Atomistry » Zinc » PDB 5sva-5t6b » 5t5m
Atomistry »
  Zinc »
    PDB 5sva-5t6b »
      5t5m »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy