Atomistry » Calcium » PDB 5yj7-5z1q » 5yrv
Atomistry »
  Calcium »
    PDB 5yj7-5z1q »
      5yrv »

Calcium 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
Potassium (K) 8 atoms
Chlorine (Cl) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal, PDB code: 5yrv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5yrv

Go back to Calcium Binding Sites List in 5yrv
Calcium binding site 1 out of 4 in the Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca601

b:15.5
occ:1.00
 O A:SER362 2.3 18.1 1.0
OE1 A:GLU170 2.3 13.9 1.0
OE1 A:GLU221 2.3 15.7 1.0
O2 A:PGO604 2.3 16.4 1.0
OE1 A:GLN141 2.3 18.3 1.0
OE1 A:GLN296 2.4 16.6 1.0
O1 A:PGO604 2.5 17.4 1.0
C2 A:PGO604 3.1 28.5 1.0
C1 A:PGO604 3.2 27.0 1.0
CD A:GLU170 3.3 13.0 1.0
CD A:GLU221 3.4 15.1 1.0
CD A:GLN296 3.4 12.6 1.0
C A:SER362 3.4 15.3 1.0
CD A:GLN141 3.4 16.8 1.0
OE2 A:GLU170 3.7 15.8 1.0
NE2 A:GLN296 3.8 14.5 1.0
OE2 A:GLU221 3.8 15.1 1.0
NE2 A:GLN141 3.9 16.9 1.0
CB A:SER362 4.0 13.8 1.0
OG A:SER362 4.1 13.7 1.0
NE2 A:GLN200 4.2 14.3 1.0
NE2 A:HIS143 4.2 12.7 1.0
OD2 A:ASP335 4.2 20.8 1.0
CA A:SER362 4.2 12.9 1.0
N A:GLY363 4.4 15.4 1.0
CA A:GLY363 4.4 14.8 1.0
CD2 A:HIS143 4.5 15.5 1.0
C3 A:PGO604 4.5 29.2 1.0
CG A:GLU221 4.6 16.0 1.0
CG A:GLU170 4.6 15.9 1.0
CG A:GLN141 4.7 16.7 1.0
CG A:GLN296 4.7 11.6 1.0
CB A:GLU170 4.7 16.7 1.0

Calcium binding site 2 out of 4 in 5yrv

Go back to Calcium Binding Sites List in 5yrv
Calcium binding site 2 out of 4 in the Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
D:Ca601

b:16.6
occ:1.00
 O D:SER362 2.2 20.6 1.0
OE1 D:GLN141 2.3 22.4 1.0
OE1 D:GLU170 2.3 17.3 1.0
OE1 D:GLU221 2.3 16.4 1.0
O2 D:PGO604 2.4 19.6 1.0
OE1 D:GLN296 2.4 17.7 1.0
O1 D:PGO604 2.5 21.4 1.0
C2 D:PGO604 3.2 28.4 1.0
C1 D:PGO604 3.2 30.6 1.0
CD D:GLU170 3.3 16.7 1.0
C D:SER362 3.4 20.0 1.0
CD D:GLU221 3.4 18.5 1.0
CD D:GLN296 3.4 20.8 1.0
CD D:GLN141 3.4 18.2 1.0
OE2 D:GLU170 3.7 16.9 1.0
OE2 D:GLU221 3.8 16.6 1.0
NE2 D:GLN296 3.8 16.9 1.0
NE2 D:GLN141 4.0 17.1 1.0
CB D:SER362 4.0 15.8 1.0
OG D:SER362 4.2 16.6 1.0
NE2 D:GLN200 4.2 18.2 1.0
NE2 D:HIS143 4.2 14.9 1.0
CA D:SER362 4.2 17.0 1.0
OD2 D:ASP335 4.2 23.4 1.0
N D:GLY363 4.3 18.8 1.0
CA D:GLY363 4.4 15.6 1.0
CD2 D:HIS143 4.5 16.3 1.0
CG D:GLU170 4.6 17.0 1.0
C3 D:PGO604 4.6 29.5 1.0
CG D:GLU221 4.6 20.5 1.0
CG D:GLN141 4.7 17.7 1.0
CB D:GLU170 4.7 16.8 1.0
CG D:GLN296 4.7 17.6 1.0

Calcium binding site 3 out of 4 in 5yrv

Go back to Calcium Binding Sites List in 5yrv
Calcium binding site 3 out of 4 in the Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
G:Ca601

b:18.1
occ:1.00
 OE1 G:GLU170 2.3 17.7 1.0
OE1 G:GLN141 2.4 18.9 1.0
OE1 G:GLU221 2.4 17.8 1.0
O G:SER362 2.4 20.8 1.0
O2 G:PGO604 2.4 22.0 1.0
OE1 G:GLN296 2.4 18.7 1.0
O1 G:PGO604 2.5 19.7 1.0
C2 G:PGO604 3.1 27.3 1.0
C1 G:PGO604 3.2 33.4 1.0
CD G:GLU170 3.4 15.9 1.0
CD G:GLN296 3.4 17.9 1.0
CD G:GLU221 3.4 20.3 1.0
C G:SER362 3.4 18.3 1.0
CD G:GLN141 3.5 15.6 1.0
NE2 G:GLN296 3.7 18.7 1.0
OE2 G:GLU170 3.7 18.4 1.0
OE2 G:GLU221 3.8 20.2 1.0
CB G:SER362 4.0 18.9 1.0
NE2 G:GLN141 4.0 17.9 1.0
OG G:SER362 4.1 17.6 1.0
NE2 G:GLN200 4.1 15.7 1.0
NE2 G:HIS143 4.2 17.1 1.0
OD2 G:ASP335 4.2 21.8 1.0
CA G:SER362 4.2 16.1 1.0
N G:GLY363 4.3 18.7 1.0
CA G:GLY363 4.4 16.1 1.0
C3 G:PGO604 4.5 22.3 1.0
CD2 G:HIS143 4.6 16.9 1.0
CG G:GLU221 4.6 18.3 1.0
CG G:GLU170 4.6 17.0 1.0
CG G:GLN296 4.7 16.4 1.0
CG G:GLN141 4.7 14.2 1.0
CB G:GLU170 4.8 16.9 1.0

Calcium binding site 4 out of 4 in 5yrv

Go back to Calcium Binding Sites List in 5yrv
Calcium binding site 4 out of 4 in the Diol Dehydratase, Adocbl/1,2-Propanediol, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
J:Ca601

b:17.0
occ:1.00
 OE1 J:GLN141 2.3 18.8 1.0
OE1 J:GLU221 2.3 17.3 1.0
OE1 J:GLU170 2.3 17.0 1.0
O J:SER362 2.3 22.9 1.0
OE1 J:GLN296 2.4 17.9 1.0
O J:HOH727 2.5 19.9 1.0
O J:HOH880 2.5 19.7 1.0
CD J:GLU221 3.3 19.9 1.0
CD J:GLU170 3.3 17.1 1.0
CD J:GLN296 3.4 16.3 1.0
CD J:GLN141 3.4 16.8 1.0
C J:SER362 3.4 20.9 1.0
OE2 J:GLU170 3.7 16.7 1.0
OE2 J:GLU221 3.7 16.0 1.0
NE2 J:GLN296 3.7 16.2 1.0
NE2 J:GLN141 3.9 17.3 1.0
CB J:SER362 4.0 18.8 1.0
OG J:SER362 4.1 17.3 1.0
NE2 J:HIS143 4.2 15.3 1.0
NE2 J:GLN200 4.2 16.1 1.0
OD2 J:ASP335 4.3 21.7 1.0
CA J:SER362 4.3 17.8 1.0
N J:GLY363 4.4 18.2 1.0
CA J:GLY363 4.4 17.7 1.0
CG J:GLU221 4.5 18.0 1.0
CD2 J:HIS143 4.6 16.9 1.0
CG J:GLU170 4.6 15.2 1.0
CG J:GLN141 4.7 15.3 1.0
CG J:GLN296 4.7 16.1 1.0
CB J:GLU170 4.7 17.6 1.0

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 Jul 15 15:34:22 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy