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Calcium 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
Potassium (K) 5 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium 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 Calcium atom.
In total 12 binding sites of Calcium where determined in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution, PDB code: 5a8k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5a8k

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Calcium binding site 1 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca562

b:23.6
occ:1.00
 O A:HOH2304 2.3 31.3 1.0
O A:HOH2306 2.3 30.8 1.0
OE2 A:GLU190 2.4 22.7 1.0
OE2 A:GLU194 2.5 21.0 1.0
O A:HOH2293 2.5 24.7 1.0
O A:HOH2294 2.5 15.9 1.0
OE1 A:GLU190 2.5 23.3 1.0
CD A:GLU190 2.8 21.8 1.0
CD A:GLU194 3.5 20.4 1.0
CG A:GLU194 4.0 17.9 1.0
NZ A:LYS197 4.2 15.3 1.0
CG A:GLU190 4.3 19.3 1.0
OD1 A:ASN185 4.4 15.0 1.0
O A:HOH2305 4.5 29.2 1.0
OE1 A:GLU194 4.6 21.7 1.0
O A:HOH2307 4.8 33.9 1.0

Calcium binding site 2 out of 12 in 5a8k

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Calcium binding site 2 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca563

b:8.4
occ:1.00
 O A:ILE60 2.3 9.7 1.0
O A:HOH2130 2.4 7.9 1.0
O A:THR62 2.4 9.4 1.0
O A:PRO58 2.4 9.6 1.0
O A:HOH2137 2.4 10.0 1.0
O A:HOH2144 2.4 9.0 1.0
O A:HOH2139 2.5 8.9 1.0
C A:THR62 3.4 9.3 1.0
C A:PRO58 3.5 8.2 1.0
C A:ILE60 3.5 9.0 1.0
C A:GLY61 4.0 9.8 1.0
N A:THR62 4.0 8.9 1.0
N A:ILE60 4.0 8.8 1.0
O A:HOH2138 4.1 11.6 1.0
O A:GLY61 4.1 9.8 1.0
CA A:PRO63 4.2 10.1 1.0
CA A:PRO58 4.2 8.5 1.0
O A:HOH2129 4.2 13.6 1.0
O A:HOH2127 4.2 9.3 1.0
N A:PRO63 4.2 9.8 1.0
C A:ASP59 4.3 10.2 1.0
CA A:THR62 4.3 8.4 1.0
CA A:ILE60 4.4 8.6 1.0
N A:ASP59 4.4 9.1 1.0
N A:GLY61 4.4 9.1 1.0
CA A:GLY61 4.5 10.1 1.0
N A:LEU64 4.6 9.2 1.0
O A:HOH2146 4.6 8.2 1.0
CA A:ASP59 4.6 10.8 1.0
O D:ALA144 4.7 7.4 1.0
O A:ASN57 4.7 7.8 1.0
O A:HOH2067 4.8 16.5 1.0
O A:ASP59 4.8 12.6 1.0
C A:PRO63 4.9 9.2 1.0

Calcium binding site 3 out of 12 in 5a8k

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Calcium binding site 3 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca564

b:25.0
occ:1.00
 O A:LYS11 2.3 20.4 1.0
O A:PHE14 2.3 18.8 1.0
O A:HOH2036 2.4 26.9 1.0
O A:HOH2026 2.4 41.4 1.0
O A:HOH2024 2.4 22.4 1.0
O A:HOH2025 2.4 30.3 1.0
O A:HOH2027 2.5 37.3 1.0
C A:LYS11 3.4 19.1 1.0
C A:PHE14 3.5 19.3 1.0
CA A:LYS11 4.1 18.1 1.0
CA A:GLU15 4.1 20.8 1.0
O A:GLU15 4.1 17.5 1.0
N A:GLU15 4.2 20.5 1.0
C A:GLU15 4.3 17.6 1.0
O A:HOH2015 4.5 29.4 1.0
N A:PHE14 4.5 18.1 1.0
N A:LYS12 4.5 19.4 1.0
CA A:PHE14 4.6 19.2 1.0
CB A:LYS11 4.6 20.3 1.0
O A:HOH2040 4.8 42.5 1.0
CA A:LYS12 4.8 21.4 1.0
C A:LYS12 4.8 20.6 1.0
O A:GLU16 4.8 16.9 1.0
O A:LYS12 4.9 21.6 1.0

Calcium binding site 4 out of 12 in 5a8k

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Calcium binding site 4 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca565

b:23.3
occ:1.00
 O A:HOH2267 2.4 26.9 1.0
O A:HOH2274 2.4 32.1 1.0
O A:HOH2276 2.4 22.6 1.0
OD1 A:ASP174 2.5 26.3 1.0
OD2 A:ASP174 2.5 25.1 1.0
O A:HOH2579 2.5 30.8 1.0
O A:HOH2278 2.6 34.2 1.0
CG A:ASP174 2.8 24.7 1.0
O A:HOH2275 4.1 24.8 1.0
ND2 A:ASN185 4.1 15.4 1.0
O A:HOH2288 4.1 31.5 1.0
CB A:ASP174 4.4 21.4 1.0
O A:ASP170 4.6 18.0 1.0
OD1 A:ASP170 4.9 18.0 1.0
OD1 A:ASP183 5.0 17.6 1.0

Calcium binding site 5 out of 12 in 5a8k

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Calcium binding site 5 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca444

b:42.6
occ:1.00
 O B:HOH2039 2.2 26.1 1.0
O B:HOH2445 2.3 44.9 1.0
O B:HOH2037 2.5 37.2 1.0
O B:HOH2444 2.6 44.2 1.0
OE2 B:GLU19 4.5 20.6 1.0
OE1 B:GLU434 4.6 24.1 1.0
OE2 B:GLU434 4.7 24.0 1.0
OE1 B:GLU19 4.8 19.2 1.0

Calcium binding site 6 out of 12 in 5a8k

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Calcium binding site 6 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca556

b:11.5
occ:1.00
 O D:LYS11 2.3 12.7 1.0
O D:HOH2035 2.4 20.2 1.0
O D:PHE14 2.4 11.5 1.0
O D:HOH2049 2.4 17.3 1.0
O D:HOH2036 2.4 12.1 1.0
O D:HOH2037 2.4 19.8 1.0
O D:HOH2038 2.5 16.1 1.0
C D:LYS11 3.4 12.7 1.0
C D:PHE14 3.6 13.1 1.0
CA D:LYS11 4.0 12.2 1.0
O D:GLU15 4.2 14.6 1.0
CA D:GLU15 4.3 15.1 1.0
N D:GLU15 4.4 13.7 1.0
C D:GLU15 4.4 13.4 1.0
N D:LYS12 4.5 13.0 1.0
N D:PHE14 4.5 13.5 1.0
CB D:LYS11 4.5 13.2 1.0
CA D:PHE14 4.6 13.6 0.6
CA D:PHE14 4.6 13.6 0.4
O D:HOH2055 4.7 33.5 1.0
CA D:LYS12 4.8 15.2 1.0
O D:HOH2027 4.8 41.2 1.0
C D:LYS12 4.8 14.7 1.0
O D:LYS12 4.8 15.5 1.0
O D:GLU16 4.9 11.2 1.0
O D:HOH2024 4.9 34.2 1.0

Calcium binding site 7 out of 12 in 5a8k

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Calcium binding site 7 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 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:Ca557

b:8.7
occ:1.00
 O D:ILE60 2.3 9.2 1.0
O D:PRO58 2.4 9.7 1.0
O D:THR62 2.4 8.9 1.0
O A:HOH2242 2.4 9.2 1.0
O A:HOH2239 2.4 8.4 1.0
O D:HOH2142 2.4 9.2 1.0
O D:HOH2140 2.5 11.4 1.0
C D:THR62 3.4 8.9 1.0
C D:PRO58 3.5 9.5 1.0
C D:ILE60 3.5 8.8 1.0
C D:GLY61 4.0 9.2 1.0
N D:THR62 4.0 8.8 1.0
N D:ILE60 4.1 9.9 1.0
O D:GLY61 4.1 10.6 1.0
O D:HOH2143 4.1 10.3 1.0
CA D:PRO63 4.2 8.9 1.0
O A:HOH2240 4.2 11.0 1.0
O D:HOH2134 4.2 13.2 1.0
CA D:PRO58 4.2 9.3 1.0
N D:PRO63 4.3 9.4 1.0
C D:ASP59 4.3 10.6 1.0
CA D:THR62 4.4 9.3 1.0
CA D:ILE60 4.4 9.4 1.0
N D:ASP59 4.4 9.6 1.0
N D:GLY61 4.4 8.6 1.0
CA D:GLY61 4.5 8.9 1.0
CA D:ASP59 4.6 10.4 1.0
N D:LEU64 4.6 8.9 1.0
O A:HOH2244 4.7 9.6 1.0
O D:ASN57 4.7 9.3 1.0
O A:ALA144 4.7 7.1 1.0
O D:HOH2141 4.7 12.9 1.0
O D:ASP59 4.9 12.8 1.0
C D:PRO63 5.0 10.1 1.0

Calcium binding site 8 out of 12 in 5a8k

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Calcium binding site 8 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 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:Ca558

b:25.6
occ:1.00
 O D:HOH2484 2.3 33.6 1.0
OD2 D:ASP170 2.4 16.6 1.0
O D:HOH2238 2.4 24.1 1.0
O D:HOH2233 2.4 20.9 1.0
O D:HOH2237 2.5 23.6 1.0
O D:HOH2235 2.6 19.5 1.0
O D:HOH2239 2.9 41.0 1.0
CG D:ASP170 3.5 14.6 1.0
CB D:ASP170 4.0 13.3 1.0
NZ D:LYS197 4.0 13.0 1.0
O D:HOH2241 4.4 30.8 1.0
O D:HOH2139 4.5 25.5 1.0
OD1 D:ASP170 4.5 15.4 1.0
OE2 D:GLU171 4.6 19.4 1.0
CE D:LYS197 4.7 12.6 1.0
O D:GLY168 4.7 14.3 1.0
OE1 D:GLU171 4.7 18.8 1.0
N D:ASP170 4.7 12.1 1.0
OE1 D:GLU194 4.9 15.4 1.0

Calcium binding site 9 out of 12 in 5a8k

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Calcium binding site 9 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 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:Ca559

b:30.7
occ:1.00
 O D:HOH2262 2.4 42.2 1.0
O D:HOH2236 2.4 30.2 1.0
O D:HOH2250 2.4 38.6 1.0
OD1 D:ASP174 2.5 28.2 1.0
O D:HOH2248 2.6 22.8 1.0
OD2 D:ASP174 2.6 27.3 1.0
CG D:ASP174 2.9 25.4 1.0
ND2 D:ASN185 4.2 13.2 1.0
O D:HOH2249 4.2 22.0 1.0
O D:HOH2244 4.4 32.4 1.0
CB D:ASP174 4.4 20.9 1.0
O D:HOH2258 4.5 26.6 1.0
O D:HOH2152 4.6 34.1 1.0
O D:ASP170 4.7 13.7 1.0

Calcium binding site 10 out of 12 in 5a8k

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Calcium binding site 10 out of 12 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 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:Ca560

b:16.7
occ:1.00
 O D:HOH2272 2.3 25.7 1.0
OE2 D:GLU194 2.3 14.5 1.0
O D:HOH2274 2.4 20.0 1.0
OE2 D:GLU190 2.5 18.1 1.0
OE1 D:GLU190 2.5 17.9 1.0
O D:HOH2261 2.5 20.0 1.0
O D:HOH2260 2.5 15.5 1.0
CD D:GLU190 2.8 17.0 1.0
CD D:GLU194 3.4 14.3 1.0
CG D:GLU194 4.0 12.5 1.0
NZ D:LYS197 4.2 13.0 1.0
CG D:GLU190 4.3 14.7 1.0
OD1 D:ASN185 4.4 13.9 1.0
OE1 D:GLU194 4.5 15.4 1.0
O D:HOH2271 4.5 17.7 1.0
O D:HOH2152 4.5 34.1 1.0
O D:HOH2239 4.5 41.0 1.0
O D:HOH2273 4.7 30.3 1.0
O D:GLU190 5.0 11.6 1.0
O D:HOH2238 5.0 24.1 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: Sat Dec 12 05:17:02 2020

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