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Nickel in PDB 4omf: The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

Enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

All present enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf was solved by S.Vitt, K.Ma, E.Warkentin, J.Moll, A.Pierik, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.71
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 233.160, 233.160, 233.160, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.1

Other elements in 4omf:

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 17 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member (pdb code 4omf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf:

Nickel binding site 1 out of 1 in 4omf

Go back to Nickel Binding Sites List in 4omf
Nickel binding site 1 out of 1 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni502

b:19.3
occ:1.00
NI A:NFU502 0.0 19.3 1.0
SG A:CYS63 2.4 17.6 1.0
SG A:CYS380 2.4 27.8 1.0
SG A:CYS66 2.4 16.8 1.0
SG A:CYS383 2.5 16.0 1.0
FE A:NFU502 2.8 15.2 1.0
CB A:CYS63 3.1 16.2 1.0
CB A:CYS380 3.3 18.8 1.0
CB A:CYS383 3.5 11.6 1.0
CB A:CYS66 3.7 14.0 1.0
C2 A:NFU502 3.7 12.6 1.0
C1 A:NFU502 3.9 13.6 1.0
N A:CYS66 3.9 15.6 1.0
CB A:VAL65 4.3 15.1 1.0
CA A:CYS66 4.4 12.7 1.0
C3 A:NFU502 4.4 12.5 1.0
CA A:CYS383 4.5 12.7 1.0
N A:CYS383 4.6 15.9 1.0
CA A:CYS63 4.6 17.2 1.0
N2 A:NFU502 4.6 14.1 1.0
NH2 A:ARG328 4.6 16.8 1.0
CD A:ARG328 4.7 14.8 1.0
CA A:CYS380 4.7 16.8 1.0
C A:VAL65 4.8 15.8 1.0
CG1 A:VAL65 4.8 15.7 1.0
N1 A:NFU502 4.8 14.2 1.0
CA A:VAL65 5.0 15.9 1.0
N A:VAL65 5.0 12.8 1.0

Reference:

S.Vitt, K.Ma, E.Warkentin, J.Moll, A.J.Pierik, S.Shima, U.Ermler. The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member. J.Mol.Biol. V. 426 2813 2014.
ISSN: ISSN 0022-2836
PubMed: 24887099
DOI: 10.1016/J.JMB.2014.05.024
Page generated: Wed Dec 16 01:34:11 2020

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