clustered Delta 1 Protocadherin-1 Involved in Respiratory Diseases. Commun Biol V. 2 354 2019.
ISSN: ESSN 2399-3642
PubMed: 31583286
DOI: 10.1038/S42003-019-0586-0
Page generated: Tue Jul 16 12:53:41 2024
|