Atomistry » Potassium » PDB 4zun-5avw » 5a8r
Atomistry »
  Potassium »
    PDB 4zun-5avw »
      5a8r »

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

Go back to Potassium Binding Sites List in 5a8r
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

Go back to Potassium Binding Sites List in 5a8r
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

Go back to Potassium Binding Sites List in 5a8r
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy