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Potassium in PDB 5a8r: Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution, PDB code: 5a8r was solved by T.Wagner, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.36 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 216.660, 246.610, 103.650, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.6

Other elements in 5a8r:

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution (pdb code 5a8r). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution, PDB code: 5a8r:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 5a8r

Go back to Potassium Binding Sites List in 5a8r
Potassium binding site 1 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:24.5
occ:1.00
 O A:ILE63 2.6 29.0 1.0
O D:HOH2064 2.7 16.6 1.0
O A:VAL65 2.7 27.4 1.0
O D:ALA147 2.9 15.4 1.0
O A:PRO61 3.1 29.3 1.0
O A:HOH2036 3.5 37.1 1.0
C A:PRO61 3.8 24.5 1.0
C A:ILE63 3.8 28.2 1.0
C A:VAL65 3.8 30.6 1.0
NE2 D:HIS141 4.0 16.3 1.0
C D:ALA147 4.0 17.7 1.0
CG1 A:VAL65 4.0 21.2 1.0
N A:VAL65 4.1 20.6 1.0
O A:HOH2035 4.1 25.2 1.0
CA A:PRO61 4.1 27.9 1.0
C A:GLY64 4.2 17.1 1.0
CA A:VAL65 4.4 22.8 1.0
O A:ASN60 4.4 19.9 1.0
N A:ILE63 4.5 19.6 1.0
O A:GLY64 4.5 22.3 1.0
CE1 D:HIS141 4.5 21.2 1.0
CA D:VAL148 4.6 21.8 1.0
CA A:ILE63 4.7 17.8 1.0
CG A:LEU67 4.7 25.7 1.0
N D:VAL148 4.7 16.8 1.0
N A:GLY64 4.7 16.4 1.0
O A:HOH2032 4.8 29.3 1.0
CA A:GLY64 4.8 17.3 1.0
N A:ASP62 4.8 21.8 1.0
CD2 D:HIS141 4.9 15.8 1.0
CB A:VAL65 4.9 31.8 1.0
OE2 D:GLU155 4.9 18.6 1.0
N A:PRO66 4.9 27.4 1.0
CA D:ALA147 5.0 16.1 1.0

Potassium binding site 2 out of 7 in 5a8r

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Potassium binding site 2 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:22.1
occ:1.00
 O D:ILE63 2.6 18.4 1.0
O D:VAL65 2.7 24.5 1.0
O A:HOH2078 2.7 22.3 1.0
O A:ALA147 2.9 16.4 1.0
O D:PRO61 3.3 23.8 1.0
O D:HOH2030 3.6 29.7 1.0
C D:VAL65 3.8 23.6 1.0
C D:ILE63 3.8 22.3 1.0
CG1 D:VAL65 3.9 15.4 1.0
C D:PRO61 3.9 24.3 1.0
NE2 A:HIS141 4.0 19.3 1.0
C A:ALA147 4.0 18.1 1.0
N D:VAL65 4.1 23.3 1.0
CA D:PRO61 4.1 23.6 1.0
C D:GLY64 4.2 20.9 1.0
O D:HOH2031 4.2 25.9 1.0
CA D:VAL65 4.4 23.7 1.0
O D:GLY64 4.4 17.0 1.0
O D:ASN60 4.5 18.4 1.0
CE1 A:HIS141 4.5 17.7 1.0
N D:ILE63 4.5 22.9 1.0
CA A:VAL148 4.6 18.1 1.0
CG D:LEU67 4.7 24.3 1.0
CA D:ILE63 4.7 25.1 1.0
N A:VAL148 4.7 11.9 1.0
N D:GLY64 4.8 24.4 1.0
CA D:GLY64 4.8 16.5 1.0
CB D:VAL65 4.8 19.3 1.0
CD2 A:HIS141 4.9 18.1 1.0
OE2 A:GLU155 4.9 19.1 1.0
CA A:ALA147 4.9 18.0 1.0
N D:PRO66 4.9 22.4 1.0
CB A:ALA147 5.0 12.3 1.0
N D:ASP62 5.0 17.6 1.0

Potassium binding site 3 out of 7 in 5a8r

Go back to Potassium Binding Sites List in 5a8r
Potassium binding site 3 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K605

b:15.6
occ:1.00
 O D:CYS221 2.7 9.3 1.0
O A:CYS221 2.8 13.7 1.0
O D:ARG219 2.9 13.8 1.0
O A:ARG219 2.9 14.4 1.0
O D:VAL218 3.0 18.3 1.0
O A:VAL218 3.0 15.9 1.0
O A:HOH2058 3.5 22.1 1.0
C D:ARG219 3.5 11.4 1.0
C A:ARG219 3.6 18.0 1.0
C D:CYS221 3.8 14.5 1.0
CA D:ARG219 3.8 14.8 1.0
C A:CYS221 3.8 13.1 1.0
O A:HOH2119 3.8 20.4 1.0
CA A:ARG219 3.8 8.0 1.0
O A:HOH2057 4.0 13.7 1.0
O A:HOH2115 4.0 14.7 1.0
C D:VAL218 4.0 13.8 1.0
C A:VAL218 4.1 13.5 1.0
N D:CYS221 4.4 9.3 1.0
N D:ARG219 4.4 9.7 1.0
N A:CYS221 4.5 9.9 1.0
N A:ARG219 4.5 11.3 1.0
C D:THR220 4.6 14.5 1.0
N D:THR220 4.6 11.1 1.0
N D:ASP222 4.6 8.0 1.0
CA A:ASP222 4.6 15.8 1.0
N A:ASP222 4.6 11.9 1.0
CA D:ASP222 4.6 10.8 1.0
CA D:CYS221 4.6 9.9 1.0
C A:THR220 4.6 15.6 1.0
N A:THR220 4.7 8.1 1.0
CA A:CYS221 4.7 12.4 1.0
NZ A:LYS105 4.8 37.7 1.0
O D:THR220 4.8 15.3 1.0
O A:THR220 4.9 18.4 1.0
NZ D:LYS105 4.9 37.5 1.0

Potassium binding site 4 out of 7 in 5a8r

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Potassium binding site 4 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:30.0
occ:1.00
 O G:ILE63 2.7 29.3 1.0
O G:VAL65 2.7 33.5 1.0
O J:HOH2056 2.8 26.7 1.0
O J:ALA147 2.9 18.6 1.0
O G:PRO61 3.2 31.9 1.0
O G:HOH2025 3.6 32.5 1.0
C G:VAL65 3.8 29.5 1.0
C G:ILE63 3.9 35.5 1.0
CG1 G:VAL65 3.9 19.4 1.0
C G:PRO61 3.9 34.9 1.0
NE2 J:HIS141 4.0 25.1 1.0
N G:VAL65 4.0 28.4 1.0
C J:ALA147 4.1 22.6 1.0
CA G:PRO61 4.2 31.1 1.0
C G:GLY64 4.2 29.5 1.0
O G:HOH2024 4.3 32.1 1.0
CA G:VAL65 4.4 25.6 1.0
O G:GLY64 4.5 25.5 1.0
CE1 J:HIS141 4.5 26.2 1.0
O G:ASN60 4.5 26.2 1.0
N G:ILE63 4.5 27.9 1.0
CA J:VAL148 4.7 28.1 1.0
CG G:LEU67 4.7 27.5 1.0
O G:HOH2021 4.7 38.0 1.0
CA G:GLY64 4.7 30.3 1.0
N G:GLY64 4.7 33.3 1.0
CA G:ILE63 4.7 26.9 1.0
N J:VAL148 4.8 19.2 1.0
CB G:VAL65 4.8 25.4 1.0
OE2 J:GLU155 4.9 19.6 1.0
N G:PRO66 4.9 28.7 1.0
CD2 J:HIS141 4.9 25.2 1.0
N G:ASP62 4.9 30.8 1.0
N G:LEU67 5.0 23.1 1.0
CA J:ALA147 5.0 23.7 1.0

Potassium binding site 5 out of 7 in 5a8r

Go back to Potassium Binding Sites List in 5a8r
Potassium binding site 5 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K604

b:19.9
occ:1.00
 O J:CYS221 2.8 19.3 1.0
O G:CYS221 2.8 16.9 1.0
O J:ARG219 2.9 17.6 1.0
O J:VAL218 2.9 16.7 1.0
O G:ARG219 3.0 14.9 1.0
O G:VAL218 3.0 13.7 1.0
O G:HOH2109 3.5 20.0 1.0
C J:ARG219 3.5 14.2 1.0
O G:HOH2045 3.6 18.1 1.0
C G:ARG219 3.6 11.2 1.0
CA J:ARG219 3.8 11.6 1.0
C J:CYS221 3.8 17.9 1.0
C G:CYS221 3.9 15.3 1.0
CA G:ARG219 3.9 14.8 1.0
C J:VAL218 4.0 24.5 1.0
O G:HOH2105 4.0 14.1 1.0
O G:HOH2044 4.1 18.8 1.0
C G:VAL218 4.1 16.1 1.0
N J:CYS221 4.4 13.1 1.0
N J:ARG219 4.4 14.6 1.0
N G:CYS221 4.5 13.9 1.0
N G:ARG219 4.5 12.2 1.0
N J:THR220 4.6 11.4 1.0
C J:THR220 4.6 21.2 1.0
CA J:ASP222 4.6 10.4 1.0
N J:ASP222 4.6 13.3 1.0
C G:THR220 4.6 18.5 1.0
N G:THR220 4.7 12.0 1.0
CA G:ASP222 4.7 17.9 1.0
CA J:CYS221 4.7 15.3 1.0
N G:ASP222 4.7 12.9 1.0
CA G:CYS221 4.7 12.3 1.0
NZ G:LYS105 4.8 39.6 1.0
NZ J:LYS105 4.8 39.2 1.0
O J:THR220 4.9 15.3 1.0
O G:THR220 4.9 14.6 1.0

Potassium binding site 6 out of 7 in 5a8r

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Potassium binding site 6 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K605

b:26.8
occ:1.00
 O J:ILE63 2.6 23.4 1.0
O J:VAL65 2.7 18.8 1.0
O G:HOH2074 2.7 28.5 1.0
O G:ALA147 2.9 13.1 1.0
O J:PRO61 3.2 18.9 1.0
O J:HOH2028 3.7 34.8 1.0
C J:ILE63 3.8 23.1 1.0
C J:VAL65 3.8 28.2 1.0
C J:PRO61 3.9 21.9 1.0
CG1 J:VAL65 3.9 16.9 1.0
NE2 G:HIS141 4.0 22.1 1.0
N J:VAL65 4.0 19.9 1.0
C G:ALA147 4.0 20.4 1.0
O J:HOH2029 4.1 37.8 1.0
CA J:PRO61 4.2 25.2 1.0
C J:GLY64 4.2 27.1 1.0
CA J:VAL65 4.4 22.9 1.0
O J:ASN60 4.5 25.6 1.0
CE1 G:HIS141 4.5 27.0 1.0
N J:ILE63 4.5 24.4 1.0
O J:GLY64 4.5 20.1 1.0
CA G:VAL148 4.6 18.4 1.0
CA J:GLY64 4.7 21.5 1.0
N J:GLY64 4.7 23.7 1.0
CA J:ILE63 4.7 22.9 1.0
N G:VAL148 4.7 16.8 1.0
CG J:LEU67 4.8 22.2 1.0
CB J:VAL65 4.8 22.7 1.0
CD2 G:HIS141 4.9 21.3 1.0
N J:ASP62 4.9 16.7 1.0
OE2 G:GLU155 4.9 24.6 1.0
CA G:ALA147 4.9 15.0 1.0
N J:PRO66 5.0 29.1 1.0
O G:HOH2073 5.0 31.4 1.0

Potassium binding site 7 out of 7 in 5a8r

Go back to Potassium Binding Sites List in 5a8r
Potassium binding site 7 out of 7 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K606

b:25.6
occ:1.00
 O J:ASN188 2.8 31.8 1.0
O J:PHE191 2.9 21.7 1.0
O J:HOH2078 2.9 28.0 1.0
O J:HOH2075 2.9 37.8 1.0
O J:LYS189 2.9 25.5 1.0
C J:LYS189 3.4 26.4 1.0
O J:HOH2074 3.5 29.9 1.0
C J:PHE191 3.7 22.0 1.0
CA J:LYS189 3.8 24.3 1.0
C J:ASN188 3.9 18.6 1.0
O J:HOH2077 4.0 4.0 1.0
N J:PHE191 4.1 18.6 1.0
N J:LYS189 4.3 23.5 1.0
N J:GLU190 4.3 16.8 1.0
N J:PRO192 4.4 20.4 1.0
C J:GLU190 4.5 23.5 1.0
CA J:PHE191 4.5 16.9 1.0
CA J:PRO192 4.6 14.9 1.0
CA J:GLU190 4.9 17.1 1.0

Reference:

T.Wagner, J.Kahnt, U.Ermler, S.Shima. Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. V. 55 10630 2016.
ISSN: ISSN 1433-7851
PubMed: 27467699
DOI: 10.1002/ANIE.201603882
Page generated: Mon Aug 12 12:52:35 2024

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