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: Sat Dec 12 05:55:07 2020

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