Atomistry » Nickel » PDB 4jzr-4ls3 » 4ko1
Atomistry »
  Nickel »
    PDB 4jzr-4ls3 »
      4ko1 »

Nickel in PDB 4ko1: High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

Enzymatic activity of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

All present enzymatic activity of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air:
1.12.99.6; 1.18.99.1;

Protein crystallography data

The structure of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko1 was solved by A.Volbeda, C.Cavazza, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.230, 108.910, 136.340, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 18.4

Other elements in 4ko1:

The structure of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air also contains other interesting chemical elements:

Iron (Fe) 26 atoms
Calcium (Ca) 7 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko1:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 1 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni502

b:16.8
occ:0.07
 NI L:NI502 0.0 16.8 0.1
SE L:SEC492 1.6 16.1 0.8
NI L:NI502 2.0 16.3 0.8
SG L:CYS495 2.3 9.5 1.0
NI L:NI502 2.5 10.9 0.1
N L:CYS495 2.7 7.9 1.0
SG L:CYS70 2.8 12.1 1.0
CB L:SEC492 2.8 13.8 0.1
CB L:CYS495 2.9 9.9 1.0
CB L:SEC492 2.9 12.7 0.8
SE L:SEC492 3.1 17.7 0.1
O L:HOH607 3.1 15.4 0.8
CB L:CYS70 3.1 10.4 1.0
CA L:CYS495 3.3 8.2 1.0
FE L:FCO501 3.7 9.7 1.0
C L:GLY494 3.7 9.0 1.0
O L:SEC492 3.9 10.2 1.0
OE1 L:GLU23 3.9 14.4 0.9
C L:SEC492 3.9 11.8 1.0
CA L:SEC492 3.9 12.4 1.0
SG L:CYS73 4.0 10.2 1.0
CA L:GLY494 4.1 10.2 1.0
C1 L:FCO501 4.1 12.2 1.0
N L:GLY494 4.1 8.6 1.0
CA L:CYS70 4.4 8.8 1.0
CD L:GLU23 4.4 14.7 0.9
O L:ILE69 4.6 8.1 1.0
N L:LEU493 4.6 10.6 1.0
C L:CYS495 4.6 8.4 1.0
N1 L:FCO501 4.7 11.8 1.0
CG L:GLU23 4.8 13.8 1.0
O L:GLY494 4.8 9.5 1.0
N L:ALA496 4.9 7.4 1.0
C3 L:FCO501 4.9 10.7 1.0
C L:LEU493 5.0 10.3 1.0
CG2 L:ILE69 5.0 8.8 1.0

Nickel binding site 2 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 2 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni502

b:16.3
occ:0.85
 NI L:NI502 0.0 16.3 0.8
NI L:NI502 0.7 10.9 0.1
O L:HOH607 1.8 15.4 0.8
NI L:NI502 2.0 16.8 0.1
SG L:CYS70 2.2 12.1 1.0
SE L:SEC492 2.3 16.1 0.8
SG L:CYS73 2.4 10.2 1.0
SG L:CYS495 2.5 9.5 1.0
SE L:SEC492 2.6 17.7 0.1
FE L:FCO501 2.7 9.7 1.0
CB L:CYS70 2.9 10.4 1.0
CB L:SEC492 3.4 13.8 0.1
CB L:SEC492 3.4 12.7 0.8
CB L:CYS73 3.6 9.8 1.0
C1 L:FCO501 3.7 12.2 1.0
C2 L:FCO501 3.8 9.2 1.0
CB L:CYS495 3.9 9.9 1.0
N L:CYS73 4.0 7.2 1.0
C3 L:FCO501 4.2 10.7 1.0
CA L:CYS70 4.4 8.8 1.0
CA L:CYS73 4.4 8.2 1.0
CB L:VAL72 4.5 8.2 1.0
NH1 L:ARG425 4.6 11.5 1.0
N L:CYS495 4.6 7.9 1.0
N1 L:FCO501 4.7 11.8 1.0
N2 L:FCO501 4.7 9.3 1.0
CD L:ARG425 4.8 8.5 1.0
CA L:SEC492 4.8 12.4 1.0
CA L:CYS495 4.8 8.2 1.0
C L:VAL72 4.9 8.3 1.0
C L:CYS70 4.9 8.3 1.0
N L:VAL72 4.9 7.1 1.0

Nickel binding site 3 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 3 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni502

b:10.9
occ:0.08
 NI L:NI502 0.0 10.9 0.1
NI L:NI502 0.7 16.3 0.8
O L:HOH607 1.7 15.4 0.8
SG L:CYS70 2.2 12.1 1.0
SE L:SEC492 2.4 17.7 0.1
SG L:CYS73 2.4 10.2 1.0
SE L:SEC492 2.5 16.1 0.8
NI L:NI502 2.5 16.8 0.1
FE L:FCO501 2.9 9.7 1.0
SG L:CYS495 3.1 9.5 1.0
CB L:CYS70 3.3 10.4 1.0
CB L:CYS73 3.4 9.8 1.0
CB L:SEC492 3.5 13.8 0.1
CB L:SEC492 3.5 12.7 0.8
N L:CYS73 3.6 7.2 1.0
C2 L:FCO501 3.7 9.2 1.0
CB L:VAL72 3.9 8.2 1.0
C1 L:FCO501 4.0 12.2 1.0
NH1 L:ARG425 4.0 11.5 1.0
CA L:CYS73 4.1 8.2 1.0
C L:VAL72 4.3 8.3 1.0
CA L:VAL72 4.5 8.8 1.0
N2 L:FCO501 4.5 9.3 1.0
CZ L:ARG425 4.5 9.2 1.0
C3 L:FCO501 4.5 10.7 1.0
CB L:CYS495 4.5 9.9 1.0
CD L:ARG425 4.5 8.5 1.0
CG1 L:VAL72 4.5 10.6 1.0
N L:VAL72 4.6 7.1 1.0
CA L:CYS70 4.6 8.8 1.0
NE L:ARG425 4.7 9.2 1.0
CG2 L:VAL72 4.8 11.3 1.0
CA L:SEC492 4.9 12.4 1.0
N1 L:FCO501 4.9 11.8 1.0
C L:CYS73 5.0 7.5 1.0
C L:CYS70 5.0 8.3 1.0

Nickel binding site 4 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 4 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni502

b:17.9
occ:0.11
 NI M:NI502 0.0 17.9 0.1
SE M:SEC492 1.6 18.9 0.8
NI M:NI502 2.0 20.1 0.8
SG M:CYS495 2.3 14.0 1.0
NI M:NI502 2.5 14.6 0.1
N M:CYS495 2.7 10.5 1.0
SG M:CYS70 2.8 15.5 1.0
CB M:SEC492 2.9 15.3 0.2
CB M:CYS495 2.9 12.9 1.0
CB M:SEC492 2.9 15.3 0.8
CB M:CYS70 3.1 12.8 1.0
SE M:SEC492 3.1 19.5 0.2
O M:HOH622 3.2 16.8 0.8
CA M:CYS495 3.3 12.2 1.0
FE M:FCO501 3.7 13.6 1.0
C M:GLY494 3.7 11.1 1.0
OE1 M:GLU23 3.8 21.2 0.9
O M:SEC492 3.9 13.2 1.0
CA M:SEC492 3.9 14.5 1.0
C M:SEC492 3.9 14.4 1.0
SG M:CYS73 4.0 14.4 1.0
CA M:GLY494 4.0 12.1 1.0
C1 M:FCO501 4.1 13.4 1.0
N M:GLY494 4.1 11.7 1.0
CA M:CYS70 4.3 12.2 1.0
CD M:GLU23 4.4 18.0 0.9
O M:ILE69 4.5 11.4 1.0
C M:CYS495 4.6 11.3 1.0
N M:LEU493 4.6 13.0 1.0
N1 M:FCO501 4.7 13.6 1.0
CG M:GLU23 4.7 16.4 1.0
O M:GLY494 4.8 12.1 1.0
N M:ALA496 4.9 11.3 1.0
C M:LEU493 4.9 12.2 1.0
C3 M:FCO501 5.0 12.1 1.0
CG2 M:ILE69 5.0 10.8 1.0

Nickel binding site 5 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 5 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni502

b:20.1
occ:0.80
 NI M:NI502 0.0 20.1 0.8
NI M:NI502 0.6 14.6 0.1
O M:HOH622 1.8 16.8 0.8
NI M:NI502 2.0 17.9 0.1
SG M:CYS70 2.2 15.5 1.0
SE M:SEC492 2.3 18.9 0.8
SG M:CYS73 2.3 14.4 1.0
SG M:CYS495 2.5 14.0 1.0
SE M:SEC492 2.6 19.5 0.2
FE M:FCO501 2.7 13.6 1.0
CB M:CYS70 2.9 12.8 1.0
CB M:SEC492 3.4 15.3 0.2
CB M:SEC492 3.4 15.3 0.8
CB M:CYS73 3.6 10.7 1.0
C1 M:FCO501 3.7 13.4 1.0
C2 M:FCO501 3.8 11.1 1.0
CB M:CYS495 3.9 12.9 1.0
N M:CYS73 4.0 10.3 1.0
C3 M:FCO501 4.2 12.1 1.0
CA M:CYS73 4.4 10.7 1.0
CA M:CYS70 4.4 12.2 1.0
CB M:VAL72 4.5 12.1 1.0
NH1 M:ARG425 4.6 15.8 1.0
N M:CYS495 4.6 10.5 1.0
N1 M:FCO501 4.6 13.6 1.0
N2 M:FCO501 4.7 12.0 1.0
CA M:SEC492 4.8 14.5 1.0
CA M:CYS495 4.8 12.2 1.0
CD M:ARG425 4.8 11.9 1.0
C M:VAL72 4.9 11.3 1.0
C M:CYS70 4.9 11.9 1.0
N M:VAL72 5.0 11.1 1.0

Nickel binding site 6 out of 6 in 4ko1

Go back to Nickel Binding Sites List in 4ko1
Nickel binding site 6 out of 6 in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni502

b:14.6
occ:0.09
 NI M:NI502 0.0 14.6 0.1
NI M:NI502 0.6 20.1 0.8
O M:HOH622 1.7 16.8 0.8
SG M:CYS70 2.2 15.5 1.0
SG M:CYS73 2.4 14.4 1.0
SE M:SEC492 2.4 19.5 0.2
SE M:SEC492 2.5 18.9 0.8
NI M:NI502 2.5 17.9 0.1
FE M:FCO501 2.9 13.6 1.0
SG M:CYS495 3.1 14.0 1.0
CB M:CYS70 3.2 12.8 1.0
CB M:CYS73 3.3 10.7 1.0
N M:CYS73 3.5 10.3 1.0
CB M:SEC492 3.5 15.3 0.8
CB M:SEC492 3.5 15.3 0.2
C2 M:FCO501 3.7 11.1 1.0
CB M:VAL72 3.9 12.1 1.0
C1 M:FCO501 4.0 13.4 1.0
CA M:CYS73 4.0 10.7 1.0
NH1 M:ARG425 4.1 15.8 1.0
C M:VAL72 4.3 11.3 1.0
CB M:CYS495 4.5 12.9 1.0
C3 M:FCO501 4.5 12.1 1.0
CA M:VAL72 4.5 11.3 1.0
N2 M:FCO501 4.5 12.0 1.0
CZ M:ARG425 4.6 13.8 1.0
CD M:ARG425 4.6 11.9 1.0
N M:VAL72 4.6 11.1 1.0
CG1 M:VAL72 4.6 14.1 1.0
CA M:CYS70 4.6 12.2 1.0
NE M:ARG425 4.7 16.3 1.0
CG2 M:VAL72 4.8 13.7 1.0
N1 M:FCO501 4.9 13.6 1.0
CA M:SEC492 4.9 14.5 1.0
C M:CYS73 4.9 10.4 1.0
C M:CYS70 5.0 11.9 1.0

Reference:

A.Volbeda, P.Amara, M.Iannello, A.L.De Lacey, C.Cavazza, J.C.Fontecilla-Camps. Structural Foundations For the O2 Resistance of Desulfomicrobium Baculatum [Nifese]-Hydrogenase. Chem.Commun.(Camb.) V. 49 7061 2013.
ISSN: ISSN 1359-7345
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Wed Oct 9 18:18:55 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy