Magnesium in PDB 5xvc: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition, PDB code: 5xvc 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)	37.86 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.970, 121.830, 99.170, 90.00, 102.93, 90.00
R / Rfree (%)	16.6 / 21.7

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

Nickel	(Ni)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Magnesium atom in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition (pdb code 5xvc). 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 A Ferricyanide-Oxidized Condition, PDB code: 5xvc:
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 A Ferricyanide-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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg601 b:7.8 occ:1.00 O L:HOH708 2.0 6.5 1.0 O L:HOH764 2.0 6.5 1.0 O L:ALA498 2.1 4.5 1.0 O L:HOH738 2.1 5.7 1.0 OE2 L:GLU42 2.2 7.8 1.0 NE2 L:HIS552 2.3 9.8 1.0 CE1 L:HIS552 3.2 8.3 1.0 CD L:GLU42 3.2 9.7 1.0 C L:ALA498 3.2 3.4 1.0 CD2 L:HIS552 3.3 6.2 1.0 OE1 L:GLU42 3.6 8.5 1.0 N L:ALA498 3.6 5.9 1.0 OE1 L:GLN497 3.9 10.4 1.0 CA L:ALA498 3.9 6.7 1.0 OE2 L:GLU329 3.9 8.7 1.0 OE1 L:GLU329 4.0 7.7 1.0 O L:HOH778 4.2 5.9 1.0 NZ L:LYS366 4.3 9.3 1.0 N L:VAL499 4.3 4.8 1.0 O L:HOH754 4.3 6.7 1.0 ND1 L:HIS552 4.3 5.8 1.0 CB L:ALA498 4.4 7.3 1.0 CD L:GLU329 4.4 7.1 1.0 CG L:HIS552 4.5 8.2 1.0 CG L:GLU42 4.5 10.7 1.0 CD L:LYS366 4.5 4.2 1.0 CA L:VAL499 4.6 3.6 1.0 C L:GLN497 4.6 6.3 1.0 CE L:LYS366 4.8 5.7 1.0 CA L:GLN497 4.9 7.7 1.0

Magnesium binding site 2 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg700 b:10.3 occ:1.00 O M:HOH821 2.0 10.3 1.0 O M:HOH876 2.1 8.3 1.0 O M:ALA498 2.1 8.8 1.0 O M:HOH875 2.1 13.2 1.0 OE2 M:GLU42 2.2 8.7 1.0 NE2 M:HIS552 2.2 9.7 1.0 CE1 M:HIS552 3.1 10.4 1.0 C M:ALA498 3.2 7.8 1.0 CD M:GLU42 3.2 9.2 1.0 CD2 M:HIS552 3.3 7.1 1.0 OE1 M:GLU42 3.6 7.3 1.0 N M:ALA498 3.7 8.9 1.0 CA M:ALA498 4.0 11.3 1.0 OE2 M:GLU329 4.0 10.1 1.0 OE1 M:GLN497 4.0 12.4 1.0 OE1 M:GLU329 4.1 9.4 1.0 O M:HOH864 4.2 10.6 1.0 ND1 M:HIS552 4.3 11.9 1.0 O M:HOH909 4.3 10.0 1.0 N M:VAL499 4.3 6.1 1.0 NZ M:LYS366 4.3 12.0 1.0 CB M:ALA498 4.4 9.5 1.0 CG M:HIS552 4.4 12.1 1.0 CD M:GLU329 4.5 9.2 1.0 CG M:GLU42 4.5 12.0 1.0 CA M:VAL499 4.6 6.1 1.0 CD M:LYS366 4.6 10.0 1.0 CE M:LYS366 4.7 8.4 1.0 C M:GLN497 4.7 10.1 1.0 CA M:GLN497 5.0 8.0 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