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Potassium in PDB 5yrv: Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal, PDB code: 5yrv was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.777, 95.666, 114.514, 80.61, 87.77, 81.25
R / Rfree (%) 15.5 / 18.1

Other elements in 5yrv:

The structure of Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal (pdb code 5yrv). 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/1,2-Propanediol, Anaerobically-Prepared Crystal, PDB code: 5yrv:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 1 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:15.0
occ:1.00
 OE1 A:GLU265 2.7 13.8 1.0
O A:GLY261 2.7 14.4 1.0
OE1 A:GLU280 2.8 14.6 1.0
O A:HOH827 2.8 14.3 1.0
O A:HOH761 2.9 14.5 1.0
OG A:SER264 3.1 15.7 1.0
OE2 A:GLU265 3.4 13.8 1.0
C A:GLY261 3.4 11.9 1.0
CD A:GLU265 3.4 16.1 1.0
SG A:CYS283 3.4 14.9 1.0
N A:GLY261 3.7 16.1 1.0
CA A:GLU280 4.0 11.2 1.0
CD A:GLU280 4.0 15.0 1.0
N A:SER262 4.1 12.7 1.0
CA A:GLY261 4.2 12.1 1.0
CA A:SER262 4.2 11.9 1.0
CB A:GLU280 4.2 13.2 1.0
CB A:SER264 4.3 15.1 1.0
N A:GLU280 4.3 13.4 1.0
N A:SER264 4.5 12.3 1.0
CB A:CYS283 4.5 13.6 1.0
O A:LEU279 4.6 15.0 1.0
C A:LEU279 4.6 15.6 1.0
N A:GLY263 4.6 13.5 1.0
CB A:SER260 4.6 16.1 1.0
C A:SER262 4.6 15.2 1.0
N A:GLY227 4.7 17.1 1.0
CG A:GLU280 4.7 14.2 1.0
C A:SER260 4.8 16.4 1.0
CG A:GLU265 4.8 15.3 1.0
OE2 A:GLU280 4.9 14.5 1.0
N1 A:5AD605 4.9 16.2 1.0
CA A:SER264 5.0 12.9 1.0

Potassium binding site 2 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 2 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:17.4
occ:1.00
 OE1 A:GLU208 2.6 17.2 1.0
O A:LEU203 2.6 19.3 1.0
O A:THR222 2.7 15.1 1.0
OE1 A:GLU205 2.8 16.9 1.0
OG1 A:THR222 2.8 15.8 1.0
N40 B:B121601 3.2 16.2 1.0
CD A:GLU205 3.5 19.0 1.0
C A:THR222 3.5 16.9 1.0
CD A:GLU208 3.7 18.3 1.0
OE2 A:GLU205 3.8 15.7 1.0
C A:LEU203 3.8 19.4 1.0
CB A:THR222 3.9 13.6 1.0
N A:LEU203 3.9 18.5 1.0
CD1 A:ILE223 4.0 17.5 1.0
C38 B:B121601 4.1 15.9 1.0
CA A:THR222 4.2 12.8 1.0
N A:ILE223 4.3 15.2 1.0
OE2 A:GLU208 4.4 18.2 1.0
O A:HOH724 4.4 17.7 1.0
CB A:GLU208 4.5 18.1 1.0
O A:HOH834 4.5 16.1 1.0
CA A:LEU203 4.5 19.8 1.0
CA A:GLU205 4.5 16.5 1.0
CA A:ILE223 4.6 13.4 1.0
CG A:GLU205 4.6 18.8 1.0
C A:GLU204 4.6 14.3 1.0
N A:GLU205 4.6 15.0 1.0
C37 B:B121601 4.6 15.6 1.0
OG A:SER202 4.7 16.7 0.6
CG A:GLU208 4.7 16.5 1.0
N A:THR222 4.7 14.0 1.0
O A:GLU204 4.7 18.3 1.0
C A:SER202 4.8 20.4 1.0
O2' A:5AD605 4.8 17.6 1.0
CA A:SER202 4.8 15.7 0.4
CA A:SER202 4.9 15.2 0.6
N A:GLU204 4.9 18.7 1.0
O39 B:B121601 4.9 18.0 1.0

Potassium binding site 3 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 3 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:18.4
occ:1.00
 O D:GLY261 2.7 18.1 1.0
OE1 D:GLU280 2.8 18.7 1.0
OE2 D:GLU265 2.8 17.0 1.0
O D:HOH799 2.8 17.7 1.0
O D:HOH844 2.9 15.8 1.0
OG D:SER264 3.2 20.4 1.0
C D:GLY261 3.3 19.7 1.0
OE1 D:GLU265 3.4 18.4 1.0
SG D:CYS283 3.5 19.1 1.0
CD D:GLU265 3.5 21.4 1.0
N D:GLY261 3.7 18.7 1.0
CD D:GLU280 4.0 16.5 1.0
CA D:GLU280 4.0 15.1 1.0
N D:SER262 4.0 16.5 1.0
CA D:GLY261 4.1 19.1 1.0
CA D:SER262 4.2 15.9 1.0
CB D:GLU280 4.2 14.3 1.0
CB D:SER264 4.3 19.7 1.0
N D:GLU280 4.3 16.9 1.0
N D:SER264 4.5 17.7 1.0
CB D:CYS283 4.5 18.9 1.0
O D:LEU279 4.5 19.5 1.0
C D:LEU279 4.6 18.5 1.0
N D:GLY263 4.6 16.6 1.0
C D:SER262 4.6 16.7 1.0
N D:GLY227 4.6 17.9 1.0
CB D:SER260 4.7 18.5 1.0
CG D:GLU280 4.7 13.3 1.0
C D:SER260 4.7 18.2 1.0
CG D:GLU265 4.9 20.4 1.0
OE2 D:GLU280 4.9 18.9 1.0
N1 D:5AD605 4.9 18.2 1.0
CA D:SER264 5.0 17.5 1.0

Potassium binding site 4 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 4 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:19.9
occ:1.00
 OE1 D:GLU208 2.6 20.4 1.0
O D:LEU203 2.6 19.3 1.0
O D:THR222 2.7 19.2 1.0
OE1 D:GLU205 2.8 20.3 1.0
OG1 D:THR222 2.9 19.7 1.0
N40 E:B121601 3.2 19.8 1.0
CD D:GLU205 3.4 21.3 1.0
C D:THR222 3.5 20.9 1.0
OE2 D:GLU205 3.7 21.4 1.0
CD D:GLU208 3.7 19.4 1.0
C D:LEU203 3.8 21.9 1.0
CB D:THR222 3.9 22.2 1.0
N D:LEU203 4.0 16.2 1.0
CD1 D:ILE223 4.1 24.0 1.0
C38 E:B121601 4.1 19.0 1.0
CA D:THR222 4.2 19.1 1.0
N D:ILE223 4.4 17.0 1.0
O D:HOH713 4.4 19.2 1.0
OE2 D:GLU208 4.4 20.3 1.0
CB D:GLU208 4.4 20.8 1.0
CA D:GLU205 4.5 23.9 1.0
CG D:GLU205 4.5 21.8 1.0
O D:HOH714 4.5 22.6 1.0
CA D:LEU203 4.5 19.9 1.0
C D:GLU204 4.6 24.9 1.0
N D:GLU205 4.6 21.5 1.0
C37 E:B121601 4.6 19.2 1.0
CA D:ILE223 4.6 18.1 1.0
CG D:GLU208 4.7 19.5 1.0
N D:THR222 4.7 17.5 1.0
OG D:SER202 4.7 17.1 0.5
O D:GLU204 4.7 23.9 1.0
O2' D:5AD605 4.8 19.3 1.0
C D:SER202 4.8 18.1 1.0
N D:GLU204 4.8 18.9 1.0
CA D:SER202 4.9 16.0 0.5
CA D:SER202 4.9 15.9 0.5
O39 E:B121601 4.9 20.8 1.0

Potassium binding site 5 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 5 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K602

b:18.4
occ:1.00
 OE2 G:GLU265 2.7 18.4 1.0
O G:GLY261 2.7 18.0 1.0
OE1 G:GLU280 2.8 17.5 1.0
O G:HOH870 2.8 18.0 1.0
O G:HOH802 2.8 18.2 1.0
OG G:SER264 3.2 18.4 1.0
C G:GLY261 3.4 16.6 1.0
OE1 G:GLU265 3.4 19.6 1.0
CD G:GLU265 3.4 18.0 1.0
SG G:CYS283 3.5 19.1 1.0
N G:GLY261 3.7 18.4 1.0
CD G:GLU280 4.0 17.3 1.0
CA G:GLU280 4.0 16.1 1.0
N G:SER262 4.1 17.5 1.0
CA G:GLY261 4.1 17.5 1.0
CA G:SER262 4.2 19.1 1.0
CB G:GLU280 4.2 16.0 1.0
CB G:SER264 4.3 17.5 1.0
N G:GLU280 4.3 18.8 1.0
CB G:CYS283 4.5 16.5 1.0
O G:LEU279 4.5 17.6 1.0
N G:SER264 4.5 15.0 1.0
CB G:SER260 4.6 19.9 1.0
C G:LEU279 4.6 18.3 1.0
N G:GLY263 4.6 19.3 1.0
N G:GLY227 4.7 20.3 1.0
CG G:GLU280 4.7 17.3 1.0
C G:SER262 4.7 17.5 1.0
C G:SER260 4.8 19.0 1.0
CG G:GLU265 4.9 19.7 1.0
OE2 G:GLU280 4.9 18.3 1.0
N1 G:5AD605 4.9 20.4 1.0

Potassium binding site 6 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 6 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K603

b:18.6
occ:1.00
 OE1 G:GLU208 2.6 18.2 1.0
O G:LEU203 2.6 19.0 1.0
O G:THR222 2.7 18.8 1.0
OE1 G:GLU205 2.8 20.8 1.0
OG1 G:THR222 2.9 19.8 1.0
N40 H:B121601 3.2 17.3 1.0
CD G:GLU205 3.4 16.7 1.0
C G:THR222 3.5 20.0 1.0
OE2 G:GLU205 3.7 17.4 1.0
CD G:GLU208 3.7 17.9 1.0
C G:LEU203 3.8 18.9 1.0
CB G:THR222 3.9 17.2 1.0
N G:LEU203 3.9 18.0 1.0
CD1 G:ILE223 4.0 20.7 1.0
C38 H:B121601 4.1 18.1 1.0
CA G:THR222 4.2 18.3 1.0
N G:ILE223 4.3 17.0 1.0
OE2 G:GLU208 4.4 20.1 1.0
O G:HOH712 4.4 17.2 1.0
CB G:GLU208 4.5 17.1 1.0
O G:HOH789 4.5 17.6 1.0
CA G:LEU203 4.5 19.1 1.0
CA G:GLU205 4.5 18.1 1.0
CG G:GLU205 4.6 17.7 1.0
OG G:SER202 4.6 17.6 0.5
C37 H:B121601 4.6 16.6 1.0
CA G:ILE223 4.6 18.1 1.0
C G:GLU204 4.6 17.1 1.0
CG G:GLU208 4.7 17.1 1.0
N G:GLU205 4.7 16.9 1.0
N G:THR222 4.7 18.2 1.0
O G:GLU204 4.8 18.9 1.0
O2' G:5AD605 4.8 17.7 1.0
C G:SER202 4.8 20.3 1.0
N G:GLU204 4.9 16.6 1.0
CA G:SER202 4.9 19.1 0.5
CA G:SER202 4.9 19.0 0.5
O39 H:B121601 4.9 21.9 1.0

Potassium binding site 7 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 7 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K602

b:17.1
occ:1.00
 OE2 J:GLU265 2.7 18.9 1.0
OE1 J:GLU280 2.7 17.3 1.0
O J:GLY261 2.7 16.5 1.0
O J:HOH764 2.8 17.6 1.0
O J:HOH743 2.8 16.8 1.0
OG J:SER264 3.1 16.7 1.0
C J:GLY261 3.4 12.0 1.0
OE1 J:GLU265 3.4 15.8 1.0
CD J:GLU265 3.4 15.9 1.0
SG J:CYS283 3.4 17.0 1.0
N J:GLY261 3.7 14.0 1.0
CD J:GLU280 3.9 16.6 1.0
CA J:GLU280 4.0 15.8 1.0
N J:SER262 4.1 15.9 1.0
CA J:GLY261 4.1 11.3 1.0
CB J:GLU280 4.1 14.6 1.0
CA J:SER262 4.3 17.0 1.0
CB J:SER264 4.3 17.0 1.0
N J:GLU280 4.3 15.1 1.0
CB J:CYS283 4.5 17.0 1.0
N J:SER264 4.5 17.4 1.0
CB J:SER260 4.6 19.4 1.0
O J:LEU279 4.6 14.4 1.0
CG J:GLU280 4.6 13.3 1.0
N J:GLY263 4.6 16.1 1.0
C J:LEU279 4.6 16.4 1.0
C J:SER262 4.7 14.8 1.0
N J:GLY227 4.7 16.1 1.0
C J:SER260 4.8 15.7 1.0
CG J:GLU265 4.8 19.0 1.0
OE2 J:GLU280 4.9 18.6 1.0
N1 J:5AD604 4.9 18.0 1.0
CA J:SER264 5.0 15.0 1.0

Potassium binding site 8 out of 8 in 5yrv

Go back to Potassium Binding Sites List in 5yrv
Potassium binding site 8 out of 8 in the Diol Dehydratase, Adocbl/1,2-Propanediol, 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/1,2-Propanediol, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K603

b:17.8
occ:1.00
 O J:LEU203 2.6 17.9 1.0
OE1 J:GLU208 2.6 16.5 1.0
O J:THR222 2.8 17.7 1.0
OE1 J:GLU205 2.8 19.1 1.0
OG1 J:THR222 2.8 16.6 1.0
N40 K:B121601 3.1 16.6 1.0
CD J:GLU205 3.4 17.7 1.0
C J:THR222 3.5 18.2 1.0
OE2 J:GLU205 3.7 17.9 1.0
CD J:GLU208 3.7 17.7 1.0
C J:LEU203 3.8 18.1 1.0
CB J:THR222 3.9 17.1 1.0
N J:LEU203 3.9 18.1 1.0
C38 K:B121601 4.0 17.2 1.0
CD1 J:ILE223 4.1 19.2 1.0
CA J:THR222 4.2 16.0 1.0
N J:ILE223 4.4 16.7 1.0
O J:HOH710 4.4 17.4 1.0
OE2 J:GLU208 4.4 18.7 1.0
CB J:GLU208 4.4 18.1 1.0
CA J:GLU205 4.5 17.7 1.0
O J:HOH739 4.5 19.3 1.0
CG J:GLU205 4.5 18.2 1.0
CA J:LEU203 4.5 16.4 1.0
C37 K:B121601 4.6 14.2 1.0
C J:GLU204 4.6 20.6 1.0
N J:GLU205 4.6 18.7 1.0
CA J:ILE223 4.6 17.5 1.0
CG J:GLU208 4.7 16.4 1.0
OG J:SER202 4.7 15.8 0.5
O J:GLU204 4.7 17.7 1.0
N J:THR222 4.8 15.8 1.0
O39 K:B121601 4.8 18.0 1.0
C J:SER202 4.8 19.8 1.0
O2' J:5AD604 4.8 18.2 1.0
N J:GLU204 4.8 16.9 1.0
CA J:SER202 4.9 14.2 0.5
CA J:SER202 4.9 14.5 0.5

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: Sat Aug 9 10:18:26 2025

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