Magnesium in PDB 4c3o: Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella

All present enzymatic activity of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella:
1.12.7.2;

The structure of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella, PDB code: 4c3o was solved by L.Bowman, L.Flanagan, P.K.Fyfe, A.Parkin, W.N.Hunter, F.Sargent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.52 / 3.20
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.460, 122.210, 227.820, 90.00, 95.56, 90.00
R / Rfree (%)	15.811 / 20.467

The structure of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Iron	(Fe)	36 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Magnesium atom in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella (pdb code 4c3o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella, PDB code: 4c3o:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1586 b:41.1 occ:1.00 OE2 C:GLU57 2.2 71.4 1.0 O C:CYS531 2.7 77.4 1.0 O C:HOH2019 2.7 50.5 1.0 NE2 C:HIS585 2.8 84.2 1.0 OE2 C:GLU347 2.9 89.6 1.0 CD C:GLU57 3.0 72.6 1.0 OE1 C:GLU57 3.0 73.7 1.0 OE1 C:GLN530 3.3 95.7 1.0 CE C:LYS402 3.4 97.3 1.0 NZ C:LYS402 3.6 98.3 1.0 CE1 C:HIS585 3.7 83.9 1.0 O C:HOH2026 3.7 82.1 1.0 CD C:GLU347 3.8 85.5 1.0 CD2 C:HIS585 3.8 84.2 1.0 C C:CYS531 3.8 77.8 1.0 CD C:LYS402 3.8 94.8 1.0 OE1 C:GLU347 3.9 83.9 1.0 N C:CYS531 4.2 79.2 1.0 CG C:LYS402 4.3 92.2 1.0 OG1 C:THR372 4.4 0.1 1.0 CG C:GLU57 4.4 72.1 1.0 CD C:GLN530 4.6 93.4 1.0 CA C:CYS531 4.6 77.2 1.0 CB C:LYS402 4.8 89.0 1.0 ND1 C:HIS585 4.8 82.6 1.0 N C:VAL532 4.8 73.9 1.0 CG C:HIS585 4.9 85.0 1.0

Magnesium binding site 2 out of 3 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:56.9 occ:1.00 OE2 A:GLU57 2.3 71.2 1.0 NE2 A:HIS585 2.5 82.4 1.0 O A:CYS531 2.6 89.6 1.0 CD A:GLU57 3.1 78.1 1.0 OE1 A:GLU57 3.1 83.7 1.0 OE2 A:GLU347 3.1 94.2 1.0 CE1 A:HIS585 3.3 83.9 1.0 CD2 A:HIS585 3.6 82.3 1.0 CE A:LYS402 3.6 82.3 1.0 OE1 A:GLN530 3.7 89.1 1.0 C A:CYS531 3.8 84.3 1.0 NZ A:LYS402 3.9 83.6 1.0 CD A:GLU347 3.9 96.1 1.0 OE1 A:GLU347 3.9 91.0 1.0 CD A:LYS402 3.9 84.0 1.0 O A:HOH2030 4.0 46.5 1.0 CG A:LYS402 4.2 82.0 1.0 O A:HOH2031 4.3 51.7 1.0 N A:CYS531 4.4 84.9 1.0 ND1 A:HIS585 4.5 82.9 1.0 CG A:GLU57 4.5 80.2 1.0 OG1 A:THR372 4.6 91.4 1.0 CA A:CYS531 4.6 83.8 1.0 CG A:HIS585 4.6 80.8 1.0 CB A:LYS402 4.7 82.3 1.0 N A:VAL532 4.8 80.9 1.0 CD A:GLN530 4.9 94.4 1.0 CA A:VAL532 5.0 84.5 1.0

Magnesium binding site 3 out of 3 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1005 b:50.0 occ:1.00 O E:CYS531 2.2 83.2 1.0 NE2 E:HIS585 2.3 84.3 1.0 OE2 E:GLU57 2.5 0.5 1.0 CE1 E:HIS585 2.9 85.4 1.0 O E:HOH2027 3.0 59.6 1.0 OE2 E:GLU347 3.2 0.2 1.0 C E:CYS531 3.5 87.3 1.0 CD E:GLU57 3.5 0.8 1.0 CD2 E:HIS585 3.5 83.4 1.0 OE1 E:GLU57 3.6 98.5 1.0 OE1 E:GLU347 3.7 0.8 1.0 O E:HOH2004 3.8 79.5 1.0 CD E:GLU347 3.9 0.3 1.0 CE E:LYS402 4.1 0.4 1.0 OE1 E:GLN530 4.1 92.4 1.0 ND1 E:HIS585 4.2 82.8 1.0 CD E:LYS402 4.3 0.9 1.0 N E:CYS531 4.3 92.9 1.0 N E:VAL532 4.4 83.2 1.0 NZ E:LYS402 4.4 0.8 1.0 CA E:CYS531 4.4 89.9 1.0 CG E:LYS402 4.4 0.9 1.0 CA E:VAL532 4.5 82.5 1.0 CG E:HIS585 4.5 81.8 1.0 CB E:LYS402 4.8 0.4 1.0 CB E:CYS531 4.8 89.8 1.0 CG E:GLU57 4.8 0.9 1.0 CG2 E:VAL532 4.9 87.5 1.0 CG2 E:THR536 4.9 91.9 1.0

L.Bowman, L.Flanagan, P.K.Fyfe, A.Parkin, W.N.Hunter, F.Sargent. How the Structure of the Large Subunit Controls Function in An Oxygen-Tolerant [Nife]-Hydrogenase. Biochem.J. V. 458 449 2014.
ISSN: ISSN 0264-6021
PubMed: 24428762
DOI: 10.1042/BJ20131520