Calcium in PDB 3gin: Crystal Structure of E454K-CBD1
Protein crystallography data
The structure of Crystal Structure of E454K-CBD1, PDB code: 3gin
was solved by
V.Chaptal,
G.Mercado-Besserer,
J.Abramson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
64.96 /
2.40
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.858,
91.858,
65.590,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
25.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of E454K-CBD1
(pdb code 3gin). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Crystal Structure of E454K-CBD1, PDB code: 3gin:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 1 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1
b:51.3
occ:1.00
|
OD2
|
A:ASP498
|
2.0
|
30.4
|
1.0
|
O
|
A:ILE449
|
2.3
|
36.6
|
1.0
|
OD2
|
A:ASP500
|
2.4
|
29.2
|
1.0
|
OD1
|
A:ASP447
|
2.5
|
36.1
|
1.0
|
OE1
|
A:GLU385
|
2.6
|
30.2
|
1.0
|
CG
|
A:ASP498
|
2.8
|
24.9
|
1.0
|
OE2
|
A:GLU385
|
2.9
|
30.3
|
1.0
|
CD
|
A:GLU385
|
3.0
|
30.7
|
1.0
|
OD1
|
A:ASP498
|
3.0
|
28.2
|
1.0
|
C
|
A:ILE449
|
3.4
|
36.5
|
1.0
|
CG
|
A:ASP500
|
3.5
|
27.6
|
1.0
|
CG
|
A:ASP447
|
3.5
|
36.8
|
1.0
|
OD2
|
A:ASP447
|
3.8
|
40.5
|
1.0
|
CA
|
A:CA2
|
3.9
|
61.9
|
1.0
|
CB
|
A:ASP500
|
3.9
|
27.6
|
1.0
|
N
|
A:ILE449
|
4.0
|
37.6
|
1.0
|
CB
|
A:ASP498
|
4.1
|
22.7
|
1.0
|
N
|
A:PHE450
|
4.3
|
36.1
|
1.0
|
CA
|
A:ILE449
|
4.3
|
37.5
|
1.0
|
O
|
A:ASP447
|
4.4
|
34.9
|
1.0
|
CA
|
A:PHE450
|
4.4
|
35.5
|
1.0
|
CG
|
A:GLU385
|
4.4
|
29.6
|
1.0
|
OD1
|
A:ASP500
|
4.5
|
28.3
|
1.0
|
C
|
A:ASP447
|
4.5
|
34.9
|
1.0
|
CA
|
A:ASP498
|
4.5
|
22.2
|
1.0
|
OD1
|
A:ASP499
|
4.6
|
29.3
|
1.0
|
N
|
A:GLU451
|
4.6
|
32.8
|
1.0
|
N
|
A:ASP500
|
4.6
|
26.5
|
1.0
|
CA
|
A:CA7
|
4.6
|
64.8
|
1.0
|
N
|
A:ASP499
|
4.7
|
23.2
|
1.0
|
C
|
A:ASP448
|
4.7
|
37.8
|
1.0
|
CG
|
A:GLU451
|
4.7
|
33.9
|
1.0
|
N
|
A:ASP448
|
4.8
|
36.3
|
1.0
|
CB
|
A:ASP447
|
4.9
|
34.2
|
1.0
|
CB
|
A:ILE449
|
4.9
|
38.3
|
1.0
|
C
|
A:PHE450
|
4.9
|
34.4
|
1.0
|
CA
|
A:ASP500
|
4.9
|
28.1
|
1.0
|
CA
|
A:ASP448
|
4.9
|
37.8
|
1.0
|
OE2
|
A:GLU451
|
5.0
|
42.1
|
1.0
|
|
Calcium binding site 2 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 2 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2
b:61.9
occ:1.00
|
OD1
|
A:ASP499
|
2.3
|
29.3
|
1.0
|
OD2
|
A:ASP500
|
2.3
|
29.2
|
1.0
|
O
|
A:ASP447
|
2.3
|
34.9
|
1.0
|
OE1
|
A:GLU385
|
2.7
|
30.2
|
1.0
|
OD1
|
A:ASP446
|
2.7
|
32.3
|
1.0
|
OD1
|
A:ASP500
|
2.9
|
28.3
|
1.0
|
CG
|
A:ASP500
|
2.9
|
27.6
|
1.0
|
O
|
A:HOH510
|
3.1
|
52.0
|
1.0
|
CG
|
A:ASP499
|
3.3
|
26.2
|
1.0
|
C
|
A:ASP447
|
3.5
|
34.9
|
1.0
|
OD2
|
A:ASP499
|
3.6
|
32.3
|
1.0
|
CD
|
A:GLU385
|
3.8
|
30.7
|
1.0
|
CG
|
A:ASP446
|
3.8
|
31.6
|
1.0
|
OD1
|
A:ASP447
|
3.8
|
36.1
|
1.0
|
CA
|
A:CA1
|
3.9
|
51.3
|
1.0
|
N
|
A:ASP447
|
4.0
|
32.7
|
1.0
|
OD2
|
A:ASP446
|
4.2
|
35.9
|
1.0
|
CA
|
A:ASP448
|
4.2
|
37.8
|
1.0
|
CB
|
A:GLU385
|
4.3
|
27.3
|
1.0
|
N
|
A:ASP448
|
4.3
|
36.3
|
1.0
|
CB
|
A:ASP500
|
4.3
|
27.6
|
1.0
|
CA
|
A:ASP447
|
4.4
|
34.1
|
1.0
|
N
|
A:ASP500
|
4.5
|
26.5
|
1.0
|
OE2
|
A:GLU385
|
4.5
|
30.3
|
1.0
|
C
|
A:ASP499
|
4.6
|
25.1
|
1.0
|
CB
|
A:ASP499
|
4.6
|
24.7
|
1.0
|
N
|
A:ASP499
|
4.6
|
23.2
|
1.0
|
CG
|
A:GLU385
|
4.7
|
29.6
|
1.0
|
CA
|
A:ASP500
|
4.8
|
28.1
|
1.0
|
CA
|
A:ASP499
|
4.8
|
24.4
|
1.0
|
CG
|
A:ASP447
|
4.9
|
36.8
|
1.0
|
|
Calcium binding site 3 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 3 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca5
b:37.0
occ:0.80
|
O
|
A:HOH46
|
2.0
|
27.0
|
1.0
|
O
|
A:HOH22
|
2.2
|
24.0
|
1.0
|
O
|
A:HOH48
|
2.2
|
21.4
|
1.0
|
O
|
A:HOH45
|
2.3
|
24.2
|
1.0
|
O
|
A:HOH44
|
2.3
|
25.1
|
1.0
|
O
|
A:HOH47
|
4.0
|
27.4
|
1.0
|
O
|
A:HOH94
|
4.0
|
33.8
|
1.0
|
O
|
A:HOH78
|
4.2
|
32.0
|
1.0
|
OD1
|
A:ASP453
|
4.2
|
20.7
|
1.0
|
OD2
|
A:ASP453
|
4.3
|
23.2
|
1.0
|
O
|
A:HOH77
|
4.4
|
33.9
|
1.0
|
O
|
A:ASP498
|
4.5
|
20.7
|
1.0
|
CG
|
A:ASP453
|
4.7
|
22.9
|
1.0
|
O
|
A:HOH49
|
4.8
|
31.2
|
1.0
|
CD2
|
A:PHE497
|
4.8
|
19.0
|
1.0
|
|
Calcium binding site 4 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 4 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca7
b:64.8
occ:1.00
|
OD2
|
A:ASP447
|
2.4
|
40.5
|
1.0
|
OE2
|
A:GLU385
|
2.6
|
30.3
|
1.0
|
OD1
|
A:ASP421
|
3.2
|
30.1
|
1.0
|
CG
|
A:ASP447
|
3.3
|
36.8
|
1.0
|
OE2
|
A:GLU451
|
3.4
|
42.1
|
1.0
|
CD
|
A:GLU385
|
3.8
|
30.7
|
1.0
|
OD1
|
A:ASP447
|
3.9
|
36.1
|
1.0
|
O
|
A:HOH3
|
4.1
|
22.3
|
1.0
|
CB
|
A:ASP447
|
4.3
|
34.2
|
1.0
|
CG
|
A:ASP421
|
4.4
|
27.8
|
1.0
|
CD
|
A:GLU451
|
4.4
|
35.9
|
1.0
|
CG
|
A:GLU385
|
4.5
|
29.6
|
1.0
|
O
|
A:ILE445
|
4.5
|
24.4
|
1.0
|
CA
|
A:CA1
|
4.6
|
51.3
|
1.0
|
O
|
A:SER420
|
4.8
|
27.1
|
1.0
|
NZ
|
A:LYS454
|
4.8
|
30.2
|
1.0
|
CG
|
A:GLU451
|
4.8
|
33.9
|
1.0
|
CB
|
A:ASP421
|
4.8
|
26.1
|
1.0
|
OE1
|
A:GLU385
|
4.9
|
30.2
|
1.0
|
CA
|
A:ASP421
|
4.9
|
26.1
|
1.0
|
O
|
A:HOH4
|
4.9
|
17.1
|
1.0
|
N
|
A:ASP447
|
5.0
|
32.7
|
1.0
|
|
Calcium binding site 5 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 5 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca3
b:49.4
occ:1.00
|
O
|
B:ASP447
|
2.3
|
31.1
|
1.0
|
OD2
|
B:ASP500
|
2.4
|
34.1
|
1.0
|
OD1
|
B:ASP499
|
2.4
|
29.0
|
1.0
|
OE1
|
B:GLU385
|
2.5
|
29.4
|
1.0
|
OD1
|
B:ASP446
|
2.6
|
25.4
|
1.0
|
OD1
|
B:ASP500
|
2.9
|
31.4
|
1.0
|
CG
|
B:ASP500
|
2.9
|
31.1
|
1.0
|
O
|
B:HOH2
|
3.0
|
39.8
|
1.0
|
CA
|
B:CA4
|
3.4
|
51.5
|
1.0
|
C
|
B:ASP447
|
3.4
|
31.5
|
1.0
|
CD
|
B:GLU385
|
3.5
|
33.0
|
1.0
|
CG
|
B:ASP499
|
3.5
|
27.6
|
1.0
|
CG
|
B:ASP446
|
3.6
|
26.3
|
1.0
|
OD1
|
B:ASP447
|
3.7
|
36.0
|
1.0
|
N
|
B:ASP447
|
3.8
|
29.8
|
1.0
|
OD2
|
B:ASP446
|
4.0
|
24.2
|
1.0
|
OD2
|
B:ASP499
|
4.0
|
31.1
|
1.0
|
CA
|
B:ASP447
|
4.2
|
31.1
|
1.0
|
CG
|
B:GLU385
|
4.3
|
30.1
|
1.0
|
N
|
B:ASP448
|
4.3
|
33.9
|
1.0
|
CB
|
B:ASP500
|
4.3
|
30.4
|
1.0
|
OE2
|
B:GLU385
|
4.4
|
36.2
|
1.0
|
CB
|
B:GLU385
|
4.4
|
26.2
|
1.0
|
CA
|
B:ASP448
|
4.4
|
34.9
|
1.0
|
N
|
B:ASP499
|
4.5
|
24.7
|
1.0
|
N
|
B:ASP500
|
4.6
|
28.8
|
1.0
|
CG
|
B:ASP447
|
4.6
|
33.3
|
1.0
|
C
|
B:ASP448
|
4.7
|
34.4
|
1.0
|
C
|
B:ASP499
|
4.7
|
27.6
|
1.0
|
CB
|
B:ASP499
|
4.8
|
26.8
|
1.0
|
C
|
B:ASP446
|
4.8
|
28.0
|
1.0
|
CB
|
B:ASP446
|
4.8
|
26.3
|
1.0
|
N
|
B:ILE449
|
4.8
|
34.0
|
1.0
|
CA
|
B:ASP499
|
4.9
|
26.3
|
1.0
|
O
|
B:ILE449
|
4.9
|
33.1
|
1.0
|
CA
|
B:ASP500
|
4.9
|
30.6
|
1.0
|
CA
|
B:ASP446
|
4.9
|
26.6
|
1.0
|
|
Calcium binding site 6 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 6 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca4
b:51.5
occ:1.00
|
OD2
|
B:ASP500
|
2.2
|
34.1
|
1.0
|
OD1
|
B:ASP498
|
2.2
|
32.5
|
1.0
|
O
|
B:ILE449
|
2.2
|
33.1
|
1.0
|
OD1
|
B:ASP447
|
2.2
|
36.0
|
1.0
|
OE1
|
B:GLU385
|
2.4
|
29.4
|
1.0
|
CG
|
B:ASP498
|
2.9
|
24.5
|
1.0
|
OE2
|
B:GLU385
|
2.9
|
36.2
|
1.0
|
CD
|
B:GLU385
|
3.0
|
33.0
|
1.0
|
OD2
|
B:ASP498
|
3.1
|
24.4
|
1.0
|
CG
|
B:ASP447
|
3.3
|
33.3
|
1.0
|
CG
|
B:ASP500
|
3.3
|
31.1
|
1.0
|
C
|
B:ILE449
|
3.4
|
32.5
|
1.0
|
CA
|
B:CA3
|
3.4
|
49.4
|
1.0
|
OD2
|
B:ASP447
|
3.7
|
36.4
|
1.0
|
N
|
B:ILE449
|
3.9
|
34.0
|
1.0
|
CB
|
B:ASP500
|
4.0
|
30.4
|
1.0
|
O
|
B:ASP447
|
4.1
|
31.1
|
1.0
|
CB
|
B:ASP498
|
4.2
|
22.4
|
1.0
|
CA
|
B:ILE449
|
4.2
|
33.8
|
1.0
|
OD1
|
B:ASP500
|
4.3
|
31.4
|
1.0
|
O
|
B:HOH51
|
4.3
|
34.1
|
1.0
|
N
|
B:PHE450
|
4.3
|
31.5
|
1.0
|
C
|
B:ASP447
|
4.4
|
31.5
|
1.0
|
CA
|
B:ASP498
|
4.5
|
22.2
|
1.0
|
CG
|
B:GLU385
|
4.5
|
30.1
|
1.0
|
CA
|
B:PHE450
|
4.5
|
31.5
|
1.0
|
C
|
B:ASP448
|
4.6
|
34.4
|
1.0
|
CB
|
B:ASP447
|
4.6
|
31.6
|
1.0
|
N
|
B:ASP500
|
4.6
|
28.8
|
1.0
|
OD1
|
B:ASP499
|
4.6
|
29.0
|
1.0
|
N
|
B:ASP499
|
4.6
|
24.7
|
1.0
|
N
|
B:GLU451
|
4.7
|
30.1
|
1.0
|
CB
|
B:ILE449
|
4.8
|
33.9
|
1.0
|
N
|
B:ASP447
|
4.9
|
29.8
|
1.0
|
CA
|
B:ASP447
|
4.9
|
31.1
|
1.0
|
OE1
|
B:GLU451
|
4.9
|
35.1
|
1.0
|
CA
|
B:CA6
|
5.0
|
63.0
|
0.8
|
CA
|
B:ASP500
|
5.0
|
30.6
|
1.0
|
N
|
B:ASP448
|
5.0
|
33.9
|
1.0
|
|
Calcium binding site 7 out
of 7 in 3gin
Go back to
Calcium Binding Sites List in 3gin
Calcium binding site 7 out
of 7 in the Crystal Structure of E454K-CBD1
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 E454K-CBD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca6
b:63.0
occ:0.80
|
OD2
|
B:ASP447
|
2.3
|
36.4
|
1.0
|
O
|
B:HOH95
|
2.6
|
40.0
|
1.0
|
OD1
|
B:ASP421
|
2.7
|
26.4
|
1.0
|
OE1
|
B:GLU451
|
3.1
|
35.1
|
1.0
|
OE2
|
B:GLU385
|
3.1
|
36.2
|
1.0
|
CG
|
B:ASP447
|
3.5
|
33.3
|
1.0
|
CG
|
B:ASP421
|
3.8
|
23.6
|
1.0
|
O
|
B:HOH51
|
4.1
|
34.1
|
1.0
|
NZ
|
B:LYS454
|
4.1
|
26.3
|
1.0
|
OD1
|
B:ASP447
|
4.2
|
36.0
|
1.0
|
O
|
B:HOH52
|
4.3
|
23.3
|
1.0
|
CD
|
B:GLU451
|
4.3
|
31.9
|
1.0
|
CD
|
B:GLU385
|
4.4
|
33.0
|
1.0
|
CD
|
B:LYS454
|
4.4
|
23.4
|
1.0
|
CB
|
B:ASP447
|
4.5
|
31.6
|
1.0
|
CB
|
B:ASP421
|
4.6
|
23.8
|
1.0
|
OD2
|
B:ASP421
|
4.6
|
25.1
|
1.0
|
CA
|
B:ASP421
|
4.8
|
23.4
|
1.0
|
O
|
B:HOH56
|
4.8
|
33.6
|
1.0
|
OE2
|
B:GLU451
|
4.8
|
35.6
|
1.0
|
O
|
B:SER420
|
4.9
|
23.9
|
1.0
|
CE
|
B:LYS454
|
4.9
|
24.1
|
1.0
|
CA
|
B:CA4
|
5.0
|
51.5
|
1.0
|
|
Reference:
V.Chaptal,
M.Ottolia,
G.Mercado-Besserer,
D.A.Nicoll,
K.D.Philipson,
J.Abramson.
Structure and Functional Analysis of A CA2+ Sensor Mutant of the Na+/CA2+ Exchanger J.Biol.Chem. V. 284 14688 2009.
ISSN: ISSN 0021-9258
PubMed: 19332552
DOI: 10.1074/JBC.C900037200
Page generated: Sat Jul 13 10:41:03 2024
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