Magnesium in PDB 9bt4: Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans

All present enzymatic activity of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans:
1.2.7.1;

The structure of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans, PDB code: 9bt4 was solved by D.Catlin, S.J.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.92
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	79.121, 79.121, 496.524, 90, 90, 120
R / Rfree (%)	17.3 / 20

The structure of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans also contains other interesting chemical elements:

Iron

(Fe)

24 atoms

The binding sites of Magnesium atom in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans (pdb code 9bt4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans, PDB code: 9bt4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:11.1 occ:1.00 OD1 C:ASN126 2.0 12.4 1.0 O C:ALA128 2.0 13.7 1.0 O2A C:TPP302 2.0 12.5 1.0 OD1 C:ASP98 2.0 13.3 1.0 O3B C:TPP302 2.0 12.3 1.0 O C:HOH442 2.4 14.5 1.0 CG C:ASP98 3.0 13.4 1.0 CG C:ASN126 3.0 12.5 1.0 C C:ALA128 3.2 14.1 1.0 PA C:TPP302 3.2 12.7 1.0 PB C:TPP302 3.3 13.1 1.0 OD2 C:ASP98 3.4 13.4 1.0 O3A C:TPP302 3.4 13.1 1.0 ND2 C:ASN126 3.5 12.7 1.0 O2B C:TPP302 3.9 13.5 1.0 O7 C:TPP302 4.0 13.6 1.0 N C:ALA128 4.0 14.0 1.0 N C:ASP98 4.0 13.6 1.0 N C:TYR129 4.1 14.5 1.0 N C:MET130 4.2 15.1 1.0 CA C:TYR129 4.2 14.9 1.0 N C:ASN126 4.2 13.4 1.0 CA C:ALA128 4.2 14.1 1.0 CB C:ASP98 4.3 13.3 1.0 CB C:ASN126 4.3 13.0 1.0 CG C:MET130 4.4 15.2 1.0 N C:GLY99 4.4 14.4 1.0 C C:ASN126 4.5 13.3 1.0 N C:GLU127 4.5 13.3 1.0 O1A C:TPP302 4.5 12.6 1.0 O1B C:TPP302 4.5 12.7 1.0 CA C:ASN126 4.5 13.2 1.0 O C:VAL124 4.5 13.4 1.0 CA C:GLY97 4.6 12.9 1.0 CA C:ASP98 4.7 13.6 1.0 C C:TYR129 4.7 14.7 1.0 C C:GLY97 4.8 13.2 1.0 CB C:MET130 4.9 15.2 1.0 O C:ASN126 4.9 13.0 1.0

Magnesium binding site 2 out of 2 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:11.1 occ:1.00 O D:ALA128 2.0 13.7 1.0 OD1 D:ASN126 2.0 12.1 1.0 O2A D:TPP302 2.0 12.6 1.0 O3B D:TPP302 2.0 12.7 1.0 OD1 D:ASP98 2.0 13.4 1.0 O D:HOH443 2.4 14.6 1.0 CG D:ASP98 3.0 13.9 1.0 CG D:ASN126 3.1 12.3 1.0 PA D:TPP302 3.2 13.2 1.0 C D:ALA128 3.2 14.2 1.0 PB D:TPP302 3.3 13.7 1.0 OD2 D:ASP98 3.4 14.4 1.0 O3A D:TPP302 3.4 13.6 1.0 ND2 D:ASN126 3.6 12.4 1.0 O2B D:TPP302 3.9 14.5 1.0 N D:ALA128 4.0 14.1 1.0 O7 D:TPP302 4.0 14.2 1.0 N D:ASP98 4.0 13.8 1.0 N D:TYR129 4.1 14.4 1.0 CA D:TYR129 4.2 15.0 1.0 N D:ASN126 4.2 13.4 1.0 N D:MET130 4.2 15.0 1.0 CA D:ALA128 4.3 14.0 1.0 CB D:ASP98 4.3 13.7 1.0 CB D:ASN126 4.3 12.8 1.0 CG D:MET130 4.4 15.3 1.0 N D:GLY99 4.5 14.8 1.0 N D:GLU127 4.5 13.8 1.0 C D:ASN126 4.5 13.7 1.0 O1B D:TPP302 4.5 13.4 1.0 CA D:ASN126 4.5 13.3 1.0 O1A D:TPP302 4.5 12.8 1.0 O D:VAL124 4.5 13.9 1.0 CA D:GLY97 4.6 13.5 1.0 CA D:ASP98 4.7 13.9 1.0 C D:TYR129 4.7 14.6 1.0 C D:GLY97 4.8 13.7 1.0 CB D:MET130 4.9 15.0 1.0 O D:ASN126 4.9 13.8 1.0

M.Cossu, D.Catlin, S.J.Elliott, W.W.Metcalf, S.K.Nair. Structural Organization of Pyruvate: Ferredoxin Oxidoreductase From the Methanogenic Archaeon Methanosarcina Acetivorans. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 39265575
DOI: 10.1016/J.STR.2024.08.011