Nickel 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:

Magnesium	(Mg)	3 atoms
Iron	(Fe)	36 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Nickel 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 Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella, PDB code: 4c3o:
Jump to Nickel binding site number: 1; 2; 3;

Nickel 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 Nickel with other atoms in the Ni 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 A:Ni1004 b:73.0 occ:1.00 NI A:NFU1004 0.0 73.0 1.0 SG A:CYS79 2.2 74.0 1.0 SG A:CYS579 2.3 70.3 1.0 SG A:CYS76 2.4 62.4 1.0 SG A:CYS582 2.6 75.1 1.0 CB A:CYS582 2.7 68.0 1.0 CB A:CYS79 2.8 68.7 1.0 FE A:NFU1004 2.9 71.6 1.0 CB A:CYS579 3.1 72.7 1.0 CB A:CYS76 3.3 65.6 1.0 C2 A:NFU1004 3.7 70.4 1.0 N A:CYS79 3.7 69.2 1.0 CA A:CYS79 3.8 71.1 1.0 NH1 A:ARG512 4.1 62.2 1.0 CA A:CYS582 4.1 68.3 1.0 C1 A:NFU1004 4.3 78.7 1.0 C3 A:NFU1004 4.3 69.8 1.0 CD A:ARG512 4.3 64.6 1.0 N A:CYS582 4.5 70.5 1.0 CZ A:ARG512 4.5 59.7 1.0 N2 A:NFU1004 4.5 73.7 1.0 CA A:CYS579 4.5 72.2 1.0 NE A:ARG512 4.6 61.4 1.0 CB A:VAL78 4.6 63.0 1.0 CA A:CYS76 4.8 69.5 1.0 C A:VAL78 4.8 63.7 1.0 CG A:GLU28 4.9 73.9 1.0 C A:CYS79 4.9 72.8 1.0 O A:CYS579 4.9 71.4 1.0 C A:CYS579 5.0 71.5 1.0

Nickel 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 Nickel with other atoms in the Ni 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 C:Ni1004 b:71.3 occ:1.00 NI C:NFU1004 0.0 71.3 1.0 SG C:CYS79 2.2 70.0 1.0 SG C:CYS579 2.3 75.5 1.0 SG C:CYS76 2.3 71.8 1.0 SG C:CYS582 2.5 73.9 1.0 CB C:CYS582 2.5 71.4 1.0 FE C:NFU1004 2.9 68.5 1.0 CB C:CYS79 2.9 68.5 1.0 CB C:CYS579 3.2 73.2 1.0 CB C:CYS76 3.2 71.3 1.0 C1 C:NFU1004 3.9 68.7 1.0 N C:CYS79 3.9 70.9 1.0 CA C:CYS582 3.9 71.1 1.0 CG2 C:VAL78 3.9 71.1 1.0 CA C:CYS79 4.0 71.0 1.0 N C:CYS582 4.2 75.1 1.0 C2 C:NFU1004 4.2 68.0 1.0 C3 C:NFU1004 4.4 83.2 1.0 CD C:ARG512 4.5 77.3 1.0 NH1 C:ARG512 4.6 68.0 1.0 CA C:CYS579 4.6 74.2 1.0 CA C:CYS76 4.6 75.3 1.0 NE C:ARG512 4.6 72.1 1.0 CZ C:ARG512 4.7 71.2 1.0 N1 C:NFU1004 4.8 76.0 1.0 CG C:GLU28 4.8 78.3 1.0 O C:CYS579 4.9 66.2 1.0 C C:CYS579 4.9 71.6 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni1004 b:79.4 occ:1.00 NI E:NFU1004 0.0 79.4 1.0 SG E:CYS79 2.2 82.9 1.0 SG E:CYS579 2.3 88.8 1.0 SG E:CYS76 2.4 76.4 1.0 SG E:CYS582 2.5 78.2 1.0 CB E:CYS582 2.7 75.6 1.0 CB E:CYS79 2.9 79.1 1.0 FE E:NFU1004 2.9 74.2 1.0 CB E:CYS579 3.1 89.4 1.0 CB E:CYS76 3.3 73.1 1.0 C2 E:NFU1004 3.7 86.7 1.0 N E:CYS79 3.7 85.5 1.0 CA E:CYS79 3.9 83.9 1.0 CA E:CYS582 4.1 77.0 1.0 C3 E:NFU1004 4.3 75.6 1.0 C1 E:NFU1004 4.3 80.1 1.0 CD E:ARG512 4.3 81.1 1.0 NH1 E:ARG512 4.4 76.1 1.0 N E:CYS582 4.4 82.0 1.0 NE E:ARG512 4.4 78.6 1.0 CZ E:ARG512 4.5 73.4 1.0 N2 E:NFU1004 4.5 0.8 1.0 CA E:CYS579 4.5 87.3 1.0 CB E:VAL78 4.6 78.7 1.0 CA E:CYS76 4.7 71.8 1.0 CG E:GLU28 4.9 83.0 1.0 C E:VAL78 4.9 77.7 1.0 O E:CYS579 4.9 82.8 1.0 C E:CYS579 4.9 87.0 1.0 C E:CYS79 5.0 84.3 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