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Nickel in PDB 4uqp: High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air

Enzymatic activity of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air

All present enzymatic activity of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air:
1.12.2.1;

Protein crystallography data

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp 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 / 1.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.700, 100.900, 116.700, 90.00, 105.90, 90.00
R / Rfree (%) 11.983 / 15.633

Other elements in 4uqp:

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air (pdb code 4uqp). 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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4uqp

Go back to Nickel Binding Sites List in 4uqp
Nickel binding site 1 out of 4 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1553

b:11.2
occ:0.50
NI Q:NI1553 0.0 11.2 0.5
NI Q:NI1553 0.6 11.2 0.5
SD Q:CSS543 1.9 10.8 0.5
OD Q:CSX75 1.9 9.3 0.3
O Q:HOH2701 1.9 8.4 0.5
SG Q:CYS72 2.1 10.8 1.0
SG Q:CSS543 2.2 11.8 0.5
SG Q:CSX75 2.6 8.5 1.0
SG Q:CYS546 2.6 9.0 1.0
FE Q:FCO1552 2.9 9.1 1.0
SG Q:CSS543 3.0 12.0 0.5
CB Q:CYS72 3.0 8.8 1.0
CB Q:CSS543 3.1 9.4 0.5
CB Q:CSS543 3.2 9.6 0.5
CB Q:CSX75 3.6 8.2 1.0
N Q:CSX75 3.6 8.0 1.0
CB Q:CYS546 3.6 7.7 1.0
C1 Q:FCO1552 3.9 8.4 1.0
CA Q:CSX75 4.1 8.3 1.0
C2 Q:FCO1552 4.2 8.1 1.0
CB Q:VAL74 4.4 7.6 1.0
CA Q:CYS72 4.4 7.7 1.0
C3 Q:FCO1552 4.5 9.0 1.0
CA Q:CSS543 4.6 8.7 1.0
N Q:CYS546 4.6 6.9 1.0
CA Q:CYS546 4.6 7.8 1.0
C Q:VAL74 4.7 7.8 1.0
CG Q:GLU25 4.7 8.9 1.0
N Q:VAL74 4.7 8.2 1.0
N1 Q:FCO1552 4.8 9.2 1.0
NH1 Q:ARG476 4.8 12.4 1.0
CA Q:VAL74 4.8 7.9 1.0
C Q:CSX75 4.8 7.4 1.0
C Q:CYS72 4.9 7.3 1.0
CD Q:ARG476 4.9 8.8 1.0
OE1 Q:GLU25 4.9 12.7 1.0
NE Q:ARG476 4.9 9.7 1.0
CZ Q:ARG476 4.9 9.7 1.0
CG1 Q:VAL74 5.0 8.9 1.0
O Q:CSX75 5.0 8.8 1.0
CB Q:GLU25 5.0 8.9 1.0

Nickel binding site 2 out of 4 in 4uqp

Go back to Nickel Binding Sites List in 4uqp
Nickel binding site 2 out of 4 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1553

b:11.2
occ:0.50
NI Q:NI1553 0.0 11.2 0.5
NI Q:NI1553 0.6 11.2 0.5
OD Q:CSX75 1.5 9.3 0.3
O Q:HOH2701 2.1 8.4 0.5
SD Q:CSS543 2.2 10.8 0.5
SG Q:CSX75 2.2 8.5 1.0
SG Q:CYS72 2.2 10.8 1.0
SG Q:CYS546 2.2 9.0 1.0
SG Q:CSS543 2.6 11.8 0.5
FE Q:FCO1552 2.6 9.1 1.0
CB Q:CYS72 2.7 8.8 1.0
CB Q:CSX75 3.3 8.2 1.0
CB Q:CYS546 3.5 7.7 1.0
SG Q:CSS543 3.5 12.0 0.5
CB Q:CSS543 3.5 9.4 0.5
CB Q:CSS543 3.6 9.6 0.5
N Q:CSX75 3.6 8.0 1.0
C1 Q:FCO1552 3.8 8.4 1.0
CA Q:CSX75 4.0 8.3 1.0
C2 Q:FCO1552 4.0 8.1 1.0
C3 Q:FCO1552 4.1 9.0 1.0
CA Q:CYS72 4.2 7.7 1.0
CA Q:CYS546 4.4 7.8 1.0
N Q:CYS546 4.5 6.9 1.0
C Q:CSX75 4.6 7.4 1.0
O Q:CSX75 4.6 8.8 1.0
C Q:CYS72 4.7 7.3 1.0
CB Q:VAL74 4.7 7.6 1.0
N1 Q:FCO1552 4.8 9.2 1.0
C Q:VAL74 4.8 7.8 1.0
NE2 Q:HIS79 4.8 7.7 1.0
N Q:VAL74 4.9 8.2 1.0
CA Q:CSS543 5.0 8.7 1.0

Nickel binding site 3 out of 4 in 4uqp

Go back to Nickel Binding Sites List in 4uqp
Nickel binding site 3 out of 4 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1556

b:10.6
occ:0.50
NI R:NI1556 0.0 10.6 0.5
NI R:NI1556 0.6 10.8 0.5
OD R:CSX75 1.9 8.8 0.3
O R:HOH2701 1.9 9.1 0.5
SD R:CSS543 1.9 9.6 0.5
SG R:CYS72 2.1 10.2 1.0
SG R:CSS543 2.2 11.1 0.5
SG R:CYS546 2.6 8.2 1.0
SG R:CSX75 2.7 8.4 1.0
SG R:CSS543 2.9 10.7 0.5
FE R:FCO1555 2.9 8.7 1.0
CB R:CYS72 3.0 8.8 1.0
CB R:CSS543 3.1 8.5 0.5
CB R:CSS543 3.1 8.3 0.5
CB R:CSX75 3.6 8.2 1.0
CB R:CYS546 3.6 6.4 1.0
N R:CSX75 3.6 6.5 1.0
C1 R:FCO1555 4.0 7.0 1.0
CA R:CSX75 4.1 7.7 1.0
C2 R:FCO1555 4.2 7.7 1.0
CA R:CYS72 4.4 6.8 1.0
CB R:VAL74 4.4 6.8 1.0
C3 R:FCO1555 4.5 8.0 1.0
CA R:CSS543 4.5 7.3 1.0
N R:CYS546 4.6 6.8 1.0
CA R:CYS546 4.6 6.2 1.0
C R:VAL74 4.7 6.8 1.0
CG R:GLU25 4.8 8.3 1.0
N R:VAL74 4.8 7.1 1.0
N1 R:FCO1555 4.8 8.6 1.0
C R:CSX75 4.9 7.8 1.0
CA R:VAL74 4.9 7.0 1.0
CD R:ARG476 4.9 8.3 1.0
C R:CYS72 4.9 6.5 1.0
NE R:ARG476 4.9 8.8 1.0
NH1 R:ARG476 4.9 11.2 1.0
OE1 R:GLU25 5.0 11.6 1.0
CZ R:ARG476 5.0 8.5 1.0

Nickel binding site 4 out of 4 in 4uqp

Go back to Nickel Binding Sites List in 4uqp
Nickel binding site 4 out of 4 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1556

b:10.8
occ:0.50
NI R:NI1556 0.0 10.8 0.5
NI R:NI1556 0.6 10.6 0.5
OD R:CSX75 1.5 8.8 0.3
O R:HOH2701 2.0 9.1 0.5
SD R:CSS543 2.2 9.6 0.5
SG R:CSX75 2.2 8.4 1.0
SG R:CYS546 2.2 8.2 1.0
SG R:CYS72 2.3 10.2 1.0
SG R:CSS543 2.6 11.1 0.5
FE R:FCO1555 2.6 8.7 1.0
CB R:CYS72 2.8 8.8 1.0
CB R:CSX75 3.3 8.2 1.0
SG R:CSS543 3.4 10.7 0.5
CB R:CYS546 3.4 6.4 1.0
CB R:CSS543 3.5 8.5 0.5
CB R:CSS543 3.5 8.3 0.5
N R:CSX75 3.7 6.5 1.0
C1 R:FCO1555 3.8 7.0 1.0
C2 R:FCO1555 4.0 7.7 1.0
CA R:CSX75 4.0 7.7 1.0
C3 R:FCO1555 4.1 8.0 1.0
CA R:CYS72 4.2 6.8 1.0
CA R:CYS546 4.4 6.2 1.0
N R:CYS546 4.5 6.8 1.0
C R:CSX75 4.6 7.8 1.0
O R:CSX75 4.6 8.3 1.0
C R:CYS72 4.8 6.5 1.0
N1 R:FCO1555 4.8 8.6 1.0
CB R:VAL74 4.8 6.8 1.0
C R:VAL74 4.8 6.8 1.0
NE2 R:HIS79 4.9 6.8 1.0
CA R:CSS543 4.9 7.3 1.0
N R:VAL74 4.9 7.1 1.0
N2 R:FCO1555 5.0 7.3 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 Dec 16 01:36:09 2020

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