Sodium in PDB 6o5e: Crystal Structure of the Vitronectin Hemopexin-Like Domain
Protein crystallography data
The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain, PDB code: 6o5e
was solved by
B.C.Lechtenberg,
K.Shin,
F.M.Marassi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.21 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.560,
97.360,
49.160,
90.00,
99.90,
90.00
|
R / Rfree (%)
|
17.9 /
21
|
Other elements in 6o5e:
The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain 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
(pdb code 6o5e). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of the Vitronectin Hemopexin-Like Domain, PDB code: 6o5e:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6o5e
Go back to
Sodium Binding Sites List in 6o5e
Sodium binding site 1 out
of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_01_stereo.jpg) 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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:18.9
occ:1.00
|
O
|
A:HOH689
|
2.1
|
33.6
|
1.0
|
O
|
A:ASP255
|
2.3
|
21.6
|
1.0
|
O
|
A:ASP207
|
2.3
|
24.0
|
1.0
|
O
|
A:ASP162
|
2.3
|
19.9
|
1.0
|
O
|
A:ASP347
|
2.3
|
25.0
|
1.0
|
C
|
A:ASP255
|
3.4
|
23.8
|
1.0
|
O
|
A:HOH671
|
3.4
|
51.5
|
1.0
|
C
|
A:ASP347
|
3.5
|
24.9
|
1.0
|
C
|
A:ASP207
|
3.5
|
22.5
|
1.0
|
C
|
A:ASP162
|
3.5
|
23.1
|
1.0
|
HA
|
A:ASP255
|
3.7
|
26.5
|
1.0
|
HA
|
A:ASP207
|
3.8
|
29.4
|
1.0
|
HA
|
A:ASP162
|
3.8
|
28.7
|
1.0
|
HA
|
A:ALA348
|
3.9
|
23.0
|
1.0
|
HB2
|
A:ALA348
|
3.9
|
22.6
|
1.0
|
HA
|
A:ASP347
|
4.0
|
31.0
|
1.0
|
HA
|
A:ALA256
|
4.1
|
24.5
|
1.0
|
HB2
|
A:ALA163
|
4.1
|
23.4
|
1.0
|
CA
|
A:ASP255
|
4.1
|
22.1
|
1.0
|
HA
|
A:ALA208
|
4.2
|
26.7
|
1.0
|
CA
|
A:ASP162
|
4.2
|
23.9
|
1.0
|
CA
|
A:ASP207
|
4.2
|
24.6
|
1.0
|
HA
|
A:ALA163
|
4.2
|
22.8
|
1.0
|
HB3
|
A:ASP162
|
4.2
|
25.6
|
1.0
|
HB2
|
A:ALA208
|
4.3
|
23.8
|
1.0
|
N
|
A:ALA348
|
4.3
|
20.0
|
1.0
|
CA
|
A:ASP347
|
4.3
|
25.8
|
1.0
|
HB2
|
A:ALA256
|
4.4
|
27.8
|
1.0
|
CA
|
A:ALA348
|
4.4
|
19.3
|
1.0
|
HB3
|
A:ASP255
|
4.4
|
25.9
|
1.0
|
N
|
A:ALA256
|
4.5
|
23.0
|
1.0
|
N
|
A:ALA208
|
4.5
|
23.3
|
1.0
|
N
|
A:ALA163
|
4.5
|
19.9
|
1.0
|
HB3
|
A:ASP347
|
4.6
|
40.1
|
1.0
|
CB
|
A:ALA348
|
4.6
|
19.0
|
1.0
|
CA
|
A:ALA256
|
4.7
|
20.4
|
1.0
|
HB3
|
A:ASP207
|
4.7
|
30.9
|
1.0
|
CA
|
A:ALA163
|
4.7
|
19.2
|
1.0
|
CA
|
A:ALA208
|
4.7
|
22.2
|
1.0
|
O
|
A:ILE206
|
4.7
|
28.7
|
1.0
|
CB
|
A:ASP162
|
4.8
|
21.5
|
1.0
|
CB
|
A:ALA163
|
4.9
|
19.4
|
1.0
|
CB
|
A:ASP255
|
4.9
|
21.6
|
1.0
|
O
|
A:VAL254
|
4.9
|
29.1
|
1.0
|
CB
|
A:ALA208
|
5.0
|
19.8
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6o5e
Go back to
Sodium Binding Sites List in 6o5e
Sodium binding site 2 out
of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_02_stereo.jpg) 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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:16.2
occ:1.00
|
O
|
A:ALA209
|
2.2
|
18.0
|
1.0
|
O
|
A:ALA257
|
2.3
|
22.1
|
1.0
|
O
|
A:ALA349
|
2.3
|
18.5
|
1.0
|
O
|
A:PHE164
|
2.3
|
21.5
|
1.0
|
O
|
A:HOH621
|
2.3
|
64.4
|
1.0
|
CL
|
A:CL502
|
2.7
|
19.0
|
1.0
|
H
|
A:ALA209
|
3.2
|
25.2
|
1.0
|
H
|
A:PHE164
|
3.3
|
22.3
|
1.0
|
H
|
A:ALA257
|
3.3
|
26.1
|
1.0
|
C
|
A:ALA209
|
3.4
|
19.0
|
1.0
|
C
|
A:ALA257
|
3.4
|
22.5
|
1.0
|
C
|
A:ALA349
|
3.4
|
20.4
|
1.0
|
H
|
A:ALA349
|
3.5
|
22.9
|
1.0
|
C
|
A:PHE164
|
3.5
|
20.1
|
1.0
|
HA
|
A:MET350
|
3.7
|
24.6
|
1.0
|
HB2
|
A:PHE164
|
3.7
|
26.1
|
1.0
|
HA
|
A:LEU258
|
3.8
|
27.9
|
1.0
|
HA
|
A:PHE210
|
3.9
|
26.4
|
1.0
|
N
|
A:ALA209
|
3.9
|
21.0
|
1.0
|
HB3
|
A:MET350
|
4.0
|
26.5
|
1.0
|
HB3
|
A:ALA209
|
4.0
|
20.8
|
1.0
|
N
|
A:PHE164
|
4.0
|
18.8
|
1.0
|
N
|
A:ALA257
|
4.0
|
21.7
|
1.0
|
HA
|
A:THR165
|
4.0
|
24.2
|
1.0
|
HB3
|
A:PHE210
|
4.1
|
26.1
|
1.0
|
HB3
|
A:ALA257
|
4.1
|
26.5
|
1.0
|
HB3
|
A:ALA349
|
4.1
|
25.5
|
1.0
|
CA
|
A:ALA209
|
4.2
|
16.8
|
1.0
|
N
|
A:ALA349
|
4.2
|
19.1
|
1.0
|
CA
|
A:PHE164
|
4.2
|
20.7
|
1.0
|
CA
|
A:ALA257
|
4.2
|
19.9
|
1.0
|
HB3
|
A:LEU258
|
4.3
|
28.4
|
1.0
|
N
|
A:MET350
|
4.3
|
18.4
|
1.0
|
CA
|
A:ALA349
|
4.3
|
18.8
|
1.0
|
CA
|
A:MET350
|
4.4
|
20.5
|
1.0
|
N
|
A:LEU258
|
4.4
|
20.2
|
1.0
|
N
|
A:PHE210
|
4.4
|
22.1
|
1.0
|
CB
|
A:PHE164
|
4.4
|
21.7
|
1.0
|
CA
|
A:LEU258
|
4.5
|
23.2
|
1.0
|
CA
|
A:PHE210
|
4.5
|
22.0
|
1.0
|
N
|
A:THR165
|
4.5
|
18.8
|
1.0
|
CA
|
A:THR165
|
4.6
|
20.1
|
1.0
|
CB
|
A:ALA209
|
4.6
|
17.3
|
1.0
|
CB
|
A:MET350
|
4.7
|
22.1
|
1.0
|
HB3
|
A:PHE164
|
4.7
|
26.1
|
1.0
|
HB1
|
A:ALA208
|
4.7
|
23.8
|
1.0
|
CB
|
A:ALA257
|
4.7
|
22.1
|
1.0
|
CB
|
A:PHE210
|
4.8
|
21.7
|
1.0
|
CB
|
A:ALA349
|
4.8
|
21.2
|
1.0
|
OD1
|
A:ASP166
|
4.8
|
26.0
|
1.0
|
C
|
A:THR165
|
4.8
|
24.1
|
1.0
|
HB1
|
A:ALA163
|
4.8
|
23.4
|
1.0
|
CB
|
A:LEU258
|
4.9
|
23.6
|
1.0
|
HB1
|
A:ALA256
|
4.9
|
27.8
|
1.0
|
HA
|
A:ALA208
|
4.9
|
26.7
|
1.0
|
HA
|
A:ALA163
|
5.0
|
22.8
|
1.0
|
O
|
A:THR165
|
5.0
|
27.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6o5e
Go back to
Sodium Binding Sites List in 6o5e
Sodium binding site 3 out
of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Vitronectin Hemopexin-Like Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:22.9
occ:1.00
|
O
|
B:HOH664
|
2.1
|
33.2
|
1.0
|
O
|
B:ASP207
|
2.2
|
24.1
|
1.0
|
O
|
B:ASP255
|
2.2
|
26.4
|
1.0
|
O
|
B:ASP162
|
2.2
|
26.6
|
1.0
|
O
|
B:ASP347
|
2.4
|
25.4
|
1.0
|
C
|
B:ASP162
|
3.2
|
27.6
|
1.0
|
C
|
B:ASP255
|
3.3
|
26.8
|
1.0
|
C
|
B:ASP207
|
3.3
|
24.4
|
1.0
|
HA
|
B:ASP162
|
3.3
|
33.5
|
1.0
|
C
|
B:ASP347
|
3.5
|
25.5
|
1.0
|
HA
|
B:ASP255
|
3.5
|
29.4
|
1.0
|
HA
|
B:ASP207
|
3.7
|
30.8
|
1.0
|
CA
|
B:ASP162
|
3.8
|
28.1
|
1.0
|
HA
|
B:ALA256
|
3.9
|
26.5
|
1.0
|
HA
|
B:ASP347
|
3.9
|
31.9
|
1.0
|
CA
|
B:ASP255
|
4.0
|
24.4
|
1.0
|
HA
|
B:ALA348
|
4.0
|
28.0
|
1.0
|
HA
|
B:ALA208
|
4.0
|
29.7
|
1.0
|
CA
|
B:ASP207
|
4.1
|
25.6
|
1.0
|
HB3
|
B:ASP162
|
4.1
|
35.3
|
1.0
|
HB2
|
B:ALA348
|
4.2
|
27.9
|
1.0
|
HB2
|
B:ALA208
|
4.2
|
33.6
|
1.0
|
HA
|
B:ALA163
|
4.2
|
33.6
|
1.0
|
N
|
B:ALA256
|
4.3
|
22.6
|
1.0
|
HB2
|
B:ALA163
|
4.3
|
35.6
|
1.0
|
CA
|
B:ASP347
|
4.3
|
26.8
|
1.0
|
N
|
B:ALA208
|
4.3
|
26.9
|
1.0
|
N
|
B:ALA163
|
4.3
|
28.3
|
1.0
|
HB2
|
B:ALA256
|
4.4
|
27.7
|
1.0
|
N
|
B:ALA348
|
4.4
|
24.6
|
1.0
|
HB3
|
B:ASP255
|
4.4
|
30.9
|
1.0
|
O
|
B:HOH637
|
4.4
|
50.9
|
1.0
|
HB3
|
B:ASP347
|
4.5
|
37.0
|
1.0
|
CA
|
B:ALA256
|
4.5
|
22.1
|
1.0
|
CA
|
B:ALA348
|
4.5
|
23.5
|
1.0
|
CA
|
B:ALA208
|
4.5
|
24.7
|
1.0
|
CB
|
B:ASP162
|
4.6
|
29.6
|
1.0
|
HB3
|
B:ASP207
|
4.6
|
33.8
|
1.0
|
CA
|
B:ALA163
|
4.7
|
28.1
|
1.0
|
CB
|
B:ASP255
|
4.8
|
25.7
|
1.0
|
O
|
B:VAL254
|
4.8
|
27.4
|
1.0
|
CB
|
B:ALA348
|
4.8
|
23.3
|
1.0
|
O
|
B:PHE161
|
4.8
|
28.0
|
1.0
|
CB
|
B:ALA208
|
4.9
|
28.0
|
1.0
|
O
|
B:ILE206
|
4.9
|
28.8
|
1.0
|
CB
|
B:ALA256
|
4.9
|
23.0
|
1.0
|
CB
|
B:ASP207
|
5.0
|
28.1
|
1.0
|
CB
|
B:ALA163
|
5.0
|
29.6
|
1.0
|
CB
|
B:ASP347
|
5.0
|
30.8
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6o5e
Go back to
Sodium Binding Sites List in 6o5e
Sodium binding site 4 out
of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/o5/6o5e-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Vitronectin Hemopexin-Like Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:22.2
occ:1.00
|
O
|
B:ALA257
|
2.2
|
22.8
|
1.0
|
O
|
B:ALA349
|
2.2
|
21.2
|
1.0
|
O
|
B:ALA209
|
2.3
|
22.9
|
1.0
|
O
|
B:PHE164
|
2.3
|
28.1
|
1.0
|
CL
|
B:CL502
|
2.8
|
22.9
|
1.0
|
O2
|
B:SO4504
|
2.8
|
46.9
|
1.0
|
C
|
B:ALA349
|
3.3
|
22.6
|
1.0
|
C
|
B:ALA257
|
3.4
|
23.0
|
1.0
|
H
|
B:ALA349
|
3.4
|
26.8
|
1.0
|
H
|
B:ALA209
|
3.4
|
22.3
|
1.0
|
H
|
B:ALA257
|
3.4
|
27.7
|
1.0
|
C
|
B:ALA209
|
3.5
|
21.1
|
1.0
|
H
|
B:PHE164
|
3.5
|
33.9
|
1.0
|
C
|
B:PHE164
|
3.5
|
29.3
|
1.0
|
HA
|
B:MET350
|
3.6
|
25.0
|
1.0
|
HA
|
B:LEU258
|
3.6
|
34.9
|
1.0
|
HA
|
B:THR165
|
3.8
|
36.9
|
1.0
|
HA
|
B:PHE210
|
3.9
|
27.7
|
1.0
|
HB3
|
B:PHE210
|
3.9
|
27.8
|
1.0
|
HB3
|
B:LEU258
|
4.0
|
32.2
|
1.0
|
HB
|
B:THR165
|
4.0
|
37.8
|
1.0
|
HB3
|
B:ALA349
|
4.1
|
29.4
|
1.0
|
N
|
B:ALA349
|
4.1
|
22.4
|
1.0
|
N
|
B:ALA209
|
4.1
|
18.5
|
1.0
|
N
|
B:ALA257
|
4.2
|
23.0
|
1.0
|
HB3
|
B:ALA209
|
4.2
|
29.6
|
1.0
|
N
|
B:PHE164
|
4.2
|
28.4
|
1.0
|
HB2
|
B:MET350
|
4.2
|
29.2
|
1.0
|
N
|
B:MET350
|
4.2
|
21.2
|
1.0
|
CA
|
B:ALA349
|
4.2
|
23.4
|
1.0
|
S
|
B:SO4504
|
4.3
|
35.1
|
1.0
|
HB2
|
B:PHE164
|
4.3
|
33.6
|
1.0
|
N
|
B:LEU258
|
4.3
|
26.4
|
1.0
|
CA
|
B:MET350
|
4.3
|
20.8
|
1.0
|
HB3
|
B:ALA257
|
4.3
|
29.2
|
1.0
|
CA
|
B:ALA257
|
4.3
|
23.4
|
1.0
|
CA
|
B:LEU258
|
4.3
|
29.0
|
1.0
|
CA
|
B:ALA209
|
4.3
|
21.7
|
1.0
|
CA
|
B:PHE164
|
4.4
|
29.2
|
1.0
|
N
|
B:PHE210
|
4.4
|
21.6
|
1.0
|
CA
|
B:THR165
|
4.4
|
30.9
|
1.0
|
CA
|
B:PHE210
|
4.4
|
23.1
|
1.0
|
N
|
B:THR165
|
4.5
|
30.8
|
1.0
|
CB
|
B:PHE210
|
4.6
|
23.1
|
1.0
|
CB
|
B:LEU258
|
4.6
|
26.8
|
1.0
|
CB
|
B:ALA349
|
4.7
|
24.5
|
1.0
|
CB
|
B:THR165
|
4.7
|
31.6
|
1.0
|
CB
|
B:PHE164
|
4.7
|
28.1
|
1.0
|
CB
|
B:ALA209
|
4.8
|
24.6
|
1.0
|
CB
|
B:MET350
|
4.8
|
24.3
|
1.0
|
O3
|
B:SO4504
|
4.8
|
44.0
|
1.0
|
CB
|
B:ALA257
|
4.8
|
24.3
|
1.0
|
HB3
|
B:PHE164
|
4.8
|
33.6
|
1.0
|
HG3
|
B:MET350
|
4.9
|
38.1
|
1.0
|
HB1
|
B:ALA163
|
4.9
|
35.6
|
1.0
|
HB2
|
B:PHE210
|
4.9
|
27.8
|
1.0
|
HB2
|
B:LEU258
|
4.9
|
32.2
|
1.0
|
O4
|
B:SO4504
|
4.9
|
41.3
|
1.0
|
HB1
|
B:ALA256
|
4.9
|
27.7
|
1.0
|
HB1
|
B:ALA348
|
4.9
|
27.9
|
1.0
|
HB1
|
B:ALA208
|
5.0
|
33.6
|
1.0
|
|
Reference:
K.Shin,
B.C.Lechtenberg,
L.M.Fujimoto,
Y.Yao,
S.S.Bartra,
G.V.Plano,
F.M.Marassi.
Structure of Human Vitronectin C-Terminal Domain and Interaction Withyersinia Pestisouter Membrane Protein Ail. Sci Adv V. 5 X5068 2019.
ISSN: ESSN 2375-2548
PubMed: 31535027
DOI: 10.1126/SCIADV.AAX5068
Page generated: Tue Dec 15 12:40:57 2020
|