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

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

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
Iron	(Fe)	32 atoms
Sodium	(Na)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:10.8 occ:1.00 O L:HOH745 2.1 12.4 1.0 O L:HOH747 2.1 13.2 1.0 OE2 L:GLU42 2.1 12.2 1.0 O L:ALA498 2.2 12.3 1.0 NE2 L:HIS552 2.2 12.3 1.0 O L:HOH791 2.2 12.6 1.0 CE1 L:HIS552 3.1 12.3 1.0 CD L:GLU42 3.2 13.1 1.0 CD2 L:HIS552 3.2 11.9 1.0 C L:ALA498 3.3 11.6 1.0 OE1 L:GLU42 3.5 12.8 1.0 N L:ALA498 3.7 10.3 1.0 CA L:ALA498 4.0 11.3 1.0 OE1 L:GLN497 4.0 18.1 1.0 OE2 L:GLU329 4.1 19.2 1.0 OE1 L:GLU329 4.2 20.6 1.0 O L:HOH912 4.2 11.4 1.0 ND1 L:HIS552 4.2 11.8 1.0 O L:HOH778 4.3 15.0 1.0 CG L:HIS552 4.3 11.2 1.0 CB L:ALA498 4.4 12.3 1.0 N L:VAL499 4.4 10.6 1.0 NZ L:LYS366 4.4 13.9 1.0 CG L:GLU42 4.5 13.5 1.0 CD L:LYS366 4.6 13.8 1.0 CD L:GLU329 4.6 18.4 1.0 C L:GLN497 4.7 11.7 1.0 CA L:VAL499 4.7 11.0 1.0 CE L:LYS366 4.8 14.7 1.0 CA L:GLN497 4.9 11.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:13.0 occ:1.00 O M:HOH724 2.1 15.8 1.0 O M:HOH786 2.1 14.3 1.0 O M:HOH729 2.1 16.4 1.0 OE2 M:GLU42 2.1 15.1 1.0 O M:ALA498 2.2 13.8 1.0 NE2 M:HIS552 2.2 14.0 1.0 CE1 M:HIS552 3.1 13.7 1.0 CD M:GLU42 3.1 15.4 1.0 CD2 M:HIS552 3.2 12.6 1.0 C M:ALA498 3.3 13.5 1.0 OE1 M:GLU42 3.5 16.2 1.0 N M:ALA498 3.7 14.1 1.0 OE1 M:GLN497 4.0 19.5 1.0 CA M:ALA498 4.0 14.3 1.0 OE2 M:GLU329 4.1 23.7 1.0 OE1 M:GLU329 4.2 22.6 1.0 O M:HOH797 4.2 16.7 1.0 ND1 M:HIS552 4.3 15.2 1.0 O M:HOH830 4.3 15.2 1.0 CG M:HIS552 4.3 14.5 1.0 NZ M:LYS366 4.3 16.0 1.0 N M:VAL499 4.4 14.4 1.0 CB M:ALA498 4.4 14.1 1.0 CG M:GLU42 4.4 16.2 1.0 CD M:LYS366 4.5 16.9 1.0 CD M:GLU329 4.6 22.2 1.0 CA M:VAL499 4.7 12.8 1.0 C M:GLN497 4.7 14.3 1.0 CE M:LYS366 4.7 16.2 1.0 CA M:GLN497 4.9 13.2 1.0 CD M:GLN497 5.0 18.6 1.0

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