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Sodium in PDB 1zv8: A Structure-Based Mechanism of Sars Virus Membrane Fusion

Protein crystallography data

The structure of A Structure-Based Mechanism of Sars Virus Membrane Fusion, PDB code: 1zv8 was solved by Y.Deng, J.Liu, Q.Zheng, W.Yong, J.Dai, M.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 1.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 31.054, 55.565, 71.678, 81.26, 87.08, 84.10
R / Rfree (%) 20.3 / 27.4

Other elements in 1zv8:

The structure of A Structure-Based Mechanism of Sars Virus Membrane Fusion also contains other interesting chemical elements:

Arsenic (As) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the A Structure-Based Mechanism of Sars Virus Membrane Fusion (pdb code 1zv8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the A Structure-Based Mechanism of Sars Virus Membrane Fusion, PDB code: 1zv8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1zv8

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Sodium binding site 1 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:41.5
occ:1.00
 OE1 A:GLU18 2.3 32.8 1.0
O A:HOH215 2.6 49.5 1.0
OE2 A:GLU18 2.9 33.6 1.0
CD A:GLU18 2.9 32.4 1.0
NH2 B:ARG18 3.4 32.5 1.0
CZ B:ARG18 3.7 34.1 1.0
NH1 B:ARG18 4.2 35.3 1.0
NE B:ARG18 4.3 30.6 1.0
CG A:GLU18 4.3 25.9 1.0
OG1 A:THR22 4.4 14.5 1.0
OG1 A:THR21 4.8 17.7 1.0
CB A:GLU18 5.0 15.2 1.0

Sodium binding site 2 out of 6 in 1zv8

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Sodium binding site 2 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:56.6
occ:1.00
 OE1 B:GLU21 2.0 17.0 1.0
OE2 B:GLU21 2.6 13.6 1.0
CD B:GLU21 2.7 17.1 1.0
CG B:GLU21 4.2 15.1 1.0
O B:HOH209 4.5 54.2 1.0

Sodium binding site 3 out of 6 in 1zv8

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Sodium binding site 3 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na208

b:50.7
occ:1.00
 O G:HOH220 2.3 50.9 1.0
O G:HOH213 2.3 34.9 1.0
OD1 G:ASP32 2.4 31.5 1.0
O L:HOH44 3.0 58.7 1.0
CG G:ASP32 3.5 24.6 1.0
NE2 G:GLN31 3.6 12.4 1.0
O G:HOH212 3.9 41.1 1.0
OD2 G:ASP32 4.0 32.0 1.0
O G:HOH215 4.0 39.3 1.0
OE1 L:GLN13 4.2 17.1 1.0
CD G:GLN31 4.6 16.0 1.0
CB G:ASP32 4.7 19.4 1.0
O G:GLY28 4.8 14.6 1.0
CA G:ASP32 4.8 16.8 1.0
CG G:GLN31 4.8 12.9 1.0
N G:ASP32 5.0 16.4 1.0

Sodium binding site 4 out of 6 in 1zv8

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Sodium binding site 4 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na210

b:45.9
occ:1.00
 O H:HOH229 2.0 55.8 1.0
O H:HOH226 2.3 50.8 1.0
O H:HOH225 2.5 69.6 1.0
OD2 H:ASP32 2.9 30.1 1.0
CG H:ASP32 4.1 24.9 1.0
O H:HOH220 4.6 45.1 1.0
OD1 H:ASP32 4.9 26.1 1.0
CB H:ASP32 5.0 19.9 1.0

Sodium binding site 5 out of 6 in 1zv8

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Sodium binding site 5 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na207

b:35.5
occ:1.00
 OE2 J:GLU28 1.8 26.8 1.0
OE1 F:GLU21 1.8 34.2 1.0
O J:HOH217 2.2 47.7 1.0
O E:HOH59 2.7 46.7 1.0
CD J:GLU28 2.8 29.8 1.0
CD F:GLU21 3.0 32.1 1.0
OE1 J:GLU28 3.3 37.0 1.0
OE2 F:GLU21 3.6 35.5 1.0
NH1 F:ARG18 3.7 8.4 1.0
O J:HOH210 3.9 42.0 1.0
CG J:GLU28 4.0 22.9 1.0
CG F:GLU21 4.2 25.8 1.0
CB F:GLU21 4.3 16.9 1.0
CD F:ARG18 4.4 16.1 1.0
CA F:ARG18 4.7 15.2 1.0
CZ F:ARG18 4.9 8.0 1.0
CB F:ARG18 5.0 16.5 1.0

Sodium binding site 6 out of 6 in 1zv8

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Sodium binding site 6 out of 6 in the A Structure-Based Mechanism of Sars Virus Membrane Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Structure-Based Mechanism of Sars Virus Membrane Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na205

b:36.6
occ:1.00
 O K:HOH220 1.7 41.6 1.0
OD1 K:ASP32 2.1 22.6 1.0
O K:HOH219 2.2 46.8 1.0
O K:HOH223 2.3 48.1 1.0
CG K:ASP32 3.1 22.4 1.0
OD2 K:ASP32 3.4 25.3 1.0
NE2 K:GLN31 3.7 12.6 1.0
OE1 J:GLN13 4.1 11.4 1.0
O J:HOH214 4.1 52.4 1.0
CB K:ASP32 4.4 12.1 1.0
O K:GLY28 4.5 11.7 1.0
CA K:ASP32 4.7 13.8 1.0
CD K:GLN31 4.7 14.1 1.0
CG K:GLN31 4.8 11.5 1.0
N K:ASP32 4.9 13.1 1.0
CB K:GLN31 5.0 7.8 1.0

Reference:

Y.Deng, J.Liu, Q.Zheng, W.Yong, M.Lu. Structures and Polymorphic Interactions of Two Heptad-Repeat Regions of the Sars Virus S2 Protein. Structure V. 14 889 2006.
ISSN: ISSN 0969-2126
PubMed: 16698550
DOI: 10.1016/J.STR.2006.03.007
Page generated: Mon Oct 7 01:45:39 2024

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