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Nickel in PDB 4ucw: Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucw was solved by A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.Delacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.200, 99.590, 181.840, 90.00, 92.47, 90.00
R / Rfree (%) 19.185 / 23.552

Other elements in 4ucw:

The structure of Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

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

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ucw). 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 the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucw:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 4ucw

Go back to Nickel Binding Sites List in 4ucw
Nickel binding site 1 out of 3 in the Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-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 the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1551

b:13.6
occ:1.00
O Q:HOH2009 1.9 12.6 1.0
OD Q:CSO75 2.0 13.7 1.0
SG Q:CYS72 2.2 11.0 1.0
SG Q:CYS543 2.2 11.7 1.0
SG Q:CYS546 2.5 10.3 1.0
SG Q:CSO75 2.5 9.0 1.0
FE Q:FCO1550 3.0 12.8 1.0
CB Q:CYS72 3.0 10.1 1.0
CB Q:CYS543 3.0 11.4 1.0
CB Q:CYS546 3.4 10.1 1.0
C1 Q:FCO1550 3.8 12.4 1.0
CB Q:CSO75 3.9 9.9 1.0
N Q:CSO75 3.9 9.9 1.0
C2 Q:FCO1550 4.3 15.0 1.0
N Q:CYS546 4.3 10.8 1.0
CA Q:CYS546 4.4 9.8 1.0
CA Q:CSO75 4.4 10.2 1.0
CA Q:CYS543 4.5 11.5 1.0
CA Q:CYS72 4.5 9.7 1.0
C3 Q:FCO1550 4.5 13.4 1.0
CD Q:ARG476 4.5 11.1 1.0
NE Q:ARG476 4.6 11.4 1.0
N1 Q:FCO1550 4.6 11.8 1.0
CZ Q:ARG476 4.7 11.5 1.0
CB Q:VAL74 4.8 9.5 1.0
NH1 Q:ARG476 4.8 11.3 1.0
CB Q:GLU25 4.8 13.0 1.0
OE1 Q:GLU25 4.8 21.1 1.0
CG Q:GLU25 4.9 16.3 1.0

Nickel binding site 2 out of 3 in 4ucw

Go back to Nickel Binding Sites List in 4ucw
Nickel binding site 2 out of 3 in the Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-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 the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1551

b:17.3
occ:1.00
OD R:CSO75 1.9 15.1 1.0
SG R:CYS543 2.0 19.4 1.0
O R:HOH2006 2.0 25.5 1.0
SG R:CYS72 2.1 18.4 1.0
SG R:CSO75 2.5 14.8 1.0
SG R:CYS546 2.6 18.1 1.0
CB R:CYS72 2.9 18.0 1.0
FE R:FCO1550 2.9 14.9 1.0
CB R:CYS543 3.0 18.1 1.0
CB R:CYS546 3.5 17.6 1.0
C1 R:FCO1550 3.8 15.6 1.0
CB R:CSO75 3.8 15.0 1.0
N R:CSO75 3.9 15.3 1.0
C2 R:FCO1550 4.1 15.6 1.0
N R:CYS546 4.4 16.3 1.0
CA R:CSO75 4.4 14.7 1.0
CA R:CYS72 4.4 16.9 1.0
CA R:CYS546 4.4 17.4 1.0
CA R:CYS543 4.5 18.3 1.0
C3 R:FCO1550 4.5 15.3 1.0
NH1 R:ARG476 4.5 16.6 1.0
N1 R:FCO1550 4.7 16.5 1.0
CD R:ARG476 4.7 15.7 1.0
CZ R:ARG476 4.7 16.0 1.0
CB R:VAL74 4.7 18.2 1.0
NE R:ARG476 4.7 15.4 1.0
OE1 R:GLU25 4.8 22.4 1.0
CG R:GLU25 4.9 21.9 1.0
CB R:GLU25 4.9 19.0 1.0
C R:VAL74 4.9 15.9 1.0
N R:VAL74 5.0 16.5 1.0
C R:CYS72 5.0 16.5 1.0
C R:CSO75 5.0 14.3 1.0
O R:CSO75 5.0 13.6 1.0

Nickel binding site 3 out of 3 in 4ucw

Go back to Nickel Binding Sites List in 4ucw
Nickel binding site 3 out of 3 in the Structure of the T18V Small Subunit Mutant of D. Fructosovorans Nife-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 the T18V Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ni1551

b:23.1
occ:1.00
OD S:CSO75 1.9 19.7 1.0
O S:HOH2006 1.9 24.8 1.0
SG S:CYS543 2.1 22.0 1.0
SG S:CYS72 2.2 25.2 1.0
SG S:CYS546 2.5 18.2 1.0
SG S:CSO75 2.5 19.2 1.0
FE S:FCO1550 3.0 17.5 1.0
CB S:CYS543 3.0 20.6 1.0
CB S:CYS72 3.1 24.3 1.0
CB S:CYS546 3.4 17.0 1.0
C1 S:FCO1550 3.8 16.2 1.0
CB S:CSO75 3.9 21.4 1.0
N S:CSO75 4.0 22.3 1.0
N S:CYS546 4.3 17.2 1.0
C2 S:FCO1550 4.3 17.3 1.0
CA S:CYS546 4.4 17.0 1.0
CA S:CYS543 4.5 19.8 1.0
N1 S:FCO1550 4.5 16.2 1.0
CD S:ARG476 4.5 22.7 1.0
CA S:CYS72 4.5 24.8 1.0
CA S:CSO75 4.5 22.8 1.0
C3 S:FCO1550 4.5 17.3 1.0
NE S:ARG476 4.6 24.1 1.0
OE1 S:GLU25 4.7 20.7 1.0
CZ S:ARG476 4.7 22.7 1.0
NH1 S:ARG476 4.8 21.9 1.0
CB S:VAL74 4.8 24.8 1.0
CB S:GLU25 4.9 19.3 1.0
CG S:GLU25 5.0 21.4 1.0
N S:VAL74 5.0 23.7 1.0

Reference:

A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.De Lacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin. A Threonine Stabilizes the Nic and Nir Catalytic Intermediates of [Nife]-Hydrogenase During Catalysis in Nife-Hydrogenase J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.630491
Page generated: Wed Dec 16 01:35:21 2020

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