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

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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

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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: Wed Dec 16 10:53:55 2020

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