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Potassium in PDB 5a8k: Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution, PDB code: 5a8k 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) 48.47 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.140, 150.540, 187.090, 90.00, 90.00, 90.00
R / Rfree (%) 11.4 / 14

Other elements in 5a8k:

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 1 atom
Calcium (Ca) 12 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution (pdb code 5a8k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution, PDB code: 5a8k:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 5a8k

Go back to Potassium Binding Sites List in 5a8k
Potassium binding site 1 out of 5 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 From Methanothermobacter Wolfeii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K561

b:11.3
occ:1.00
 O A:CYS218 2.7 6.5 1.0
O D:CYS218 2.7 6.3 1.0
O D:ARG216 2.8 6.7 1.0
O A:ARG216 2.8 6.6 1.0
O D:SER215 3.3 6.7 1.0
O A:SER215 3.3 7.4 1.0
NH1 A:ARG102 3.5 7.5 1.0
NH1 D:ARG102 3.5 7.9 1.0
C D:ARG216 3.6 5.8 1.0
C A:ARG216 3.6 6.9 1.0
O A:HOH2188 3.8 8.2 1.0
C A:CYS218 3.8 5.5 1.0
C D:CYS218 3.8 5.6 1.0
O A:HOH2324 3.8 9.7 1.0
CA D:ARG216 3.9 5.8 1.0
CA A:ARG216 3.9 6.1 1.0
CZ D:ARG102 4.0 8.0 1.0
NH2 D:ARG102 4.0 8.1 1.0
CZ A:ARG102 4.0 7.6 1.0
NH2 A:ARG102 4.1 7.4 1.0
C D:SER215 4.3 6.2 1.0
N A:CYS218 4.4 5.3 1.0
C A:SER215 4.4 7.1 1.0
N D:CYS218 4.4 5.7 1.0
C D:THR217 4.6 5.3 1.0
C A:THR217 4.6 5.4 1.0
CA A:ASP219 4.6 6.8 1.0
N A:ASP219 4.6 6.1 1.0
CA D:ASP219 4.6 6.1 1.0
N D:ARG216 4.6 5.5 1.0
N D:ASP219 4.6 5.5 1.0
N A:ARG216 4.6 6.5 1.0
N D:THR217 4.6 5.6 1.0
N A:THR217 4.7 5.5 1.0
CA D:CYS218 4.7 5.4 1.0
CA A:CYS218 4.7 5.6 1.0
O D:THR217 4.8 6.1 1.0
O A:THR217 4.8 6.2 1.0
NE A:ARG102 5.0 8.2 1.0
NE D:ARG102 5.0 8.1 1.0

Potassium binding site 2 out of 5 in 5a8k

Go back to Potassium Binding Sites List in 5a8k
Potassium binding site 2 out of 5 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 From Methanothermobacter Wolfeii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K566

b:18.6
occ:0.55
 O A:HOH2269 2.5 35.2 0.5
O A:HOH2265 2.5 33.2 1.0
OD2 A:ASP170 2.6 20.5 1.0
O A:HOH2312 2.6 25.9 0.7
O A:HOH2140 2.6 40.4 1.0
O A:HOH2268 2.6 32.5 0.6
O A:HOH2266 2.7 27.4 1.0
CG A:ASP170 3.6 18.6 1.0
CB A:ASP170 4.0 17.5 1.0
NZ A:LYS197 4.4 15.3 1.0
O A:GLY168 4.5 15.9 1.0
O A:HOH2136 4.6 31.1 1.0
N A:ASP170 4.6 16.4 1.0
OD1 A:ASP170 4.7 18.0 1.0
CE A:LYS197 4.9 15.3 1.0
CA A:ASP170 4.9 16.4 1.0

Potassium binding site 3 out of 5 in 5a8k

Go back to Potassium Binding Sites List in 5a8k
Potassium binding site 3 out of 5 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 From Methanothermobacter Wolfeii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K250

b:15.7
occ:1.00
 O C:HOH2093 2.4 15.5 1.0
O C:ALA78 2.4 13.1 1.0
O C:HOH2096 2.4 14.8 1.0
O C:HOH2140 2.5 27.6 1.0
OG C:SER51 2.5 16.3 1.0
O C:HOH2090 2.5 21.2 1.0
O C:HOH2097 2.5 20.9 1.0
CB C:SER51 3.6 16.1 1.0
C C:ALA78 3.6 11.9 1.0
CA C:SER51 4.4 15.3 1.0
O C:HOH2091 4.4 33.1 1.0
CB C:ALA78 4.5 12.6 1.0
CA C:ALA78 4.5 12.9 1.0
C C:GLY79 4.5 11.4 1.0
O C:HOH2170 4.5 26.5 1.0
N C:GLY79 4.5 10.5 1.0
CA C:GLY79 4.6 11.5 1.0
O C:HOH2035 4.6 29.4 1.0
O C:GLY79 4.6 11.8 1.0
O C:HOH2036 4.6 35.8 1.0
O C:TYR49 4.6 19.5 1.0
O C:PRO50 4.7 17.1 1.0
OD1 C:ASP80 4.7 14.4 1.0
O C:HIS53 4.7 13.2 1.0
CG C:PRO55 4.7 14.1 1.0
O C:HOH2058 4.8 33.0 1.0
N C:ASP80 4.8 10.7 1.0
CD C:PRO55 5.0 13.9 1.0

Potassium binding site 4 out of 5 in 5a8k

Go back to Potassium Binding Sites List in 5a8k
Potassium binding site 4 out of 5 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 From Methanothermobacter Wolfeii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K561

b:13.1
occ:0.58
 O D:VAL124 2.4 13.6 1.0
O D:HOH2187 2.5 26.0 1.0
O D:HOH2487 2.5 31.6 1.0
O D:HOH2199 2.5 23.6 1.0
O D:HOH2188 2.6 26.4 1.0
O1 D:ETX1552 2.7 31.2 1.0
C D:VAL124 3.6 12.6 1.0
C1 D:ETX1552 3.8 30.9 1.0
OE2 D:GLU117 3.9 29.0 1.0
O2 D:ETX1552 4.4 31.1 1.0
N D:VAL124 4.4 14.4 1.0
N D:THR125 4.5 11.2 1.0
CA D:THR125 4.5 11.8 1.0
CA D:VAL124 4.5 12.7 1.0
CG2 D:THR125 4.5 12.5 1.0
C2 D:ETX1552 4.8 30.1 1.0
CB D:VAL124 4.9 13.0 1.0

Potassium binding site 5 out of 5 in 5a8k

Go back to Potassium Binding Sites List in 5a8k
Potassium binding site 5 out of 5 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 From Methanothermobacter Wolfeii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K445

b:20.9
occ:1.00
 O E:LYS7 2.4 12.6 1.0
O E:HOH2012 2.4 20.4 1.0
O E:HOH2013 2.5 17.0 1.0
O E:HOH2282 2.6 31.9 1.0
C E:LYS7 3.6 10.3 1.0
O E:HOH2008 4.1 37.7 1.0
N E:LYS7 4.2 9.2 1.0
CA E:LYS7 4.4 10.4 1.0
OH E:TYR243 4.4 11.4 1.0
OD2 E:ASP249 4.5 11.0 1.0
N E:VAL8 4.6 9.0 1.0
O E:HOH2347 4.6 24.5 1.0
NE2 E:GLN21 4.6 22.2 1.0
CA E:VAL8 4.7 9.0 1.0
OE1 E:GLN21 4.7 23.2 1.0
CB E:LYS7 4.8 11.4 1.0
OD1 E:ASP249 4.9 10.6 1.0
O E:HOH2317 5.0 24.5 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 12:52:09 2024

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