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Zinc 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:

Nickel (Ni) 1 atom
Magnesium (Mg) 4 atoms
Iron (Fe) 17 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where 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:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4omf

Go back to Zinc Binding Sites List in 4omf
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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
G:Zn304

b:60.6
occ:0.50
ZN G:DTZ304 0.0 60.6 0.5
S1 G:DTZ304 2.5 54.6 0.5
O G:HOH565 2.6 31.7 0.5
SG G:CYS206 2.6 45.4 1.0
SG G:CYS208 2.7 21.8 0.5
ZN G:DTZ304 2.9 54.0 0.5
CB G:CYS208 3.6 19.7 0.5
CB G:CYS208 3.6 19.2 0.5
SG G:CYS208 3.6 25.6 0.5
CB G:CYS206 3.8 26.6 1.0
NZ G:LYS251 4.1 27.0 1.0
N G:CYS208 4.2 16.5 1.0
CA G:CYS208 4.5 17.7 1.0
CD2 G:LEU244 4.7 20.7 1.0
N G:GLY207 4.9 18.9 1.0

Zinc binding site 2 out of 2 in 4omf

Go back to Zinc Binding Sites List in 4omf
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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
G:Zn304

b:54.0
occ:0.50
ZN G:DTZ304 0.0 54.0 0.5
S1 G:DTZ304 2.2 54.6 0.5
ZN G:DTZ304 2.9 60.6 0.5
NZ G:LYS251 3.9 27.0 1.0
SG G:CYS208 4.3 25.6 0.5
SG G:CYS208 4.6 21.8 0.5
SG G:CYS206 4.6 45.4 1.0
O G:HOH565 4.8 31.7 0.5
CB G:CYS206 5.0 26.6 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 05:39:17 2020

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