Atomistry » Potassium » PDB 5x24-5ze2 » 5yrv
Atomistry »
  Potassium »
    PDB 5x24-5ze2 »
      5yrv »

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: Mon Aug 12 15:14:52 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