Nickel in PDB 3cur: Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase

All present enzymatic activity of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase:
1.12.2.1;

The structure of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase, PDB code: 3cur was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.600, 99.900, 183.000, 90.00, 91.60, 90.00
R / Rfree (%)	15 / 19.4

The structure of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Iron	(Fe)	36 atoms

The binding sites of Nickel atom in the Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase (pdb code 3cur). 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 of A Double Methionine Mutant of Ni-Fe Hydrogenase, PDB code: 3cur:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni551 b:48.5 occ:1.00 O1 H:PER552 1.9 49.6 1.0 O2 H:PER552 2.1 49.7 0.6 SG H:CYS543 2.2 41.0 0.7 SG H:CYS72 2.3 46.4 1.0 SG H:CYS75 2.4 40.9 1.0 SG H:CYS546 2.6 41.1 1.0 SG H:CYS543 2.8 40.1 0.3 FE H:FCO550 2.8 40.5 1.0 CB H:CYS72 2.9 40.9 1.0 CB H:CYS543 3.2 39.5 0.7 CB H:CYS543 3.2 40.0 0.3 CB H:CYS75 3.5 41.2 1.0 N H:CYS75 3.5 41.0 1.0 CB H:CYS546 3.6 41.5 1.0 C1 H:FCO550 3.8 40.0 1.0 CA H:CYS75 4.1 41.7 1.0 C2 H:FCO550 4.1 41.3 1.0 CA H:CYS72 4.3 41.4 1.0 C3 H:FCO550 4.3 40.3 1.0 CB H:MET74 4.5 41.0 1.0 C H:MET74 4.6 42.8 1.0 CA H:CYS546 4.6 40.9 1.0 N H:CYS546 4.6 39.9 1.0 NH1 H:ARG476 4.6 45.8 1.0 CA H:CYS543 4.7 40.2 1.0 N1 H:FCO550 4.7 41.6 1.0 N H:MET74 4.7 41.3 1.0 C H:CYS75 4.8 41.2 1.0 CA H:MET74 4.8 42.6 1.0 C H:CYS72 4.8 40.6 1.0 CD H:ARG476 4.8 44.2 1.0 CZ H:ARG476 4.9 45.0 1.0 O H:CYS75 4.9 41.1 1.0 NE H:ARG476 4.9 43.0 1.0 CG H:GLU25 4.9 45.1 1.0

Nickel binding site 2 out of 3 in the Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni551 b:45.5 occ:1.00 O1 I:PER552 1.9 49.6 1.0 SG I:CYS543 2.1 52.3 1.0 SG I:CYS72 2.2 46.0 1.0 O2 I:PER552 2.2 49.8 0.6 SG I:CYS75 2.3 39.8 1.0 SG I:CYS546 2.6 40.8 1.0 FE I:FCO550 2.8 40.0 1.0 CB I:CYS72 2.9 41.1 1.0 CB I:CYS75 3.3 40.6 1.0 CB I:CYS543 3.4 43.5 1.0 N I:CYS75 3.5 40.7 1.0 CB I:CYS546 3.6 40.5 1.0 C1 I:FCO550 3.9 39.4 1.0 CA I:CYS75 4.0 41.4 1.0 C2 I:FCO550 4.1 41.1 1.0 C3 I:FCO550 4.3 41.2 1.0 CA I:CYS72 4.3 41.4 1.0 CB I:MET74 4.5 40.5 1.0 C I:MET74 4.6 41.7 1.0 CA I:CYS546 4.6 40.7 1.0 C I:CYS75 4.7 42.4 1.0 N I:CYS546 4.7 39.6 1.0 O I:CYS75 4.7 42.9 1.0 N1 I:FCO550 4.7 40.6 1.0 NH1 I:ARG476 4.7 46.1 1.0 N I:MET74 4.8 42.2 1.0 CA I:CYS543 4.8 41.0 1.0 C I:CYS72 4.8 41.1 1.0 CA I:MET74 4.9 42.4 1.0 CD I:ARG476 4.9 43.5 1.0 CZ I:ARG476 5.0 46.4 1.0 CG I:GLU25 5.0 45.5 1.0

Nickel binding site 3 out of 3 in the Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni551 b:45.0 occ:1.00 O1 J:PER552 1.9 49.5 1.0 O2 J:PER552 2.1 50.2 0.6 SG J:CYS543 2.2 40.8 0.7 SG J:CYS72 2.2 45.1 1.0 SG J:CYS75 2.3 41.8 1.0 SG J:CYS546 2.6 42.8 1.0 FE J:FCO550 2.8 41.4 1.0 SG J:CYS543 2.9 39.9 0.3 CB J:CYS72 3.0 40.5 1.0 CB J:CYS543 3.3 40.5 0.3 CB J:CYS543 3.3 40.2 0.7 CB J:CYS75 3.4 41.0 1.0 CB J:CYS546 3.6 41.1 1.0 N J:CYS75 3.6 40.6 1.0 C1 J:FCO550 3.8 40.1 1.0 C2 J:FCO550 4.0 41.4 1.0 CA J:CYS75 4.1 41.5 1.0 C3 J:FCO550 4.3 40.8 1.0 CA J:CYS72 4.4 41.0 1.0 CB J:MET74 4.5 42.1 1.0 CA J:CYS546 4.6 41.1 1.0 N J:CYS546 4.6 40.1 1.0 NH1 J:ARG476 4.6 45.4 1.0 N1 J:FCO550 4.7 41.6 1.0 CA J:CYS543 4.7 40.5 1.0 C J:MET74 4.7 42.1 1.0 CD J:ARG476 4.8 43.5 1.0 C J:CYS75 4.8 42.0 1.0 O J:CYS75 4.9 41.6 1.0 CZ J:ARG476 4.9 45.6 1.0 N J:MET74 4.9 42.0 1.0 C J:CYS72 4.9 40.5 1.0 CA J:MET74 4.9 42.8 1.0 NE J:ARG476 4.9 42.5 1.0 CG J:GLU25 4.9 45.6 1.0

F.Leroux, S.Dementin, B.Burlat, L.Cournac, A.Volbeda, S.Champ, L.Martin, B.Guigliarelli, P.Bertrand, J.Fontecilla-Camps, M.Rousset. Experimental Approaches to Kinetics of Gas Diffusion in Hydrogenase Proc.Natl.Acad.Sci.Usa V. 105 11188 2008.
ISSN: ISSN 0027-8424
PubMed: 18685111
DOI: 10.1073/PNAS.0803689105