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

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 5yrt

Go back to Calcium Binding Sites List in 5yrt
Calcium binding site 1 out of 4 in the Diol Dehydratase, Adocbl/Substrate-Free, 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/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:12.2
occ:1.00
 OE1 A:GLU170 2.3 11.4 1.0
OE1 A:GLU221 2.3 11.6 1.0
O A:SER362 2.3 14.2 1.0
O A:HOH845 2.4 16.7 1.0
OE1 A:GLN141 2.4 19.9 1.0
OE1 A:GLN296 2.4 17.7 1.0
O A:HOH728 2.4 15.7 1.0
CD A:GLU170 3.3 10.5 1.0
CD A:GLU221 3.4 11.8 1.0
CD A:GLN296 3.4 14.4 1.0
C A:SER362 3.5 8.0 1.0
CD A:GLN141 3.5 15.9 1.0
OE2 A:GLU170 3.6 13.3 1.0
NE2 A:GLN296 3.8 10.6 1.0
OE2 A:GLU221 3.8 10.0 1.0
NE2 A:GLN141 4.0 16.3 1.0
CB A:SER362 4.1 10.7 1.0
NE2 A:GLN200 4.1 9.6 1.0
NE2 A:HIS143 4.1 11.6 1.0
OG A:SER362 4.2 9.5 1.0
OD2 A:ASP335 4.2 18.1 1.0
CA A:SER362 4.3 10.2 1.0
N A:GLY363 4.4 9.7 1.0
CA A:GLY363 4.4 14.5 1.0
CD2 A:HIS143 4.5 11.7 1.0
CG A:GLU221 4.6 12.1 1.0
CG A:GLU170 4.6 8.6 1.0
CB A:GLU170 4.7 13.6 1.0
CG A:GLN296 4.7 6.6 1.0
CG A:GLN141 4.8 12.6 1.0

Calcium binding site 2 out of 4 in 5yrt

Go back to Calcium Binding Sites List in 5yrt
Calcium binding site 2 out of 4 in the Diol Dehydratase, Adocbl/Substrate-Free, 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/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:13.1
occ:1.00
 O D:SER362 2.3 17.8 1.0
OE1 D:GLU170 2.3 11.8 1.0
OE1 D:GLN141 2.4 20.1 1.0
OE1 D:GLU221 2.4 12.7 1.0
O D:HOH838 2.4 15.4 1.0
OE1 D:GLN296 2.5 12.6 1.0
O D:HOH720 2.5 15.6 1.0
CD D:GLU170 3.3 11.4 1.0
C D:SER362 3.4 15.4 1.0
CD D:GLU221 3.4 11.4 1.0
CD D:GLN296 3.4 13.6 1.0
CD D:GLN141 3.5 16.0 1.0
OE2 D:GLU170 3.7 15.4 1.0
NE2 D:GLN296 3.8 9.8 1.0
OE2 D:GLU221 3.8 12.8 1.0
NE2 D:GLN141 4.0 17.5 1.0
CB D:SER362 4.0 15.5 1.0
NE2 D:HIS143 4.1 11.6 1.0
NE2 D:GLN200 4.1 12.8 1.0
OD2 D:ASP335 4.2 23.8 1.0
OG D:SER362 4.2 11.6 1.0
CA D:SER362 4.3 14.1 1.0
N D:GLY363 4.3 16.5 1.0
CA D:GLY363 4.4 9.8 1.0
CD2 D:HIS143 4.5 12.9 1.0
CG D:GLU170 4.6 10.6 1.0
CG D:GLU221 4.6 9.2 1.0
CG D:GLN141 4.7 12.3 1.0
CB D:GLU170 4.7 10.9 1.0
CG D:GLN296 4.8 10.7 1.0

Calcium binding site 3 out of 4 in 5yrt

Go back to Calcium Binding Sites List in 5yrt
Calcium binding site 3 out of 4 in the Diol Dehydratase, Adocbl/Substrate-Free, 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/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:11.8
occ:1.00
 O G:SER362 2.3 16.0 1.0
OE1 G:GLN141 2.3 17.7 1.0
OE1 G:GLU221 2.4 11.4 1.0
OE1 G:GLU170 2.4 9.8 1.0
OE1 G:GLN296 2.4 12.0 1.0
O G:HOH900 2.4 16.1 1.0
O G:HOH725 2.5 17.1 1.0
CD G:GLU170 3.3 15.4 1.0
CD G:GLU221 3.4 12.6 1.0
CD G:GLN296 3.4 11.8 1.0
C G:SER362 3.4 11.5 1.0
CD G:GLN141 3.5 10.4 1.0
OE2 G:GLU170 3.7 10.8 1.0
OE2 G:GLU221 3.7 12.0 1.0
NE2 G:GLN296 3.8 14.1 1.0
CB G:SER362 4.0 10.3 1.0
OG G:SER362 4.1 9.8 1.0
NE2 G:GLN141 4.1 12.0 1.0
OD2 G:ASP335 4.1 16.9 1.0
NE2 G:GLN200 4.2 13.0 1.0
NE2 G:HIS143 4.2 9.8 1.0
CA G:SER362 4.3 8.1 1.0
N G:GLY363 4.4 10.2 1.0
CA G:GLY363 4.5 10.5 1.0
CD2 G:HIS143 4.6 11.5 1.0
CG G:GLU221 4.6 13.4 1.0
CG G:GLU170 4.7 10.8 1.0
CG G:GLN296 4.7 8.8 1.0
CG G:GLN141 4.7 9.2 1.0
CB G:GLU170 4.8 11.2 1.0

Calcium binding site 4 out of 4 in 5yrt

Go back to Calcium Binding Sites List in 5yrt
Calcium binding site 4 out of 4 in the Diol Dehydratase, Adocbl/Substrate-Free, 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/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca601

b:10.5
occ:1.00
 OE1 J:GLU170 2.3 12.0 1.0
O J:SER362 2.4 17.1 1.0
OE1 J:GLU221 2.4 10.1 1.0
OE1 J:GLN141 2.4 18.1 1.0
OE1 J:GLN296 2.4 13.7 1.0
O J:HOH791 2.4 13.1 1.0
O J:HOH769 2.5 13.6 1.0
CD J:GLU170 3.3 11.8 1.0
CD J:GLN296 3.3 10.0 1.0
CD J:GLU221 3.4 14.8 1.0
C J:SER362 3.5 13.6 1.0
CD J:GLN141 3.5 12.9 1.0
OE2 J:GLU170 3.7 12.9 1.0
NE2 J:GLN296 3.7 9.3 1.0
OE2 J:GLU221 3.8 10.6 1.0
NE2 J:GLN141 4.0 10.9 1.0
CB J:SER362 4.1 16.2 1.0
NE2 J:HIS143 4.1 8.5 1.0
OG J:SER362 4.2 11.7 1.0
OD2 J:ASP335 4.2 17.5 1.0
NE2 J:GLN200 4.3 8.0 1.0
CA J:SER362 4.3 15.9 1.0
N J:GLY363 4.4 11.9 1.0
CA J:GLY363 4.4 12.3 1.0
CD2 J:HIS143 4.5 7.3 1.0
CG J:GLU221 4.6 8.2 1.0
CG J:GLU170 4.6 7.0 1.0
CG J:GLN296 4.7 8.9 1.0
CG J:GLN141 4.7 8.4 1.0
CB J:GLU170 4.8 13.9 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 15:33:33 2024

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