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Nickel in PDB 4kn9: High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

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

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

Protein crystallography data

The structure of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kn9 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 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.260, 108.730, 136.500, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.8

Other elements in 4kn9:

The structure of High-Resolution 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
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4kn9). 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-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kn9:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4kn9

Go back to Nickel Binding Sites List in 4kn9
Nickel binding site 1 out of 6 in the High-Resolution 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-Resolution 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:17.8
occ:0.12
 NI L:NI502 0.0 17.8 0.1
SE L:SEC492 1.6 16.3 0.7
NI L:NI502 1.9 16.9 0.7
SG L:CYS495 2.2 10.2 1.0
SE L:SEC492 2.3 21.7 0.1
NI L:NI502 2.5 10.9 0.2
N L:CYS495 2.7 8.3 1.0
CB L:SEC492 2.8 13.5 0.2
SG L:CYS70 2.8 12.4 0.9
CB L:SEC492 2.9 14.3 0.1
CB L:SEC492 2.9 12.5 0.7
CB L:CYS495 2.9 10.4 1.0
CB L:CYS70 3.0 10.3 0.1
O L:HOH607 3.0 14.1 0.8
SG L:CYS70 3.0 10.9 0.1
SE L:SEC492 3.1 19.4 0.2
CB L:CYS70 3.1 10.1 0.9
CA L:CYS495 3.3 8.2 1.0
FE L:FCO501 3.7 10.4 1.0
C L:GLY494 3.8 9.5 1.0
O L:SEC492 3.9 10.9 1.0
CA L:SEC492 3.9 12.3 1.0
C L:SEC492 3.9 12.1 1.0
OE1 L:GLU23 3.9 15.7 0.9
SG L:CYS73 4.0 10.7 1.0
C1 L:FCO501 4.0 12.6 1.0
CA L:GLY494 4.1 10.6 1.0
N L:GLY494 4.1 9.0 1.0
CA L:CYS70 4.4 9.5 0.9
CD L:GLU23 4.5 16.3 0.9
CA L:CYS70 4.5 9.3 0.1
N L:LEU493 4.6 10.7 1.0
O L:ILE69 4.6 9.4 1.0
C L:CYS495 4.6 8.9 1.0
N1 L:FCO501 4.6 12.0 1.0
CG L:GLU23 4.7 15.3 1.0
O L:GLY494 4.8 10.0 1.0
N L:ALA496 4.9 8.2 1.0
C3 L:FCO501 4.9 11.1 1.0
C L:LEU493 5.0 10.8 1.0

Nickel binding site 2 out of 6 in 4kn9

Go back to Nickel Binding Sites List in 4kn9
Nickel binding site 2 out of 6 in the High-Resolution 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-Resolution 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:16.9
occ:0.69
 NI L:NI502 0.0 16.9 0.7
NI L:NI502 0.7 10.9 0.2
O L:HOH607 1.8 14.1 0.8
SG L:CYS70 1.9 10.9 0.1
NI L:NI502 1.9 17.8 0.1
SG L:CYS70 2.2 12.4 0.9
SE L:SEC492 2.3 16.3 0.7
SE L:SEC492 2.3 21.7 0.1
SG L:CYS73 2.4 10.7 1.0
SG L:CYS495 2.5 10.2 1.0
SE L:SEC492 2.7 19.4 0.2
FE L:FCO501 2.7 10.4 1.0
CB L:CYS70 2.9 10.1 0.9
CB L:CYS70 3.0 10.3 0.1
CB L:SEC492 3.4 13.5 0.2
CB L:SEC492 3.4 14.3 0.1
CB L:SEC492 3.4 12.5 0.7
CB L:CYS73 3.6 10.6 1.0
C1 L:FCO501 3.8 12.6 1.0
C2 L:FCO501 3.8 10.0 1.0
CB L:CYS495 3.9 10.4 1.0
N L:CYS73 4.0 7.1 1.0
C3 L:FCO501 4.2 11.1 1.0
CA L:CYS70 4.4 9.5 0.9
CA L:CYS73 4.4 8.2 1.0
CA L:CYS70 4.5 9.3 0.1
CB L:VAL72 4.5 8.2 1.0
N L:CYS495 4.6 8.3 1.0
NH1 L:ARG425 4.6 11.9 1.0
N1 L:FCO501 4.7 12.0 1.0
N2 L:FCO501 4.7 9.7 1.0
CA L:CYS495 4.8 8.2 1.0
CA L:SEC492 4.8 12.3 1.0
CD L:ARG425 4.8 9.0 1.0
C L:VAL72 4.9 8.7 1.0
C L:CYS70 4.9 8.2 1.0
N L:VAL72 4.9 7.4 1.0
CA L:VAL72 5.0 9.5 1.0

Nickel binding site 3 out of 6 in 4kn9

Go back to Nickel Binding Sites List in 4kn9
Nickel binding site 3 out of 6 in the High-Resolution 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-Resolution 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:0.19
 NI L:NI502 0.0 10.9 0.2
NI L:NI502 0.7 16.9 0.7
O L:HOH607 1.7 14.1 0.8
SG L:CYS70 1.9 10.9 0.1
SG L:CYS70 2.1 12.4 0.9
SE L:SEC492 2.2 21.7 0.1
SE L:SEC492 2.4 19.4 0.2
SE L:SEC492 2.5 16.3 0.7
SG L:CYS73 2.5 10.7 1.0
NI L:NI502 2.5 17.8 0.1
FE L:FCO501 3.0 10.4 1.0
SG L:CYS495 3.1 10.2 1.0
CB L:CYS70 3.2 10.1 0.9
CB L:CYS70 3.3 10.3 0.1
CB L:CYS73 3.4 10.6 1.0
CB L:SEC492 3.5 13.5 0.2
CB L:SEC492 3.5 12.5 0.7
CB L:SEC492 3.5 14.3 0.1
N L:CYS73 3.6 7.1 1.0
C2 L:FCO501 3.8 10.0 1.0
CB L:VAL72 3.9 8.2 1.0
NH1 L:ARG425 4.1 11.9 1.0
C1 L:FCO501 4.1 12.6 1.0
CA L:CYS73 4.1 8.2 1.0
C L:VAL72 4.3 8.7 1.0
CA L:VAL72 4.5 9.5 1.0
CG1 L:VAL72 4.5 10.3 1.0
N L:VAL72 4.5 7.4 1.0
CZ L:ARG425 4.5 10.0 1.0
CB L:CYS495 4.5 10.4 1.0
C3 L:FCO501 4.6 11.1 1.0
CD L:ARG425 4.6 9.0 1.0
N2 L:FCO501 4.6 9.7 1.0
CA L:CYS70 4.6 9.5 0.9
CA L:CYS70 4.7 9.3 0.1
NE L:ARG425 4.7 10.6 1.0
CG2 L:VAL72 4.8 11.8 1.0
CA L:SEC492 4.9 12.3 1.0
C L:CYS70 5.0 8.2 1.0
N1 L:FCO501 5.0 12.0 1.0
C L:CYS73 5.0 8.1 1.0

Nickel binding site 4 out of 6 in 4kn9

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Nickel binding site 4 out of 6 in the High-Resolution 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-Resolution 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:19.9
occ:0.12
 NI M:NI502 0.0 19.9 0.1
SE M:SEC492 1.6 19.6 0.7
NI M:NI502 2.0 20.8 0.7
SG M:CYS495 2.3 14.1 1.0
SE M:SEC492 2.3 23.4 0.1
NI M:NI502 2.5 16.9 0.2
N M:CYS495 2.7 11.3 1.0
SG M:CYS70 2.8 15.4 0.9
CB M:CYS70 2.9 13.0 0.1
CB M:SEC492 2.9 17.3 0.2
CB M:CYS495 2.9 14.1 1.0
CB M:SEC492 2.9 17.3 0.7
CB M:SEC492 3.0 17.4 0.1
SG M:CYS70 3.0 12.1 0.1
CB M:CYS70 3.1 13.2 0.9
SE M:SEC492 3.2 24.2 0.2
O M:HOH616 3.2 16.2 0.8
CA M:CYS495 3.3 14.1 1.0
FE M:FCO501 3.7 14.2 1.0
C M:GLY494 3.7 12.2 1.0
OE1 M:GLU23 3.8 20.7 0.9
O M:SEC492 3.9 13.8 1.0
CA M:SEC492 3.9 15.8 1.0
SG M:CYS73 4.0 14.8 1.0
C M:SEC492 4.0 15.7 1.0
CA M:GLY494 4.0 13.3 1.0
N M:GLY494 4.1 12.8 1.0
C1 M:FCO501 4.1 14.6 1.0
CA M:CYS70 4.3 13.0 0.9
CD M:GLU23 4.4 19.1 0.9
CA M:CYS70 4.4 12.7 0.1
O M:ILE69 4.5 11.9 1.0
C M:CYS495 4.7 12.1 1.0
N M:LEU493 4.7 14.0 1.0
N1 M:FCO501 4.7 14.6 1.0
CG M:GLU23 4.7 18.1 1.0
O M:GLY494 4.7 12.3 1.0
N M:ALA496 5.0 11.7 1.0
C3 M:FCO501 5.0 11.9 1.0
C M:LEU493 5.0 13.3 1.0
CG2 M:ILE69 5.0 12.2 1.0

Nickel binding site 5 out of 6 in 4kn9

Go back to Nickel Binding Sites List in 4kn9
Nickel binding site 5 out of 6 in the High-Resolution 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-Resolution 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:20.8
occ:0.69
 NI M:NI502 0.0 20.8 0.7
NI M:NI502 0.6 16.9 0.2
O M:HOH616 1.8 16.2 0.8
NI M:NI502 2.0 19.9 0.1
SG M:CYS70 2.0 12.1 0.1
SG M:CYS70 2.2 15.4 0.9
SE M:SEC492 2.2 23.4 0.1
SE M:SEC492 2.3 19.6 0.7
SG M:CYS73 2.4 14.8 1.0
SG M:CYS495 2.5 14.1 1.0
SE M:SEC492 2.7 24.2 0.2
FE M:FCO501 2.7 14.2 1.0
CB M:CYS70 2.9 13.2 0.9
CB M:CYS70 3.1 13.0 0.1
CB M:SEC492 3.4 17.3 0.2
CB M:SEC492 3.4 17.3 0.7
CB M:SEC492 3.4 17.4 0.1
CB M:CYS73 3.6 12.0 1.0
C1 M:FCO501 3.7 14.6 1.0
C2 M:FCO501 3.8 12.1 1.0
CB M:CYS495 3.9 14.1 1.0
N M:CYS73 4.0 10.9 1.0
C3 M:FCO501 4.2 11.9 1.0
CA M:CYS73 4.4 11.9 1.0
CA M:CYS70 4.4 13.0 0.9
CB M:VAL72 4.5 13.8 1.0
CA M:CYS70 4.5 12.7 0.1
NH1 M:ARG425 4.6 16.5 1.0
N M:CYS495 4.6 11.3 1.0
N1 M:FCO501 4.6 14.6 1.0
N2 M:FCO501 4.7 13.6 1.0
CA M:SEC492 4.8 15.8 1.0
CA M:CYS495 4.8 14.1 1.0
CD M:ARG425 4.8 12.3 1.0
C M:VAL72 4.9 11.9 1.0
C M:CYS70 4.9 13.5 1.0
N M:VAL72 4.9 12.4 1.0

Nickel binding site 6 out of 6 in 4kn9

Go back to Nickel Binding Sites List in 4kn9
Nickel binding site 6 out of 6 in the High-Resolution 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-Resolution 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:16.9
occ:0.19
 NI M:NI502 0.0 16.9 0.2
NI M:NI502 0.6 20.8 0.7
O M:HOH616 1.7 16.2 0.8
SG M:CYS70 2.1 12.1 0.1
SG M:CYS70 2.2 15.4 0.9
SE M:SEC492 2.2 23.4 0.1
SG M:CYS73 2.4 14.8 1.0
SE M:SEC492 2.4 24.2 0.2
SE M:SEC492 2.5 19.6 0.7
NI M:NI502 2.5 19.9 0.1
FE M:FCO501 2.9 14.2 1.0
SG M:CYS495 3.1 14.1 1.0
CB M:CYS70 3.2 13.2 0.9
CB M:CYS73 3.4 12.0 1.0
CB M:CYS70 3.4 13.0 0.1
CB M:SEC492 3.5 17.3 0.7
CB M:SEC492 3.5 17.3 0.2
CB M:SEC492 3.5 17.4 0.1
N M:CYS73 3.6 10.9 1.0
C2 M:FCO501 3.7 12.1 1.0
CB M:VAL72 3.9 13.8 1.0
C1 M:FCO501 4.0 14.6 1.0
CA M:CYS73 4.1 11.9 1.0
NH1 M:ARG425 4.1 16.5 1.0
C M:VAL72 4.4 11.9 1.0
CB M:CYS495 4.5 14.1 1.0
C3 M:FCO501 4.5 11.9 1.0
CA M:VAL72 4.5 12.4 1.0
N2 M:FCO501 4.5 13.6 1.0
N M:VAL72 4.6 12.4 1.0
CZ M:ARG425 4.6 14.1 1.0
CD M:ARG425 4.6 12.3 1.0
CA M:CYS70 4.6 13.0 0.9
CG1 M:VAL72 4.6 15.9 1.0
CA M:CYS70 4.7 12.7 0.1
NE M:ARG425 4.7 16.9 1.0
CG2 M:VAL72 4.8 15.1 1.0
N1 M:FCO501 4.9 14.6 1.0
CA M:SEC492 4.9 15.8 1.0
C M:CYS73 5.0 11.4 1.0
C M:CYS70 5.0 13.5 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 18:18:31 2024

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