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Nickel in PDB 6z7r: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1, PDB code: 6z7r was solved by S.Zacarias, A.Temporao, P.Carpentier, P.Van Der Linden, I.A.C.Pereira, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.05 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.125, 93.686, 98.433, 90.00, 93.26, 90.00
R / Rfree (%) 18.8 / 24.2

Other elements in 6z7r:

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 also contains other interesting chemical elements:

Krypton (Kr) 42 atoms
Iron (Fe) 36 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 (pdb code 6z7r). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1, PDB code: 6z7r:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z7r

Go back to Nickel Binding Sites List in 6z7r
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:18.9
occ:0.89
 S B:H2S504 2.0 13.9 0.8
SG B:CYS492 2.2 12.7 1.0
SE B:SEC489 2.3 21.8 0.6
SG B:CSD75 2.3 17.9 1.0
SE B:SEC489 2.3 16.6 0.1
FE B:FCO501 2.3 17.6 1.0
SG B:CYS78 2.4 16.0 1.0
HB2 B:SEC489 2.8 21.0 0.3
OD1 B:CSD75 3.0 17.4 0.8
SE B:SEC489 3.0 26.9 0.3
HB2 B:CSD75 3.2 22.6 1.0
CB B:CSD75 3.2 18.7 1.0
HB2 B:CYS492 3.2 19.8 1.0
C1 B:FCO501 3.2 22.8 1.0
HB3 B:CSD75 3.3 22.6 1.0
CB B:SEC489 3.3 17.4 0.3
C2 B:FCO501 3.3 16.4 1.0
HB2 B:SEC489 3.3 20.9 0.1
HB3 B:CYS78 3.4 11.9 1.0
CB B:CYS492 3.4 16.4 1.0
OD2 B:CSD75 3.4 16.2 0.8
HB3 B:SEC489 3.5 21.0 0.3
CB B:SEC489 3.5 17.3 0.1
CB B:CYS78 3.5 9.8 1.0
HB3 B:SEC489 3.6 20.3 0.6
H B:CYS78 3.6 20.5 1.0
CB B:SEC489 3.7 16.8 0.6
HB3 B:SEC489 3.8 20.9 0.1
H B:CYS492 3.8 11.4 1.0
HE2 B:HIS82 3.9 28.7 1.0
HD2 B:CSD75 4.0 19.6 0.8
HB3 B:CYS492 4.0 19.8 1.0
HD2 B:ARG422 4.0 16.4 1.0
C3 B:FCO501 4.0 19.8 1.0
HB2 B:SEC489 4.1 20.3 0.6
N1 B:FCO501 4.1 11.8 1.0
HB B:VAL77 4.1 21.4 1.0
N B:CYS78 4.2 16.9 1.0
HB2 B:CYS78 4.2 11.9 1.0
N2 B:FCO501 4.3 17.7 1.0
N B:CYS492 4.4 9.4 1.0
CA B:CYS492 4.4 16.4 1.0
CA B:CYS78 4.5 14.9 1.0
CA B:CSD75 4.6 13.8 1.0
HH11 B:ARG422 4.6 15.8 1.0
HA B:CYS492 4.7 19.8 1.0
O B:SEC489 4.7 13.6 0.1
NE2 B:HIS82 4.7 23.8 1.0
HD3 B:ARG422 4.7 16.4 1.0
CD B:ARG422 4.8 13.5 1.0
CA B:SEC489 4.8 16.9 0.3
CA B:SEC489 4.8 16.9 0.1
O B:SEC489 4.8 12.6 0.6
H B:VAL77 4.9 14.4 1.0
HA B:CSD75 4.9 16.7 1.0
NH1 B:ARG422 5.0 13.1 1.0
CA B:SEC489 5.0 16.9 0.6
HG22 B:ILE74 5.0 24.9 1.0
HD2 B:HIS82 5.0 27.7 1.0

Nickel binding site 2 out of 2 in 6z7r

Go back to Nickel Binding Sites List in 6z7r
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:21.2
occ:0.95
 S D:H2S504 2.0 15.6 0.8
SG D:CYS492 2.2 14.5 1.0
FE D:FCO501 2.3 17.8 1.0
SG D:CYS78 2.3 13.8 1.0
SE D:SEC489 2.3 29.8 0.3
SE D:SEC489 2.3 17.2 0.4
SG D:CSD75 2.3 19.9 1.0
HB2 D:SEC489 2.9 23.8 0.3
OD1 D:CSD75 3.0 16.6 0.8
HB2 D:CSD75 3.1 19.7 1.0
SE D:SEC489 3.1 24.1 0.3
C1 D:FCO501 3.2 27.4 1.0
CB D:CSD75 3.2 16.3 1.0
HB3 D:SEC489 3.2 23.8 0.3
CB D:SEC489 3.2 19.7 0.3
C2 D:FCO501 3.2 17.2 1.0
HB3 D:CYS78 3.3 6.8 1.0
HB2 D:CYS492 3.3 12.3 1.0
HB2 D:SEC489 3.3 24.2 0.3
HB3 D:SEC489 3.4 21.9 0.4
HB3 D:CSD75 3.4 19.7 1.0
CB D:SEC489 3.4 20.1 0.3
CB D:CYS78 3.4 6.0 1.0
CB D:CYS492 3.5 10.2 1.0
CB D:SEC489 3.5 18.1 0.4
H D:CYS78 3.6 13.7 1.0
OD2 D:CSD75 3.6 12.6 0.8
HB3 D:SEC489 3.7 24.2 0.3
HB2 D:SEC489 3.9 21.9 0.4
HD2 D:ARG422 4.0 22.6 1.0
H D:CYS492 4.0 16.1 1.0
HB D:VAL77 4.0 13.2 1.0
N1 D:FCO501 4.0 17.4 1.0
C3 D:FCO501 4.0 17.6 1.0
HB3 D:CYS492 4.1 12.3 1.0
HB2 D:CYS78 4.1 6.8 1.0
N D:CYS78 4.2 11.3 1.0
HE2 D:HIS82 4.2 16.6 1.0
HD2 D:CSD75 4.2 15.3 0.8
N2 D:FCO501 4.2 14.1 1.0
CA D:CYS78 4.4 6.0 1.0
N D:CYS492 4.5 13.3 1.0
CA D:CYS492 4.5 10.0 1.0
HD3 D:ARG422 4.6 22.6 1.0
CA D:CSD75 4.7 10.1 1.0
CD D:ARG422 4.7 18.7 1.0
H D:VAL77 4.7 16.6 1.0
HA D:CYS492 4.7 12.2 1.0
CA D:SEC489 4.8 19.5 0.3
CA D:SEC489 4.8 19.5 0.3
HH11 D:ARG422 4.8 25.8 1.0
O D:SEC489 4.9 17.3 0.3
CA D:SEC489 4.9 19.4 0.4
O D:SEC489 4.9 17.1 0.4
NE2 D:HIS82 4.9 13.7 1.0
CB D:VAL77 4.9 10.9 1.0
HG3 D:GLU28 5.0 22.0 1.0

Reference:

S.Zacarias, A.Temporao, P.Carpentier, P.Van Der Linden, I.A.C.Pereira, P.M.Matias. Exploring the Gas Access Routes in A [Nifese] Hydrogenase Using Crystals Pressurized with Krypton and Oxygen. J.Biol.Inorg.Chem. V. 25 863 2020.
ISSN: ESSN 1432-1327
PubMed: 32865640
DOI: 10.1007/S00775-020-01814-Y
Page generated: Wed Dec 16 01:57:37 2020

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