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Sodium in PDB 5xvd: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition

Protein crystallography data

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd was solved by K.Nishikawa, H.Matsuura, N.D.Muhd Noor, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.72 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.940, 118.980, 96.810, 90.00, 100.57, 90.00
R / Rfree (%) 12.1 / 16.6

Other elements in 5xvd:

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 32 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition (pdb code 5xvd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5xvd

Go back to Sodium Binding Sites List in 5xvd
Sodium binding site 1 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na605

b:11.9
occ:1.00
O2 L:GOL604 3.1 22.3 1.0
O L:HOH1089 3.1 39.4 1.0
N L:GLU271 3.3 15.5 1.0
NE2 L:GLN178 3.3 16.4 1.0
C L:TYR269 3.6 13.4 1.0
CB L:GLU271 3.6 19.6 1.0
N L:PRO270 3.6 15.8 1.0
CD L:PRO270 3.6 16.2 1.0
CA L:TYR269 3.7 13.2 1.0
CD1 L:TRP272 3.8 12.8 1.0
C2 L:GOL604 3.8 26.3 1.0
CG L:GLU271 3.9 25.3 1.0
CA L:GLU271 3.9 16.9 1.0
OE1 L:GLN178 4.0 17.3 1.0
CG L:PRO270 4.1 17.3 1.0
O L:TYR269 4.1 12.7 1.0
CD L:GLN178 4.1 15.8 1.0
NE1 L:TRP272 4.2 13.7 1.0
C L:PRO270 4.3 15.5 1.0
O3 L:GOL604 4.3 18.1 1.0
CD L:GLU271 4.4 30.8 1.0
CB L:TYR269 4.4 12.6 1.0
CA L:PRO270 4.4 15.7 1.0
N L:TRP272 4.5 13.0 1.0
O L:PHE268 4.5 14.2 1.0
CD1 L:TYR269 4.5 11.9 1.0
OE2 L:GLU271 4.6 33.1 1.0
C L:GLU271 4.6 14.8 1.0
C3 L:GOL604 4.6 23.9 1.0
N L:TYR269 4.8 12.2 1.0
CB L:PRO270 4.9 18.2 1.0
O1 L:GOL604 4.9 33.6 1.0
CG L:TYR269 4.9 12.1 1.0
CG L:TRP272 5.0 12.1 1.0
OE1 L:GLU271 5.0 33.4 1.0

Sodium binding site 2 out of 2 in 5xvd

Go back to Sodium Binding Sites List in 5xvd
Sodium binding site 2 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na603

b:30.0
occ:1.00
NE2 M:GLN178 3.2 29.1 1.0
N M:GLU271 3.3 26.8 1.0
CB M:GLU271 3.4 30.8 1.0
C M:TYR269 3.5 23.3 1.0
CG M:GLU271 3.6 35.5 1.0
O M:HOH937 3.6 42.6 1.0
CA M:TYR269 3.6 20.7 1.0
N M:PRO270 3.7 24.8 1.0
CD M:PRO270 3.7 26.1 1.0
CD1 M:TRP272 3.8 19.7 1.0
OE1 M:GLN178 3.8 29.4 1.0
CA M:GLU271 3.9 28.0 1.0
O M:TYR269 4.0 22.7 1.0
CD M:GLN178 4.0 28.6 1.0
NE1 M:TRP272 4.2 20.2 1.0
CB M:TYR269 4.3 19.9 1.0
C M:PRO270 4.4 26.4 1.0
CG M:PRO270 4.4 26.9 1.0
O M:PHE268 4.4 23.6 1.0
O M:HOH817 4.4 27.6 1.0
N M:TRP272 4.5 23.4 1.0
CD1 M:TYR269 4.5 20.4 1.0
C M:GLU271 4.6 25.3 1.0
CA M:PRO270 4.6 26.7 1.0
N M:TYR269 4.7 21.1 1.0
CD M:GLU271 4.8 39.9 1.0
CG M:TYR269 4.9 19.7 1.0
CG M:TRP272 5.0 20.5 1.0
C M:PHE268 5.0 22.7 1.0

Reference:

N.D.M.Noor, H.Matsuura, K.Nishikawa, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, S.Kubota, Y.Shomura, Y.Higuchi. Redox-Dependent Conformational Changes of A Proximal [4FE-4S] Cluster in Hyb-Type [Nife]-Hydrogenase to Protect the Active Site From O2. Chem.Commun.(Camb.) V. 54 12385 2018.
ISSN: ESSN 1364-548X
PubMed: 30328414
DOI: 10.1039/C8CC06261G
Page generated: Tue Dec 15 11:50:35 2020

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