Atomistry » Zinc » PDB 5svc-5t72 » 5t5i
Atomistry »
  Zinc »
    PDB 5svc-5t72 »
      5t5i »

Zinc in PDB 5t5i: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A

Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A

All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A:
1.2.99.5;

Protein crystallography data

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i 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) 48.49 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.644, 174.576, 205.425, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.2

Other elements in 5t5i:

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A also contains other interesting chemical elements:

Tungsten (W) 2 atoms
Magnesium (Mg) 2 atoms
Potassium (K) 18 atoms
Iron (Fe) 88 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A (pdb code 5t5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5t5i

Go back to Zinc Binding Sites List in 5t5i
Zinc binding site 1 out of 4 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 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, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:25.9
occ:1.00
 O A:HOH797 2.0 19.9 1.0
OQ2 A:KCX178 2.0 22.3 1.0
ND1 A:HIS231 2.1 20.6 1.0
NE2 A:HIS271 2.2 18.9 1.0
CX A:KCX178 2.9 19.0 1.0
CE1 A:HIS271 3.1 19.3 1.0
OQ1 A:KCX178 3.1 17.5 1.0
CG A:HIS231 3.1 18.8 1.0
CE1 A:HIS231 3.1 19.8 1.0
ZN A:ZN602 3.2 24.4 1.0
CD2 A:HIS271 3.2 19.9 1.0
O A:HOH717 3.3 23.5 1.0
CB A:HIS231 3.4 16.9 1.0
OD2 A:ASP385 4.1 18.3 1.0
NZ A:KCX178 4.2 19.0 1.0
NE2 A:HIS57 4.2 19.6 1.0
ND1 A:HIS271 4.3 21.4 1.0
NE2 A:HIS231 4.3 19.9 1.0
CG2 A:THR270 4.3 20.2 1.0
CD2 A:HIS231 4.3 20.6 1.0
CG A:HIS271 4.3 20.7 1.0
OD1 A:ASP385 4.3 21.1 1.0
CE1 A:HIS57 4.4 19.2 1.0
CG A:ASP385 4.5 20.0 1.0
CG2 A:THR318 4.7 21.9 1.0
CA A:HIS231 4.7 17.6 1.0
CG2 A:VAL180 4.7 21.6 1.0
CE A:KCX178 4.8 18.5 1.0
O A:HOH801 4.8 30.8 1.0
NE2 A:HIS59 4.9 24.6 1.0
CB A:THR318 5.0 22.3 1.0
CG1 A:VAL180 5.0 20.3 1.0

Zinc binding site 2 out of 4 in 5t5i

Go back to Zinc Binding Sites List in 5t5i
Zinc binding site 2 out of 4 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 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, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:24.4
occ:1.00
 O A:HOH797 2.0 19.9 1.0
NE2 A:HIS59 2.1 24.6 1.0
NE2 A:HIS57 2.1 19.6 1.0
OD1 A:ASP385 2.1 21.1 1.0
OQ1 A:KCX178 2.3 17.5 1.0
CE1 A:HIS59 3.0 24.5 1.0
CE1 A:HIS57 3.1 19.2 1.0
CG A:ASP385 3.1 20.0 1.0
CD2 A:HIS57 3.1 20.1 1.0
CD2 A:HIS59 3.2 25.5 1.0
ZN A:ZN601 3.2 25.9 1.0
CX A:KCX178 3.2 19.0 1.0
OQ2 A:KCX178 3.4 22.3 1.0
OD2 A:ASP385 3.5 18.3 1.0
O A:HOH717 3.8 23.5 1.0
CD2 A:HIS271 4.0 19.9 1.0
NE2 A:HIS271 4.1 18.9 1.0
CB A:ALA115 4.1 25.1 1.0
ND1 A:HIS59 4.2 25.3 1.0
ND1 A:HIS57 4.3 20.1 1.0
CG A:HIS59 4.3 24.0 1.0
CG A:HIS57 4.3 19.9 1.0
NZ A:KCX178 4.3 19.0 1.0
CB A:ASP385 4.5 18.3 1.0
ND2 A:ASN388 4.6 22.9 1.0
CA A:ASP385 4.9 17.9 1.0
O A:ASP385 4.9 19.3 1.0

Zinc binding site 3 out of 4 in 5t5i

Go back to Zinc Binding Sites List in 5t5i
Zinc binding site 3 out of 4 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn601

b:23.0
occ:1.00
 O I:HOH706 2.0 18.7 1.0
NE2 I:HIS59 2.1 20.7 1.0
OD1 I:ASP385 2.1 17.9 1.0
NE2 I:HIS57 2.1 17.8 1.0
OQ2 I:KCX178 2.3 17.3 1.0
CE1 I:HIS59 3.0 20.9 1.0
CG I:ASP385 3.1 19.7 1.0
CD2 I:HIS57 3.1 18.3 1.0
CE1 I:HIS57 3.2 17.3 1.0
CD2 I:HIS59 3.2 21.4 1.0
ZN I:ZN602 3.2 24.5 1.0
CX I:KCX178 3.2 19.4 1.0
OQ1 I:KCX178 3.4 17.5 1.0
OD2 I:ASP385 3.4 19.4 1.0
O I:HOH764 3.8 20.7 1.0
CD2 I:HIS271 4.0 19.9 1.0
NE2 I:HIS271 4.1 18.4 1.0
CB I:ALA115 4.1 21.5 1.0
ND1 I:HIS59 4.2 22.5 1.0
CG I:HIS59 4.3 20.6 1.0
CG I:HIS57 4.3 18.0 1.0
ND1 I:HIS57 4.3 18.7 1.0
NZ I:KCX178 4.3 19.3 1.0
CB I:ASP385 4.5 19.9 1.0
ND2 I:ASN388 4.6 20.4 1.0
CA I:ASP385 4.9 18.0 1.0
O I:ASP385 4.9 18.3 1.0

Zinc binding site 4 out of 4 in 5t5i

Go back to Zinc Binding Sites List in 5t5i
Zinc binding site 4 out of 4 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn602

b:24.5
occ:1.00
 OQ1 I:KCX178 2.0 17.5 1.0
O I:HOH706 2.0 18.7 1.0
NE2 I:HIS271 2.1 18.4 1.0
ND1 I:HIS231 2.1 18.7 1.0
CX I:KCX178 2.9 19.4 1.0
CE1 I:HIS271 3.1 17.9 1.0
CG I:HIS231 3.1 17.3 1.0
CE1 I:HIS231 3.1 17.4 1.0
CD2 I:HIS271 3.2 19.9 1.0
OQ2 I:KCX178 3.2 17.3 1.0
ZN I:ZN601 3.2 23.0 1.0
O I:HOH764 3.3 20.7 1.0
CB I:HIS231 3.4 15.1 1.0
OD2 I:ASP385 4.1 19.4 1.0
NZ I:KCX178 4.2 19.3 1.0
NE2 I:HIS57 4.2 17.8 1.0
ND1 I:HIS271 4.2 19.3 1.0
CG2 I:THR270 4.3 20.1 1.0
CG I:HIS271 4.3 18.9 1.0
NE2 I:HIS231 4.3 17.4 1.0
CD2 I:HIS231 4.3 18.7 1.0
OD1 I:ASP385 4.4 17.9 1.0
CE1 I:HIS57 4.4 17.3 1.0
CG I:ASP385 4.5 19.7 1.0
CA I:HIS231 4.7 15.8 1.0
CG2 I:THR318 4.7 19.9 1.0
CG2 I:VAL180 4.8 18.3 1.0
CE I:KCX178 4.8 17.6 1.0
O I:HOH837 4.9 29.5 1.0
NE2 I:HIS59 5.0 20.7 1.0
CG1 I:VAL180 5.0 18.1 1.0
CB I:THR318 5.0 22.6 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

Na in 3PZB
Na in 3PXS
Na in 3PYX
Na in 3PYM
Na in 3PXT
Na in 3PXW
Na in 3PNX
Na in 3PWS
Na in 3PQH
Na in 3PWM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy