Sodium in PDB 7rj9: Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium
Protein crystallography data
The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium, PDB code: 7rj9
was solved by
A.E.Aleshin,
F.M.Marassi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.69 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.832,
125.575,
40.883,
90,
119.25,
90
|
R / Rfree (%)
|
17.1 /
21
|
Other elements in 7rj9:
The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium
(pdb code 7rj9). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium, PDB code: 7rj9:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 7rj9
Go back to
Sodium Binding Sites List in 7rj9
Sodium binding site 1 out
of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:11.9
occ:1.00
|
O
|
A:ALA209
|
2.3
|
12.5
|
1.0
|
O
|
A:PHE164
|
2.3
|
17.4
|
1.0
|
O
|
A:ALA349
|
2.3
|
15.4
|
1.0
|
O
|
A:ALA257
|
2.3
|
13.9
|
1.0
|
CL
|
A:CL502
|
2.8
|
13.9
|
1.0
|
C
|
A:ALA349
|
3.4
|
15.7
|
1.0
|
C
|
A:ALA209
|
3.5
|
13.7
|
1.0
|
C
|
A:PHE164
|
3.5
|
16.9
|
1.0
|
C
|
A:ALA257
|
3.5
|
12.8
|
1.0
|
N
|
A:PHE164
|
4.1
|
15.0
|
1.0
|
N
|
A:ALA209
|
4.1
|
12.9
|
1.0
|
N
|
A:ALA257
|
4.2
|
12.2
|
1.0
|
N
|
A:ALA349
|
4.2
|
13.2
|
1.0
|
CA
|
A:PHE164
|
4.3
|
17.1
|
1.0
|
OD1
|
A:ASP166
|
4.3
|
25.5
|
1.0
|
CA
|
A:ALA209
|
4.3
|
13.5
|
1.0
|
N
|
A:MET350
|
4.3
|
16.1
|
1.0
|
CA
|
A:ALA349
|
4.3
|
14.3
|
1.0
|
CA
|
A:MET350
|
4.4
|
17.8
|
1.0
|
CA
|
A:ALA257
|
4.4
|
12.2
|
1.0
|
N
|
A:LEU258
|
4.4
|
13.3
|
1.0
|
N
|
A:PHE210
|
4.4
|
12.9
|
1.0
|
CA
|
A:LEU258
|
4.5
|
13.9
|
1.0
|
N
|
A:THR165
|
4.5
|
18.5
|
1.0
|
CA
|
A:PHE210
|
4.5
|
15.0
|
1.0
|
CB
|
A:PHE164
|
4.5
|
16.7
|
1.0
|
C
|
A:THR165
|
4.6
|
21.9
|
1.0
|
CA
|
A:THR165
|
4.6
|
19.2
|
1.0
|
CB
|
A:ALA209
|
4.7
|
14.4
|
1.0
|
CB
|
A:ALA349
|
4.7
|
14.6
|
1.0
|
O
|
A:THR165
|
4.8
|
25.2
|
1.0
|
CB
|
A:LEU258
|
4.8
|
14.8
|
1.0
|
CB
|
A:PHE210
|
4.8
|
14.4
|
1.0
|
CG
|
A:ASP166
|
4.9
|
21.7
|
1.0
|
CB
|
A:ALA257
|
4.9
|
12.6
|
1.0
|
OD2
|
A:ASP166
|
5.0
|
22.8
|
1.0
|
N
|
A:ASP166
|
5.0
|
20.5
|
1.0
|
|
Sodium binding site 2 out
of 2 in 7rj9
Go back to
Sodium Binding Sites List in 7rj9
Sodium binding site 2 out
of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:11.3
occ:1.00
|
O
|
B:ALA209
|
2.3
|
11.1
|
1.0
|
O
|
B:ALA349
|
2.3
|
12.7
|
1.0
|
O
|
B:PHE164
|
2.3
|
12.9
|
1.0
|
O
|
B:ALA257
|
2.4
|
11.1
|
1.0
|
O2
|
B:SO4504
|
2.6
|
27.4
|
0.8
|
CL
|
B:CL502
|
2.9
|
12.9
|
1.0
|
C
|
B:ALA349
|
3.4
|
14.2
|
1.0
|
C
|
B:ALA209
|
3.5
|
11.1
|
1.0
|
C
|
B:PHE164
|
3.5
|
13.4
|
1.0
|
C
|
B:ALA257
|
3.6
|
12.7
|
1.0
|
S
|
B:SO4504
|
4.0
|
26.8
|
0.8
|
N
|
B:PHE164
|
4.2
|
11.8
|
1.0
|
N
|
B:ALA209
|
4.2
|
10.1
|
1.0
|
CA
|
B:MET350
|
4.2
|
17.8
|
1.0
|
N
|
B:MET350
|
4.3
|
15.7
|
1.0
|
N
|
B:ALA349
|
4.3
|
11.0
|
1.0
|
N
|
B:ALA257
|
4.3
|
12.2
|
1.0
|
CA
|
B:ALA209
|
4.3
|
11.7
|
1.0
|
CA
|
B:PHE164
|
4.4
|
13.6
|
1.0
|
N
|
B:PHE210
|
4.4
|
10.4
|
1.0
|
CA
|
B:ALA349
|
4.4
|
12.9
|
1.0
|
CA
|
B:PHE210
|
4.4
|
11.0
|
1.0
|
CA
|
B:LEU258
|
4.4
|
14.3
|
1.0
|
N
|
B:THR165
|
4.5
|
15.0
|
1.0
|
CA
|
B:ALA257
|
4.5
|
11.2
|
1.0
|
N
|
B:LEU258
|
4.5
|
11.6
|
1.0
|
CA
|
B:THR165
|
4.5
|
15.0
|
1.0
|
O3
|
B:SO4504
|
4.6
|
27.4
|
0.8
|
CB
|
B:THR165
|
4.6
|
16.3
|
1.0
|
CB
|
B:ALA209
|
4.7
|
13.5
|
1.0
|
CB
|
B:MET350
|
4.7
|
19.7
|
1.0
|
CB
|
B:PHE210
|
4.7
|
11.2
|
1.0
|
O1
|
B:SO4504
|
4.7
|
34.2
|
0.8
|
CB
|
B:LEU258
|
4.7
|
16.5
|
1.0
|
O4
|
B:SO4504
|
4.7
|
24.8
|
0.8
|
CB
|
B:PHE164
|
4.8
|
14.1
|
1.0
|
CB
|
B:ALA349
|
4.9
|
12.7
|
1.0
|
CB
|
B:ALA257
|
4.9
|
12.2
|
1.0
|
|
Reference:
A.E.Aleshin,
F.M.Marassi.
Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium To Be Published.
Page generated: Fri Apr 7 16:00:06 2023
|