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Nickel in PDB 3cus: Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution

Enzymatic activity of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution

All present enzymatic activity of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution:
1.12.2.1;

Protein crystallography data

The structure of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.400, 99.960, 182.690, 90.00, 92.23, 90.00
R / Rfree (%) 18.5 / 22.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution (pdb code 3cus). 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 Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3cus

Go back to Nickel Binding Sites List in 3cus
Nickel binding site 1 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


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 Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni551

b:15.1
occ:1.00
SG Q:CYS75 2.1 14.2 1.0
SG Q:CYS72 2.2 13.5 1.0
SG Q:CSO543 2.3 16.1 1.0
FE Q:FCO550 2.5 15.1 1.0
SG Q:CYS546 2.6 13.2 1.0
CB Q:CYS72 3.0 13.6 1.0
CB Q:CYS75 3.2 14.2 1.0
OD Q:CSO543 3.2 16.4 1.0
CB Q:CSO543 3.3 15.1 1.0
N Q:CYS75 3.6 14.7 1.0
C1 Q:FCO550 3.6 14.6 1.0
C2 Q:FCO550 3.7 15.7 1.0
CB Q:CYS546 3.7 13.9 1.0
CA Q:CYS75 3.9 14.3 1.0
C3 Q:FCO550 4.1 14.1 1.0
NH1 Q:ARG476 4.3 14.4 1.0
CD Q:ARG476 4.4 13.7 1.0
CA Q:CYS72 4.5 14.0 1.0
N1 Q:FCO550 4.5 14.0 1.0
CZ Q:ARG476 4.5 14.7 1.0
NE Q:ARG476 4.6 14.1 1.0
N2 Q:FCO550 4.6 15.8 1.0
C Q:CYS75 4.7 14.2 1.0
CA Q:CSO543 4.7 15.2 1.0
C Q:ILE74 4.7 15.3 1.0
CB Q:ILE74 4.7 14.9 1.0
O Q:CYS75 4.8 13.8 1.0
CA Q:CYS546 4.8 13.6 1.0
N Q:CYS546 4.9 14.2 1.0

Nickel binding site 2 out of 3 in 3cus

Go back to Nickel Binding Sites List in 3cus
Nickel binding site 2 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


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 Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni551

b:15.2
occ:1.00
SG R:CYS75 2.1 14.8 1.0
SG R:CSO543 2.2 14.9 1.0
SG R:CYS72 2.2 14.6 1.0
FE R:FCO550 2.5 14.0 1.0
SG R:CYS546 2.5 13.8 1.0
CB R:CYS72 3.0 14.7 1.0
OD R:CSO543 3.1 16.2 1.0
CB R:CYS75 3.2 14.6 1.0
CB R:CSO543 3.3 14.3 1.0
CB R:CYS546 3.6 14.0 1.0
N R:CYS75 3.6 14.6 1.0
C1 R:FCO550 3.6 13.5 1.0
C2 R:FCO550 3.7 14.2 1.0
CA R:CYS75 3.9 14.8 1.0
C3 R:FCO550 4.1 13.9 1.0
CA R:CYS72 4.5 14.4 1.0
CD R:ARG476 4.5 14.1 1.0
NH1 R:ARG476 4.5 14.7 1.0
N1 R:FCO550 4.5 14.0 1.0
NE R:ARG476 4.6 14.1 1.0
CZ R:ARG476 4.6 14.6 1.0
C R:CYS75 4.7 14.8 1.0
CA R:CYS546 4.7 13.8 1.0
CA R:CSO543 4.7 14.6 1.0
N2 R:FCO550 4.7 13.7 1.0
CB R:ILE74 4.8 14.8 1.0
O R:CYS75 4.8 15.2 1.0
C R:ILE74 4.8 14.7 1.0
N R:CYS546 4.8 13.8 1.0

Nickel binding site 3 out of 3 in 3cus

Go back to Nickel Binding Sites List in 3cus
Nickel binding site 3 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


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 Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ni551

b:14.4
occ:1.00
SG S:CYS75 2.1 14.4 1.0
SG S:CSO543 2.1 15.4 1.0
SG S:CYS72 2.2 14.8 1.0
FE S:FCO550 2.5 14.5 1.0
SG S:CYS546 2.6 14.1 1.0
CB S:CYS72 3.0 14.9 1.0
OD S:CSO543 3.2 16.1 1.0
CB S:CYS75 3.2 14.5 1.0
CB S:CSO543 3.3 14.4 1.0
N S:CYS75 3.6 14.5 1.0
C2 S:FCO550 3.6 14.4 1.0
CB S:CYS546 3.6 14.3 1.0
C1 S:FCO550 3.6 14.8 1.0
CA S:CYS75 3.9 14.7 1.0
C3 S:FCO550 4.1 14.7 1.0
NH1 S:ARG476 4.2 15.1 1.0
CD S:ARG476 4.5 13.7 1.0
CZ S:ARG476 4.5 14.9 1.0
CA S:CYS72 4.5 15.0 1.0
N2 S:FCO550 4.6 14.8 1.0
NE S:ARG476 4.6 13.2 1.0
N1 S:FCO550 4.6 15.3 1.0
C S:CYS75 4.7 15.0 1.0
CA S:CSO543 4.7 14.8 1.0
O S:CYS75 4.7 14.8 1.0
C S:ILE74 4.7 14.6 1.0
CA S:CYS546 4.8 14.5 1.0
CB S:ILE74 4.8 14.6 1.0
N S:CYS546 4.9 14.0 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 08:20:41 2020
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