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Nickel in PDB 4uql: High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant

Enzymatic activity of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant

All present enzymatic activity of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant:
1.12.2.1;

Protein crystallography data

The structure of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4uql was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.22
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.690, 100.850, 116.700, 90.00, 105.96, 90.00
R / Rfree (%) 12.043 / 15.2

Other elements in 4uql:

The structure of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant (pdb code 4uql). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4uql:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4uql

Go back to Nickel Binding Sites List in 4uql
Nickel binding site 1 out of 4 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1551

b:8.5
occ:0.64
NI Q:NI1551 0.0 8.5 0.6
NI Q:NI1551 0.5 8.0 0.4
OD Q:CSX75 1.8 4.8 0.2
SD Q:CSS543 1.9 9.0 0.4
O Q:HOH2001 2.0 5.4 0.6
SG Q:CYS72 2.1 7.8 1.0
SG Q:CSS543 2.2 8.4 0.6
SG Q:CSX75 2.6 6.3 1.0
SG Q:CYS546 2.6 5.8 1.0
FE Q:FCO1550 2.9 6.0 1.0
SG Q:CSS543 2.9 8.9 0.4
CB Q:CYS72 3.0 6.7 1.0
CB Q:CSS543 3.1 5.5 0.4
CB Q:CSS543 3.2 6.9 0.6
CB Q:CSX75 3.5 5.3 1.0
N Q:CSX75 3.6 4.9 1.0
CB Q:CYS546 3.6 5.1 1.0
C1 Q:FCO1550 3.9 5.6 1.0
CA Q:CSX75 4.1 5.1 1.0
C2 Q:FCO1550 4.2 5.1 1.0
CB Q:VAL74 4.4 5.1 1.0
CA Q:CYS72 4.4 5.3 1.0
C3 Q:FCO1550 4.5 7.5 1.0
CA Q:CSS543 4.6 5.5 1.0
N Q:CYS546 4.6 5.1 1.0
CA Q:CYS546 4.6 5.5 1.0
C Q:VAL74 4.7 4.8 1.0
N1 Q:FCO1550 4.8 6.0 1.0
N Q:VAL74 4.8 4.1 1.0
C Q:CSX75 4.8 4.7 1.0
CG Q:GLU25 4.8 6.2 1.0
NH1 Q:ARG476 4.9 11.4 1.0
CD Q:ARG476 4.9 7.4 1.0
CA Q:VAL74 4.9 4.6 1.0
C Q:CYS72 4.9 4.5 1.0
NE Q:ARG476 4.9 8.3 1.0
CZ Q:ARG476 5.0 7.6 1.0
O Q:CSX75 5.0 5.5 1.0

Nickel binding site 2 out of 4 in 4uql

Go back to Nickel Binding Sites List in 4uql
Nickel binding site 2 out of 4 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1551

b:8.0
occ:0.36
NI Q:NI1551 0.0 8.0 0.4
NI Q:NI1551 0.5 8.5 0.6
OD Q:CSX75 1.5 4.8 0.2
O Q:HOH2001 2.0 5.4 0.6
SD Q:CSS543 2.1 9.0 0.4
SG Q:CSX75 2.2 6.3 1.0
SG Q:CYS72 2.3 7.8 1.0
SG Q:CYS546 2.3 5.8 1.0
SG Q:CSS543 2.6 8.4 0.6
FE Q:FCO1550 2.6 6.0 1.0
CB Q:CYS72 2.9 6.7 1.0
SG Q:CSS543 3.3 8.9 0.4
CB Q:CSX75 3.3 5.3 1.0
CB Q:CSS543 3.4 5.5 0.4
CB Q:CYS546 3.5 5.1 1.0
CB Q:CSS543 3.5 6.9 0.6
N Q:CSX75 3.6 4.9 1.0
C1 Q:FCO1550 3.8 5.6 1.0
C2 Q:FCO1550 4.0 5.1 1.0
CA Q:CSX75 4.0 5.1 1.0
C3 Q:FCO1550 4.1 7.5 1.0
CA Q:CYS72 4.3 5.3 1.0
CA Q:CYS546 4.5 5.5 1.0
N Q:CYS546 4.6 5.1 1.0
C Q:CSX75 4.6 4.7 1.0
N1 Q:FCO1550 4.7 6.0 1.0
O Q:CSX75 4.7 5.5 1.0
CB Q:VAL74 4.7 5.1 1.0
C Q:VAL74 4.8 4.8 1.0
C Q:CYS72 4.8 4.5 1.0
CA Q:CSS543 4.9 5.5 1.0
NE2 Q:HIS79 4.9 5.6 1.0
N Q:VAL74 5.0 4.1 1.0
NH1 Q:ARG476 5.0 11.4 1.0
N2 Q:FCO1550 5.0 5.9 1.0

Nickel binding site 3 out of 4 in 4uql

Go back to Nickel Binding Sites List in 4uql
Nickel binding site 3 out of 4 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1551

b:7.4
occ:0.64
NI R:NI1551 0.0 7.4 0.6
NI R:NI1551 0.5 8.3 0.4
OD R:CSX75 1.8 5.9 0.2
SD R:CSS543 1.9 8.0 0.4
O R:HOH2001 2.0 6.6 0.6
SG R:CYS72 2.1 6.4 1.0
SG R:CSS543 2.2 7.6 0.6
SG R:CSX75 2.6 5.5 1.0
SG R:CYS546 2.6 5.7 1.0
SG R:CSS543 2.9 8.2 0.4
FE R:FCO1550 2.9 5.4 1.0
CB R:CYS72 3.0 4.9 1.0
CB R:CSS543 3.1 5.3 0.4
CB R:CSS543 3.2 5.8 0.6
CB R:CSX75 3.5 5.3 1.0
CB R:CYS546 3.5 4.2 1.0
N R:CSX75 3.6 3.5 1.0
C1 R:FCO1550 3.9 5.1 1.0
CA R:CSX75 4.1 4.2 1.0
C2 R:FCO1550 4.2 5.0 1.0
CB R:VAL74 4.4 4.8 1.0
CA R:CYS72 4.4 4.1 1.0
C3 R:FCO1550 4.5 5.5 1.0
CA R:CSS543 4.6 4.5 1.0
N R:CYS546 4.6 3.9 1.0
CA R:CYS546 4.6 4.3 1.0
C R:VAL74 4.7 3.7 1.0
N1 R:FCO1550 4.7 5.6 1.0
NH1 R:ARG476 4.8 10.4 1.0
N R:VAL74 4.8 4.0 1.0
C R:CSX75 4.8 4.3 1.0
CD R:ARG476 4.9 6.5 1.0
CG R:GLU25 4.9 5.6 1.0
NE R:ARG476 4.9 7.8 1.0
CA R:VAL74 4.9 4.3 1.0
CZ R:ARG476 4.9 7.4 1.0
C R:CYS72 4.9 4.3 1.0
O R:CSX75 5.0 5.2 1.0

Nickel binding site 4 out of 4 in 4uql

Go back to Nickel Binding Sites List in 4uql
Nickel binding site 4 out of 4 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1551

b:8.3
occ:0.36
NI R:NI1551 0.0 8.3 0.4
NI R:NI1551 0.5 7.4 0.6
OD R:CSX75 1.5 5.9 0.2
O R:HOH2001 2.1 6.6 0.6
SD R:CSS543 2.1 8.0 0.4
SG R:CSX75 2.2 5.5 1.0
SG R:CYS72 2.3 6.4 1.0
SG R:CYS546 2.3 5.7 1.0
SG R:CSS543 2.6 7.6 0.6
FE R:FCO1550 2.6 5.4 1.0
CB R:CYS72 2.8 4.9 1.0
CB R:CSX75 3.3 5.3 1.0
SG R:CSS543 3.3 8.2 0.4
CB R:CYS546 3.4 4.2 1.0
CB R:CSS543 3.4 5.3 0.4
CB R:CSS543 3.5 5.8 0.6
N R:CSX75 3.7 3.5 1.0
C1 R:FCO1550 3.8 5.1 1.0
C2 R:FCO1550 4.0 5.0 1.0
CA R:CSX75 4.0 4.2 1.0
C3 R:FCO1550 4.1 5.5 1.0
CA R:CYS72 4.3 4.1 1.0
CA R:CYS546 4.4 4.3 1.0
N R:CYS546 4.5 3.9 1.0
C R:CSX75 4.6 4.3 1.0
O R:CSX75 4.7 5.2 1.0
N1 R:FCO1550 4.7 5.6 1.0
CB R:VAL74 4.8 4.8 1.0
C R:VAL74 4.8 3.7 1.0
C R:CYS72 4.8 4.3 1.0
CA R:CSS543 4.9 4.5 1.0
NE2 R:HIS79 4.9 4.4 1.0
NH1 R:ARG476 4.9 10.4 1.0
N R:VAL74 5.0 4.0 1.0

Reference:

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9
Page generated: Wed Oct 9 19:14:46 2024

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