Atomistry » Sodium » PDB 5syl-5tcd » 5t5i
Atomistry »
  Sodium »
    PDB 5syl-5tcd »
      5t5i »

Sodium 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
Zinc (Zn) 4 atoms
Iron (Fe) 88 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na606

b:21.6
occ:1.00
O A:HOH809 2.4 36.1 1.0
O A:HOH705 3.2 20.1 1.0
N A:GLY144 3.2 21.1 1.0
N A:VAL180 3.3 18.3 1.0
ND2 A:ASN145 3.5 19.8 1.0
O A:VAL180 3.6 19.0 1.0
CA A:GLY144 3.6 20.2 1.0
N A:ASN145 3.8 19.0 1.0
CB A:LEU142 3.9 18.5 1.0
CD2 A:LEU142 3.9 22.8 1.0
CB A:VAL180 3.9 21.0 1.0
CA A:VAL180 4.0 18.6 1.0
C A:GLY144 4.0 22.3 1.0
N A:PHE143 4.0 19.5 1.0
C A:VAL180 4.2 21.2 1.0
O A:KCX178 4.2 23.2 1.0
C A:ILE179 4.3 22.3 1.0
C A:PHE143 4.3 23.0 1.0
CA A:ILE179 4.3 18.9 1.0
CA A:LEU142 4.4 18.7 1.0
C A:LEU142 4.4 22.9 1.0
CG2 A:VAL180 4.5 21.6 1.0
CG A:LEU142 4.5 22.1 1.0
CG A:ASN145 4.5 28.0 1.0
CB A:ASN145 4.5 18.5 1.0
OG1 A:THR344 4.6 29.7 1.0
CA A:PHE143 4.7 19.7 1.0
CA A:ASN145 4.8 18.6 1.0
C A:KCX178 4.9 23.5 1.0
O A:GLY144 4.9 20.9 1.0
N A:ILE179 5.0 19.1 1.0

Sodium binding site 2 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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:Na610

b:25.8
occ:1.00
O A:HOH958 2.3 50.5 1.0
O A:HOH974 2.5 45.2 1.0
O A:GLY414 2.7 36.6 1.0
O A:LEU416 2.7 27.3 1.0
O A:ILE412 2.9 30.9 1.0
C A:GLY414 3.7 36.1 1.0
C A:GLU413 3.7 36.2 1.0
O A:GLU413 3.8 38.7 1.0
C A:LEU416 3.9 29.7 1.0
N A:GLY414 3.9 31.5 1.0
C A:ILE412 4.0 32.1 1.0
O A:HOH927 4.1 32.1 1.0
CA A:GLU413 4.1 29.9 1.0
N A:LEU416 4.3 28.2 1.0
CA A:GLY414 4.3 31.9 1.0
N A:GLU413 4.5 29.9 1.0
NE2 A:GLN421 4.5 35.7 1.0
C A:GLU415 4.5 34.2 1.0
CA A:LEU416 4.6 27.2 1.0
N A:GLU415 4.7 32.9 1.0
O A:LEU411 4.8 30.9 1.0
N A:LYS418 4.8 28.6 1.0
O A:HOH710 4.8 37.8 1.0
C A:HIS417 4.8 30.6 1.0
CD A:LYS418 4.9 74.4 1.0
N A:HIS417 4.9 26.8 1.0
CG A:LYS418 5.0 58.6 1.0
O A:GLU415 5.0 32.9 1.0

Sodium binding site 3 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na606

b:20.1
occ:1.00
O I:HOH819 2.8 33.6 1.0
N I:VAL180 3.2 16.8 1.0
O I:HOH721 3.2 17.7 1.0
N I:GLY144 3.2 18.4 1.0
O I:VAL180 3.5 18.4 1.0
ND2 I:ASN145 3.5 17.0 1.0
CA I:GLY144 3.5 17.9 1.0
N I:ASN145 3.8 16.6 1.0
CB I:VAL180 3.9 18.9 1.0
CD2 I:LEU142 3.9 20.6 1.0
CA I:VAL180 3.9 16.6 1.0
CB I:LEU142 3.9 16.9 1.0
C I:GLY144 4.0 21.0 1.0
N I:PHE143 4.0 16.8 1.0
C I:VAL180 4.1 19.6 1.0
O I:KCX178 4.1 19.4 1.0
C I:ILE179 4.2 21.4 1.0
CA I:ILE179 4.2 18.3 1.0
C I:PHE143 4.3 20.6 1.0
CG2 I:VAL180 4.4 18.3 1.0
CA I:LEU142 4.4 17.4 1.0
C I:LEU142 4.5 22.5 1.0
CG I:LEU142 4.5 20.4 1.0
CG I:ASN145 4.5 22.3 1.0
CB I:ASN145 4.6 18.0 1.0
OG1 I:THR344 4.7 30.9 1.0
CA I:PHE143 4.7 16.4 1.0
C I:KCX178 4.9 21.2 1.0
CA I:ASN145 4.9 15.8 1.0
N I:ILE179 4.9 19.0 1.0
O I:GLY144 4.9 18.9 1.0

Sodium binding site 4 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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:Na610

b:28.1
occ:1.00
O I:HOH1035 2.4 43.6 1.0
O I:LEU416 2.6 29.5 1.0
O I:GLY414 2.7 34.8 1.0
O I:ILE412 2.9 29.5 1.0
C I:GLY414 3.7 35.3 1.0
C I:GLU413 3.8 35.6 1.0
C I:LEU416 3.8 29.8 1.0
O I:GLU413 3.9 35.6 1.0
O I:HOH958 3.9 28.7 1.0
C I:ILE412 4.0 30.7 1.0
N I:GLY414 4.0 31.3 1.0
N I:LEU416 4.2 27.7 1.0
CA I:GLU413 4.2 30.4 1.0
CA I:GLY414 4.3 31.4 1.0
C I:GLU415 4.4 32.4 1.0
CA I:LEU416 4.4 26.3 1.0
NE2 I:GLN421 4.5 38.0 1.0
N I:GLU413 4.5 29.7 1.0
N I:GLU415 4.6 31.6 1.0
O I:HOH791 4.7 34.1 1.0
O I:LEU411 4.7 26.9 1.0
N I:HIS417 4.8 27.4 1.0
C I:HIS417 4.9 31.2 1.0
N I:LYS418 4.9 29.3 1.0
O I:GLU415 4.9 31.0 1.0
CB I:LEU416 4.9 26.1 1.0
CA I:GLU415 5.0 31.9 1.0

Sodium binding site 5 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na binding site number 5 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
L:Na201

b:22.2
occ:1.00
O L:HOH398 2.9 46.9 1.0
O L:HOH303 3.1 38.7 1.0
ND2 L:ASN36 3.5 29.8 1.0
N L:GLY74 3.5 23.9 1.0
O L:HOH345 3.5 25.0 1.0
CA L:GLU73 3.7 25.5 1.0
CE L:MET39 3.8 26.0 1.0
CB L:ASN36 4.0 24.6 1.0
CB L:MET39 4.0 23.5 1.0
C L:GLU73 4.1 27.6 1.0
CG L:ASN36 4.2 33.1 1.0
CG L:GLU73 4.2 41.0 1.0
N L:MET39 4.4 24.4 1.0
O L:PRO72 4.4 25.3 1.0
CB L:GLU73 4.5 27.6 1.0
CA L:GLY74 4.5 23.3 1.0
CA L:MET39 4.7 23.1 1.0
N L:GLU73 4.7 24.0 1.0
CG L:MET39 4.7 26.2 1.0
C L:PRO72 4.9 27.0 1.0
CB L:GLU38 5.0 32.1 1.0
SD L:MET39 5.0 28.8 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: Tue Dec 15 11:35:49 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy