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Zinc in PDB 5t5m: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.:
1.2.99.5;

Protein crystallography data

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m was solved by T.Wagner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.543, 105.543, 340.549, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.2

Other elements in 5t5m:

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. also contains other interesting chemical elements:

Tungsten (W) 1 atom
Magnesium (Mg) 3 atoms
Potassium (K) 1 atom
Iron (Fe) 44 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. (pdb code 5t5m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5t5m

Go back to Zinc Binding Sites List in 5t5m
Zinc binding site 1 out of 2 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:58.7
occ:1.00
 O A:HOH720 1.9 60.0 1.0
OQ1 A:KCX178 2.1 48.9 1.0
ND1 A:HIS231 2.2 51.2 1.0
NE2 A:HIS271 2.2 45.6 1.0
CX A:KCX178 3.0 49.6 1.0
CE1 A:HIS231 3.1 47.4 1.0
OQ2 A:KCX178 3.1 50.5 1.0
CD2 A:HIS271 3.1 47.0 1.0
CE1 A:HIS271 3.2 47.3 1.0
ZN A:ZN603 3.2 60.2 1.0
CG A:HIS231 3.2 53.0 1.0
O A:HOH746 3.4 53.9 1.0
CB A:HIS231 3.5 52.4 1.0
NE2 A:HIS57 4.1 59.0 1.0
OD2 A:ASP385 4.1 50.9 1.0
NZ A:KCX178 4.2 49.6 1.0
NE2 A:HIS231 4.2 47.8 1.0
ND1 A:HIS271 4.3 48.7 1.0
CG A:HIS271 4.3 48.2 1.0
CD2 A:HIS231 4.3 51.8 1.0
OD1 A:ASP385 4.3 48.3 1.0
CE1 A:HIS57 4.4 58.5 1.0
CG2 A:THR270 4.4 53.1 1.0
CG A:ASP385 4.5 50.1 1.0
CG2 A:VAL180 4.7 47.3 1.0
CE A:KCX178 4.7 50.1 1.0
O A:HOH742 4.7 64.5 1.0
CA A:HIS231 4.8 52.6 1.0
NE2 A:HIS59 4.9 55.2 1.0
CG2 A:THR318 4.9 44.4 1.0

Zinc binding site 2 out of 2 in 5t5m

Go back to Zinc Binding Sites List in 5t5m
Zinc binding site 2 out of 2 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:60.2
occ:1.00
 O A:HOH720 1.9 60.0 1.0
NE2 A:HIS59 2.1 55.2 1.0
OD1 A:ASP385 2.1 48.3 1.0
NE2 A:HIS57 2.2 59.0 1.0
OQ2 A:KCX178 2.3 50.5 1.0
CE1 A:HIS59 2.9 55.8 1.0
CG A:ASP385 3.1 50.1 1.0
CD2 A:HIS59 3.1 56.3 1.0
CD2 A:HIS57 3.2 57.8 1.0
CE1 A:HIS57 3.2 58.5 1.0
ZN A:ZN602 3.2 58.7 1.0
CX A:KCX178 3.3 49.6 1.0
OD2 A:ASP385 3.5 50.9 1.0
OQ1 A:KCX178 3.6 48.9 1.0
O A:HOH746 4.0 53.9 1.0
CD2 A:HIS271 4.0 47.0 1.0
ND1 A:HIS59 4.1 56.8 1.0
NE2 A:HIS271 4.2 45.6 1.0
CB A:ALA115 4.2 56.1 1.0
CG A:HIS59 4.2 56.3 1.0
ND1 A:HIS57 4.3 59.4 1.0
NZ A:KCX178 4.3 49.6 1.0
CG A:HIS57 4.3 57.8 1.0
ND2 A:ASN388 4.4 54.6 1.0
CB A:ASP385 4.5 50.4 1.0
CA A:ASP385 4.8 51.3 1.0
O A:ASP385 4.9 48.3 1.0

Reference:

T.Wagner, U.Ermler, S.Shima. The Methanogenic CO2 Reducing-and-Fixing Enzyme Is Bifunctional and Contains 46 [4FE-4S] Clusters. Science V. 354 114 2016.
ISSN: ESSN 1095-9203
PubMed: 27846502
DOI: 10.1126/SCIENCE.AAF9284
Page generated: Mon Oct 28 08:15:19 2024

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