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Potassium in PDB 5yrt: Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal, PDB code: 5yrt was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.687, 95.459, 114.567, 80.78, 87.58, 81.10
R / Rfree (%) 15 / 18.7

Other elements in 5yrt:

The structure of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Calcium (Ca) 4 atoms
Chlorine (Cl) 12 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal (pdb code 5yrt). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal, PDB code: 5yrt:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5yrt

Go back to Potassium Binding Sites List in 5yrt
Potassium binding site 1 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:12.0
occ:1.00
OE1 A:GLU265 2.7 12.5 1.0
O A:GLY261 2.7 11.7 1.0
OE1 A:GLU280 2.7 11.1 1.0
O A:HOH777 2.9 10.9 1.0
O A:HOH737 2.9 11.8 1.0
OG A:SER264 3.1 10.5 1.0
OE2 A:GLU265 3.3 10.8 1.0
CD A:GLU265 3.4 12.3 1.0
C A:GLY261 3.4 8.1 1.0
SG A:CYS283 3.4 12.9 1.0
N A:GLY261 3.7 11.6 1.0
CD A:GLU280 4.0 10.9 1.0
CA A:GLU280 4.0 7.6 1.0
N A:SER262 4.1 8.1 1.0
CA A:GLY261 4.2 11.3 1.0
CA A:SER262 4.2 11.0 1.0
CB A:SER264 4.2 12.6 1.0
CB A:GLU280 4.2 9.7 1.0
N A:GLU280 4.4 7.5 1.0
CB A:CYS283 4.5 8.9 1.0
N A:SER264 4.5 8.4 1.0
O A:LEU279 4.6 11.8 1.0
CB A:SER260 4.6 15.6 1.0
N A:GLY263 4.6 10.1 1.0
C A:LEU279 4.6 11.5 1.0
C A:SER262 4.7 14.0 1.0
N A:GLY227 4.7 11.0 1.0
CG A:GLU280 4.7 12.5 1.0
C A:SER260 4.8 13.7 1.0
CG A:GLU265 4.8 11.1 1.0
OE2 A:GLU280 4.9 10.9 1.0
N1 A:5AD604 4.9 14.7 1.0
CA A:SER264 5.0 10.3 1.0

Potassium binding site 2 out of 8 in 5yrt

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Potassium binding site 2 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:14.4
occ:1.00
O A:LEU203 2.6 13.2 1.0
OE1 A:GLU208 2.6 12.2 1.0
O A:THR222 2.7 11.2 1.0
OE1 A:GLU205 2.8 14.4 1.0
OG1 A:THR222 2.9 13.3 1.0
N40 B:B121601 3.2 12.3 1.0
C A:THR222 3.5 9.2 1.0
CD A:GLU205 3.5 15.2 1.0
CD A:GLU208 3.8 15.3 1.0
OE2 A:GLU205 3.8 12.8 1.0
C A:LEU203 3.8 12.9 1.0
CB A:THR222 3.8 8.6 1.0
N A:LEU203 3.9 11.1 1.0
C38 B:B121601 4.1 12.9 1.0
CD1 A:ILE223 4.1 10.4 1.0
CA A:THR222 4.2 7.9 1.0
N A:ILE223 4.3 10.1 1.0
CB A:GLU208 4.5 11.0 1.0
O A:HOH743 4.5 13.0 1.0
O A:HOH715 4.5 11.6 1.0
CA A:LEU203 4.5 12.3 1.0
OE2 A:GLU208 4.5 13.0 1.0
CA A:GLU205 4.5 11.2 1.0
C37 B:B121601 4.6 10.4 1.0
CA A:ILE223 4.6 8.3 1.0
C A:GLU204 4.6 12.2 1.0
N A:GLU205 4.6 10.7 1.0
CG A:GLU205 4.6 12.6 1.0
OG A:SER202 4.6 9.6 0.5
N A:THR222 4.7 10.6 1.0
CG A:GLU208 4.7 10.9 1.0
O A:GLU204 4.8 14.5 1.0
C A:SER202 4.8 12.5 1.0
O2' A:5AD604 4.8 13.9 1.0
N A:GLU204 4.8 11.2 1.0
O39 B:B121601 4.8 15.2 1.0
CA A:SER202 4.9 8.7 0.5
CA A:SER202 4.9 11.0 0.5

Potassium binding site 3 out of 8 in 5yrt

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Potassium binding site 3 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:13.3
occ:1.00
OE2 D:GLU265 2.7 13.0 1.0
O D:GLY261 2.8 11.2 1.0
O D:HOH739 2.8 12.8 1.0
OE1 D:GLU280 2.8 13.8 1.0
O D:HOH858 2.9 11.6 1.0
OG D:SER264 3.1 13.9 1.0
OE1 D:GLU265 3.4 15.3 1.0
C D:GLY261 3.4 15.4 1.0
CD D:GLU265 3.4 18.4 1.0
SG D:CYS283 3.4 13.8 1.0
N D:GLY261 3.7 12.7 1.0
CD D:GLU280 4.0 18.5 1.0
CA D:GLU280 4.0 10.4 1.0
N D:SER262 4.1 10.1 1.0
CA D:GLY261 4.2 13.7 1.0
CA D:SER262 4.2 13.5 1.0
CB D:SER264 4.3 12.2 1.0
CB D:GLU280 4.3 9.1 1.0
N D:GLU280 4.3 11.8 1.0
O D:LEU279 4.5 14.9 1.0
CB D:CYS283 4.5 11.0 1.0
N D:SER264 4.5 12.4 1.0
C D:LEU279 4.6 14.0 1.0
N D:GLY227 4.6 14.3 1.0
N D:GLY263 4.6 10.3 1.0
CB D:SER260 4.6 13.8 1.0
C D:SER262 4.7 13.3 1.0
CG D:GLU280 4.7 16.9 1.0
C D:SER260 4.8 14.5 1.0
CG D:GLU265 4.9 15.1 1.0
OE2 D:GLU280 4.9 12.0 1.0
N1 D:5AD604 5.0 15.3 1.0
CA D:SER264 5.0 10.6 1.0

Potassium binding site 4 out of 8 in 5yrt

Go back to Potassium Binding Sites List in 5yrt
Potassium binding site 4 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:15.4
occ:1.00
OE1 D:GLU208 2.6 13.4 1.0
O D:LEU203 2.6 15.4 1.0
O D:THR222 2.7 12.6 1.0
OE1 D:GLU205 2.8 15.2 1.0
OG1 D:THR222 2.9 14.9 1.0
N40 E:B121601 3.2 12.9 1.0
CD D:GLU205 3.4 12.7 1.0
C D:THR222 3.5 14.9 1.0
OE2 D:GLU205 3.7 16.8 1.0
CD D:GLU208 3.7 14.7 1.0
C D:LEU203 3.8 15.1 1.0
CB D:THR222 3.9 14.1 1.0
N D:LEU203 3.9 11.0 1.0
CD1 D:ILE223 4.0 20.4 1.0
C38 E:B121601 4.1 14.6 1.0
CA D:THR222 4.2 12.1 1.0
N D:ILE223 4.3 13.2 1.0
O D:HOH704 4.4 11.4 1.0
OE2 D:GLU208 4.4 13.1 1.0
CB D:GLU208 4.5 16.1 1.0
CA D:GLU205 4.5 16.0 1.0
CA D:LEU203 4.5 13.2 1.0
C D:GLU204 4.5 16.6 1.0
O D:HOH752 4.6 18.0 1.0
N D:GLU205 4.6 14.1 1.0
C37 E:B121601 4.6 10.6 1.0
CG D:GLU205 4.6 14.0 1.0
CA D:ILE223 4.6 14.9 1.0
N D:THR222 4.7 12.4 1.0
OG D:SER202 4.7 13.8 0.6
CG D:GLU208 4.7 14.7 1.0
O D:GLU204 4.7 16.6 1.0
O2' D:5AD604 4.8 15.1 1.0
N D:GLU204 4.8 12.6 1.0
C D:SER202 4.8 14.1 1.0
O39 E:B121601 4.9 17.7 1.0
CA D:SER202 4.9 13.9 0.4
CA D:SER202 4.9 14.6 0.6
CA D:GLU204 5.0 16.4 1.0

Potassium binding site 5 out of 8 in 5yrt

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Potassium binding site 5 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K602

b:11.7
occ:1.00
OE2 G:GLU265 2.7 10.8 1.0
O G:GLY261 2.7 9.4 1.0
OE1 G:GLU280 2.8 12.8 1.0
O G:HOH843 2.9 12.6 1.0
O G:HOH803 2.9 12.2 1.0
OG G:SER264 3.2 11.8 1.0
OE1 G:GLU265 3.4 9.8 1.0
CD G:GLU265 3.4 10.2 1.0
C G:GLY261 3.4 11.0 1.0
SG G:CYS283 3.5 13.6 1.0
N G:GLY261 3.7 11.4 1.0
CD G:GLU280 4.0 12.2 1.0
CA G:GLU280 4.0 10.1 1.0
N G:SER262 4.1 10.8 1.0
CA G:GLY261 4.2 12.1 1.0
CA G:SER262 4.3 13.0 1.0
CB G:SER264 4.3 8.6 1.0
CB G:GLU280 4.3 10.2 1.0
N G:GLU280 4.4 10.4 1.0
N G:SER264 4.5 10.4 1.0
CB G:CYS283 4.5 10.5 1.0
O G:LEU279 4.5 9.6 1.0
C G:LEU279 4.6 10.0 1.0
N G:GLY227 4.6 12.2 1.0
CB G:SER260 4.6 10.6 1.0
N G:GLY263 4.7 11.9 1.0
C G:SER262 4.7 12.2 1.0
CG G:GLU280 4.7 11.6 1.0
C G:SER260 4.8 13.7 1.0
CG G:GLU265 4.8 11.4 1.0
N1 G:5AD604 4.9 14.5 1.0
OE2 G:GLU280 4.9 13.2 1.0
CA G:SER264 5.0 8.7 1.0

Potassium binding site 6 out of 8 in 5yrt

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Potassium binding site 6 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K603

b:13.4
occ:1.00
O G:LEU203 2.6 9.0 1.0
OE1 G:GLU208 2.6 13.3 1.0
O G:THR222 2.7 11.3 1.0
OE1 G:GLU205 2.8 13.2 1.0
OG1 G:THR222 2.9 14.2 1.0
N40 H:B121601 3.2 12.4 1.0
CD G:GLU205 3.4 12.4 1.0
C G:THR222 3.5 12.6 1.0
OE2 G:GLU205 3.7 11.9 1.0
CD G:GLU208 3.8 9.6 1.0
C G:LEU203 3.8 9.4 1.0
CB G:THR222 3.9 13.4 1.0
N G:LEU203 3.9 10.7 1.0
CD1 G:ILE223 4.0 13.3 1.0
C38 H:B121601 4.0 13.1 1.0
CA G:THR222 4.2 12.3 1.0
N G:ILE223 4.3 9.6 1.0
OE2 G:GLU208 4.5 14.9 1.0
O G:HOH719 4.5 13.2 1.0
O G:HOH795 4.5 11.9 1.0
CA G:GLU205 4.5 11.4 1.0
CB G:GLU208 4.5 10.9 1.0
CA G:LEU203 4.5 11.3 1.0
CA G:ILE223 4.6 8.3 1.0
CG G:GLU205 4.6 12.2 1.0
C G:GLU204 4.6 11.8 1.0
N G:GLU205 4.6 9.8 1.0
C37 H:B121601 4.6 12.9 1.0
OG G:SER202 4.7 13.8 0.6
CG G:GLU208 4.7 11.7 1.0
N G:THR222 4.7 10.1 1.0
O39 H:B121601 4.8 13.2 1.0
O G:GLU204 4.8 14.1 1.0
C G:SER202 4.8 14.0 1.0
O2' G:5AD604 4.8 15.2 1.0
N G:GLU204 4.8 10.2 1.0
CA G:SER202 4.9 12.1 0.4
CA G:SER202 4.9 12.0 0.6

Potassium binding site 7 out of 8 in 5yrt

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Potassium binding site 7 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K602

b:12.5
occ:1.00
O J:GLY261 2.7 10.3 1.0
OE2 J:GLU265 2.7 11.9 1.0
OE1 J:GLU280 2.8 12.7 1.0
O J:HOH772 2.8 12.0 1.0
O J:HOH750 2.9 13.4 1.0
OG J:SER264 3.1 11.2 1.0
OE1 J:GLU265 3.3 9.5 1.0
C J:GLY261 3.4 12.1 1.0
CD J:GLU265 3.4 12.6 1.0
SG J:CYS283 3.5 11.6 1.0
N J:GLY261 3.7 11.0 1.0
CD J:GLU280 4.0 13.2 1.0
CA J:GLU280 4.0 10.1 1.0
N J:SER262 4.1 11.3 1.0
CA J:GLY261 4.2 10.0 1.0
CB J:GLU280 4.2 10.1 1.0
CA J:SER262 4.2 9.7 1.0
CB J:SER264 4.3 9.4 1.0
N J:GLU280 4.3 9.1 1.0
N J:SER264 4.5 9.2 1.0
CB J:CYS283 4.5 7.6 1.0
O J:LEU279 4.6 9.3 1.0
CB J:SER260 4.6 10.4 1.0
C J:LEU279 4.6 10.8 1.0
N J:GLY263 4.6 11.1 1.0
N J:GLY227 4.7 11.5 1.0
C J:SER262 4.7 8.8 1.0
CG J:GLU280 4.7 9.4 1.0
C J:SER260 4.8 11.1 1.0
CG J:GLU265 4.8 8.5 1.0
OE2 J:GLU280 4.9 12.1 1.0
CA J:SER264 5.0 8.3 1.0
N1 J:5AD604 5.0 13.6 1.0

Potassium binding site 8 out of 8 in 5yrt

Go back to Potassium Binding Sites List in 5yrt
Potassium binding site 8 out of 8 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K603

b:12.7
occ:1.00
O J:LEU203 2.6 9.6 1.0
OE1 J:GLU208 2.6 10.0 1.0
O J:THR222 2.7 11.6 1.0
OE1 J:GLU205 2.8 13.6 1.0
OG1 J:THR222 2.8 11.7 1.0
N40 K:B121601 3.1 11.0 1.0
CD J:GLU205 3.4 13.3 1.0
C J:THR222 3.5 11.7 1.0
OE2 J:GLU205 3.6 12.6 1.0
CD J:GLU208 3.8 11.2 1.0
C J:LEU203 3.8 14.1 1.0
CB J:THR222 3.9 10.4 1.0
N J:LEU203 4.0 8.4 1.0
C38 K:B121601 4.0 10.8 1.0
CD1 J:ILE223 4.1 12.4 1.0
CA J:THR222 4.2 7.9 1.0
N J:ILE223 4.3 8.4 1.0
O J:HOH730 4.5 12.3 1.0
OE2 J:GLU208 4.5 15.4 1.0
CB J:GLU208 4.5 8.9 1.0
C37 K:B121601 4.5 8.1 1.0
CG J:GLU205 4.5 12.3 1.0
O J:HOH711 4.5 12.0 1.0
CA J:GLU205 4.5 10.8 1.0
CA J:LEU203 4.5 12.0 1.0
C J:GLU204 4.6 16.1 1.0
CA J:ILE223 4.6 8.0 1.0
OG J:SER202 4.6 9.1 0.6
N J:GLU205 4.7 10.7 1.0
CG J:GLU208 4.7 11.2 1.0
N J:THR222 4.7 12.2 1.0
O J:GLU204 4.8 14.1 1.0
O39 K:B121601 4.8 12.7 1.0
N J:GLU204 4.8 10.2 1.0
C J:SER202 4.8 12.9 1.0
O2' J:5AD604 4.9 12.4 1.0
CA J:SER202 4.9 10.0 0.4
CA J:SER202 4.9 10.0 0.6

Reference:

N.Shibata, Y.Sueyoshi, Y.Higuchi, T.Toraya. Direct Participation of A Peripheral Side Chain of A Corrin Ring in Coenzyme B12CATALYSIS. Angew. Chem. Int. Ed. Engl. V. 57 7830 2018.
ISSN: ESSN 1521-3773
PubMed: 29797764
DOI: 10.1002/ANIE.201803591
Page generated: Mon Dec 14 00:14:49 2020

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