Potassium 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
Zinc (Zn) 4 atoms
Iron (Fe) 88 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 5 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Potassium 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 Potassium atom.
In total 18 binding sites of Potassium where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 18 in 5t5i

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Potassium binding site 1 out of 18 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 Potassium with other atoms in the K 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:K604

b:22.0
occ:1.00
OG A:SER76 2.6 21.7 1.0
O A:ARG69 2.7 21.2 1.0
O A:HOH713 2.8 26.3 1.0
O B:GLY305 2.8 23.1 1.0
O A:HOH894 3.0 22.6 1.0
O A:ARG72 3.0 19.6 1.0
C A:ARG69 3.6 21.6 1.0
O B:HOH754 3.6 19.0 1.0
CB A:SER76 3.7 22.3 1.0
C A:ARG72 3.7 22.3 1.0
CA A:ARG69 3.8 20.1 1.0
C B:GLY305 3.8 23.7 1.0
CA B:GLY305 4.1 21.1 1.0
N A:SER76 4.2 22.7 1.0
CB A:ARG69 4.3 19.7 1.0
N A:PRO73 4.4 20.0 1.0
CA A:PRO73 4.4 20.2 1.0
CA A:SER76 4.4 22.2 1.0
CA A:ARG72 4.6 18.6 1.0
CB A:ARG72 4.7 18.9 1.0
N A:MET70 4.8 19.0 1.0
O A:VAL94 4.8 22.6 1.0
N A:ARG72 4.8 18.1 1.0
O A:GLY68 4.9 23.8 1.0
OG A:SER90 4.9 27.6 1.0
CB A:ASP75 4.9 21.4 1.0
OD2 A:ASP75 5.0 26.0 1.0

Potassium binding site 2 out of 18 in 5t5i

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Potassium binding site 2 out of 18 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 Potassium with other atoms in the K 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:K605

b:49.8
occ:1.00
O A:HOH750 2.1 32.9 1.0
O A:ASP300 2.8 26.6 1.0
OD1 A:ASP264 3.0 32.6 1.0
O A:ASP264 3.0 27.4 1.0
O A:HOH1016 3.1 37.0 1.0
CG A:ASP264 3.5 32.1 1.0
CG2 A:THR265 3.5 28.1 1.0
C A:ASP264 3.8 28.1 1.0
C A:ASP300 3.9 27.4 1.0
OD2 A:ASP264 4.1 33.5 1.0
CB A:ASP264 4.1 29.2 1.0
CB A:ASP300 4.4 30.0 1.0
CA A:ASP300 4.5 27.1 1.0
N A:THR265 4.5 23.1 1.0
CA A:ASP264 4.6 26.7 1.0
O A:HOH749 4.6 43.7 1.0
CB A:THR265 4.7 27.2 1.0
CA A:THR265 4.7 22.0 1.0
O A:HOH1004 4.8 40.5 1.0
O A:HOH939 4.9 36.6 1.0
CG A:ASP300 5.0 44.4 1.0

Potassium binding site 3 out of 18 in 5t5i

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Potassium binding site 3 out of 18 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 Potassium with other atoms in the K 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
B:K506

b:32.1
occ:1.00
O B:VAL43 2.7 30.2 1.0
O B:SER40 2.7 24.7 1.0
O D:GLU18 2.8 27.5 1.0
O D:HOH227 2.9 28.6 1.0
O B:HOH815 2.9 52.4 1.0
O B:HOH735 3.2 44.7 1.0
O B:LYS41 3.2 28.0 1.0
O B:HOH667 3.6 31.8 1.0
C B:VAL43 3.7 31.1 1.0
C B:LYS41 3.8 26.5 1.0
C B:SER40 3.8 26.3 1.0
CA B:LYS41 3.9 23.6 1.0
C D:GLU18 4.0 27.2 1.0
O D:HOH250 4.1 53.1 1.0
CA B:HIS44 4.3 30.8 1.0
N B:LYS41 4.4 24.3 1.0
N B:HIS44 4.4 29.6 1.0
N B:VAL43 4.5 26.5 1.0
CA D:SER19 4.6 22.8 1.0
N B:ALA45 4.6 30.0 1.0
O D:SER19 4.7 31.7 1.0
N D:SER19 4.7 23.1 1.0
CA B:VAL43 4.8 26.3 0.5
CA B:VAL43 4.8 26.6 0.5
N B:PHE42 4.8 21.9 1.0
C B:PHE42 4.9 28.4 1.0
C B:HIS44 4.9 33.1 1.0
CA D:GLU18 4.9 23.4 1.0
C D:SER19 5.0 29.6 1.0
O D:HOH273 5.0 38.4 1.0

Potassium binding site 4 out of 18 in 5t5i

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Potassium binding site 4 out of 18 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 Potassium with other atoms in the K 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
F:K409

b:38.1
occ:1.00
O F:CYS249 2.6 30.5 1.0
O F:GLU247 2.9 30.9 1.0
O F:GLN246 2.9 27.0 1.0
OD1 F:ASP252 3.0 45.9 1.0
C F:GLU247 3.5 31.9 1.0
C F:CYS249 3.6 32.2 1.0
N F:CYS249 3.8 27.6 1.0
CA F:GLU247 4.0 26.1 1.0
C F:GLN246 4.0 28.3 1.0
O F:HOH512 4.0 29.4 1.0
CA F:CYS249 4.1 26.7 1.0
CG F:ASP252 4.2 47.3 1.0
C F:ILE248 4.3 32.0 1.0
N F:ILE248 4.4 28.7 1.0
CB F:CYS249 4.4 26.7 1.0
N F:GLU247 4.5 25.4 1.0
O F:HOH659 4.5 55.1 1.0
CA F:ASP252 4.7 31.8 1.0
N F:ASP252 4.7 31.6 1.0
N F:PRO250 4.8 30.1 1.0
CA F:ILE248 4.8 29.0 1.0
O F:ILE248 4.8 30.1 1.0

Potassium binding site 5 out of 18 in 5t5i

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Potassium binding site 5 out of 18 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 Potassium with other atoms in the K 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
F:K410

b:42.0
occ:1.00
O F:HOH660 2.4 47.0 1.0
O F:CYS318 2.6 25.4 1.0
O F:GLU315 2.8 27.0 1.0
O F:ARG316 3.1 27.7 1.0
C F:CYS318 3.6 27.3 1.0
C F:ARG316 3.6 27.8 1.0
CG2 F:THR321 3.7 36.1 0.5
N F:CYS318 3.9 23.9 1.0
C F:GLU315 4.0 28.4 1.0
O F:HOH501 4.0 39.1 1.0
CA F:ARG316 4.0 25.9 1.0
CA F:CYS318 4.2 22.9 1.0
O G:HOH203 4.2 46.1 1.0
OG1 F:THR321 4.4 27.6 0.5
C F:SER317 4.4 26.5 1.0
N F:ARG316 4.5 25.7 1.0
N F:SER317 4.5 23.0 1.0
CB F:CYS318 4.6 23.1 1.0
N F:PRO319 4.7 25.0 1.0
CB F:THR321 4.9 37.3 0.5
CA F:THR321 4.9 26.6 0.5
CA F:PRO319 4.9 25.3 1.0
N F:THR321 4.9 26.2 1.0
CA F:THR321 4.9 26.2 0.5
CA F:SER317 5.0 22.5 1.0

Potassium binding site 6 out of 18 in 5t5i

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Potassium binding site 6 out of 18 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 Potassium with other atoms in the K binding site number 6 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
F:K411

b:37.0
occ:1.00
O F:CYS125 2.7 27.2 1.0
OD1 F:ASP128 2.7 43.0 1.0
O F:GLU122 2.8 28.7 1.0
O F:THR123 2.8 31.8 1.0
O F:HOH679 2.9 51.4 1.0
C F:THR123 3.4 32.5 1.0
C F:CYS125 3.7 30.8 1.0
N F:CYS125 3.9 28.0 1.0
CA F:THR123 3.9 27.9 1.0
C F:GLU122 3.9 30.5 1.0
CG F:ASP128 3.9 42.9 1.0
O F:HOH595 4.0 30.2 1.0
CA F:CYS125 4.2 27.0 1.0
C F:ALA124 4.3 32.3 1.0
N F:THR123 4.3 27.5 1.0
N F:ALA124 4.3 29.4 1.0
CB F:CYS125 4.4 26.6 1.0
CA F:ASP128 4.4 32.0 1.0
N F:ASP128 4.6 31.5 1.0
CB F:ASP128 4.7 33.7 1.0
O F:ALA124 4.8 32.7 1.0
CA F:ALA124 4.8 29.1 1.0
OD2 F:ASP128 4.8 51.4 1.0
N F:PRO126 4.9 29.1 1.0

Potassium binding site 7 out of 18 in 5t5i

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Potassium binding site 7 out of 18 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 Potassium with other atoms in the K binding site number 7 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
F:K412

b:34.4
occ:1.00
OD1 F:ASP167 2.7 44.8 1.0
O F:CYS164 2.7 29.8 1.0
O F:GLU161 2.8 29.7 1.0
O F:HOH663 2.8 42.2 1.0
O F:GLU162 2.9 33.7 1.0
C F:GLU162 3.5 34.2 1.0
C F:CYS164 3.8 31.2 1.0
N F:CYS164 3.9 26.9 1.0
CG F:ASP167 3.9 47.0 1.0
C F:GLU161 3.9 32.1 1.0
O F:HOH620 4.0 61.8 1.0
O F:HOH519 4.0 31.5 1.0
CA F:GLU162 4.0 29.6 1.0
CA F:CYS164 4.2 26.4 1.0
C F:MET163 4.3 32.2 1.0
N F:MET163 4.3 30.7 1.0
CB F:CYS164 4.4 25.6 1.0
N F:GLU162 4.4 29.6 1.0
O F:HOH608 4.4 37.5 1.0
CA F:ASP167 4.5 33.0 1.0
N F:ASP167 4.5 32.8 1.0
CA F:MET163 4.7 30.2 1.0
OD2 F:ASP167 4.8 57.0 1.0
CB F:ASP167 4.8 35.0 1.0
O F:MET163 4.9 29.9 1.0
N F:PRO165 4.9 30.3 1.0

Potassium binding site 8 out of 18 in 5t5i

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Potassium binding site 8 out of 18 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 Potassium with other atoms in the K binding site number 8 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
F:K413

b:42.1
occ:1.00
O F:CYS204 2.6 35.9 1.0
O F:HOH674 2.7 67.3 1.0
O F:LYS201 2.7 36.7 1.0
OD1 F:ASP207 2.8 56.4 1.0
O F:ARG202 3.2 39.0 1.0
C F:ARG202 3.6 37.9 1.0
C F:CYS204 3.7 36.4 1.0
C F:LYS201 3.8 36.9 1.0
N F:CYS204 3.9 30.4 1.0
CA F:ARG202 3.9 34.1 1.0
CG F:ASP207 4.0 56.5 1.0
CA F:CYS204 4.1 31.1 1.0
O F:HOH541 4.3 39.8 1.0
CB F:CYS204 4.3 31.1 1.0
N F:ARG202 4.4 33.8 1.0
C F:ILE203 4.4 33.8 1.0
N F:ILE203 4.5 32.5 1.0
CA F:ASP207 4.6 40.5 1.0
N F:ASP207 4.7 39.8 1.0
OD2 F:ASP207 4.8 66.6 1.0
CB F:ASP207 4.8 43.7 1.0
N F:PRO205 4.9 34.0 1.0
O F:ILE203 4.9 32.5 1.0
CA F:ILE203 4.9 30.3 1.0

Potassium binding site 9 out of 18 in 5t5i

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Potassium binding site 9 out of 18 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 Potassium with other atoms in the K binding site number 9 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
G:K103

b:28.0
occ:1.00
O G:CYS71 2.7 23.7 1.0
O G:VAL68 2.7 24.8 1.0
O G:HOH248 2.8 33.1 1.0
O G:HOH251 2.8 46.0 1.0
O G:HOH201 2.8 28.3 1.0
OD1 G:ASP74 2.8 32.5 1.0
O G:HOH236 3.5 48.9 1.0
C G:VAL68 3.8 26.2 1.0
C G:CYS71 3.9 23.1 1.0
CG G:ASP74 4.0 35.0 1.0
CG1 G:VAL68 4.1 27.9 1.0
O G:HOH212 4.3 41.8 1.0
O G:HOH257 4.3 33.5 1.0
CA G:ASP74 4.3 23.9 1.0
N G:ASP74 4.4 23.7 1.0
CB G:CYS71 4.5 19.2 1.0
CA G:CYS71 4.5 20.2 1.0
CA G:VAL68 4.5 23.4 1.0
N G:CYS71 4.6 21.9 1.0
O G:HOH252 4.6 38.6 1.0
CB G:ASP74 4.7 25.5 1.0
N G:GLU69 4.8 24.6 1.0
OD2 G:ASP74 4.8 41.4 1.0
N G:PRO72 4.9 21.1 1.0
CA G:GLU69 4.9 25.1 1.0
O F:HOH687 5.0 38.5 1.0
CB G:VAL68 5.0 26.7 1.0

Potassium binding site 10 out of 18 in 5t5i

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Potassium binding site 10 out of 18 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 Potassium with other atoms in the K binding site number 10 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
G:K104

b:46.2
occ:1.00
O G:HOH256 2.6 63.8 1.0
OD1 G:ASN54 2.7 36.4 1.0
O G:ILE55 2.7 27.5 1.0
O G:HOH232 3.2 30.1 1.0
CG G:ASN54 3.6 42.1 1.0
C G:ILE55 3.7 29.5 1.0
N G:ILE55 3.9 25.7 1.0
ND2 G:ASN54 4.1 38.8 1.0
CA G:ILE55 4.3 26.3 1.0
O G:HOH260 4.4 50.4 1.0
C G:ASN54 4.5 27.9 1.0
CA G:ASN54 4.7 25.9 1.0
CB G:ASN54 4.7 26.9 1.0
N G:LYS56 4.8 27.7 1.0
CD G:LYS56 4.9 35.6 1.0
CB G:ILE55 4.9 29.7 1.0
O G:HOH249 4.9 65.4 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 Dec 14 00:07:38 2020

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