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

Enzymatic activity of 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;

Protein crystallography data

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

Nickel Binding Sites:

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 3cur

Go back to Nickel Binding Sites List in 3cur
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 3cur

Go back to Nickel Binding Sites List in 3cur
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 3cur

Go back to Nickel Binding Sites List in 3cur
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

Reference:

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
Page generated: Fri Sep 25 08:20:37 2020
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