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Calcium in PDB 5ysh: Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.330, 110.490, 115.480, 92.69, 95.97, 105.44
R / Rfree (%) 16.4 / 19.1

Other elements in 5ysh:

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Potassium (K) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal (pdb code 5ysh). 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 - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5ysh

Go back to Calcium Binding Sites List in 5ysh
Calcium binding site 1 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-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 - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:20.6
occ:1.00
 OE1 A:GLU170 2.3 23.0 1.0
OE1 A:GLU221 2.3 24.0 1.0
OE1 A:GLN296 2.4 21.4 1.0
O2 A:PGO604 2.4 24.7 1.0
O A:SER362 2.4 19.8 1.0
OE1 A:GLN141 2.4 26.3 1.0
O1 A:PGO604 2.4 25.4 1.0
CD A:GLU170 3.3 27.6 1.0
C2 A:PGO604 3.3 43.2 1.0
CD A:GLU221 3.3 25.8 1.0
CD A:GLN296 3.4 23.4 1.0
C1 A:PGO604 3.4 37.7 1.0
C A:SER362 3.4 22.8 1.0
CD A:GLN141 3.5 25.0 1.0
OE2 A:GLU170 3.6 31.1 1.0
NE2 A:GLN296 3.8 21.0 1.0
OE2 A:GLU221 3.8 23.6 1.0
CB A:SER362 4.0 17.1 1.0
NE2 A:HIS143 4.1 21.9 1.0
NE2 A:GLN141 4.1 20.9 1.0
OD2 A:ASP335 4.1 25.3 1.0
NE2 A:GLN200 4.2 23.6 1.0
OG A:SER362 4.2 20.9 1.0
CA A:SER362 4.3 16.3 1.0
N A:GLY363 4.4 21.3 1.0
CD2 A:HIS143 4.5 24.0 1.0
CA A:GLY363 4.5 19.1 1.0
CG A:GLU221 4.6 21.2 1.0
CG A:GLU170 4.6 25.0 1.0
CG A:GLN296 4.7 21.5 1.0
C3 A:PGO604 4.7 49.0 1.0
CB A:GLU170 4.8 24.2 1.0
CG A:GLN141 4.8 21.4 1.0

Calcium binding site 2 out of 4 in 5ysh

Go back to Calcium Binding Sites List in 5ysh
Calcium binding site 2 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-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 - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:6.3
occ:1.00
 O2 D:PGO604 2.1 18.1 1.0
OE1 D:GLU221 2.1 15.9 1.0
O D:SER362 2.2 14.8 1.0
O1 D:PGO604 2.2 19.9 1.0
OE1 D:GLU170 2.2 16.7 1.0
NE2 D:GLN296 2.3 9.2 1.0
OE1 D:GLN141 2.3 20.9 1.0
C2 D:PGO604 3.2 35.3 1.0
CD D:GLU221 3.2 16.5 1.0
C1 D:PGO604 3.3 29.2 1.0
CD D:GLU170 3.3 17.8 1.0
C D:SER362 3.3 17.1 1.0
CD D:GLN296 3.3 17.9 1.0
CD D:GLN141 3.5 16.2 1.0
OE2 D:GLU170 3.7 17.6 1.0
OE1 D:GLN296 3.7 19.5 1.0
OE2 D:GLU221 3.7 15.6 1.0
CB D:SER362 4.0 11.8 1.0
OG D:SER362 4.0 14.1 1.0
NE2 D:HIS143 4.1 12.8 1.0
NE2 D:GLN141 4.1 17.9 1.0
OD2 D:ASP335 4.1 19.7 1.0
NE2 D:GLN200 4.1 16.7 1.0
CA D:SER362 4.1 10.7 1.0
N D:GLY363 4.2 17.7 1.0
CD2 D:HIS143 4.4 13.1 1.0
CA D:GLY363 4.5 12.2 1.0
CG D:GLU221 4.5 16.8 1.0
C3 D:PGO604 4.5 42.4 1.0
CG D:GLU170 4.6 13.4 1.0
CG D:GLN296 4.6 12.0 1.0
CG D:GLN141 4.7 12.8 1.0
CB D:GLU170 4.8 13.1 1.0

Calcium binding site 3 out of 4 in 5ysh

Go back to Calcium Binding Sites List in 5ysh
Calcium binding site 3 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-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 - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:26.5
occ:1.00
 O G:SER362 2.3 26.3 1.0
OE1 G:GLU221 2.3 28.0 1.0
O1 G:PGO604 2.3 30.7 1.0
OE1 G:GLN296 2.4 24.7 1.0
OE1 G:GLU170 2.4 29.0 1.0
NE2 G:GLN141 2.4 31.0 1.0
O2 G:PGO604 2.5 33.5 1.0
CD G:GLN296 3.3 25.0 1.0
CD G:GLU221 3.3 27.5 1.0
C2 G:PGO604 3.4 49.9 1.0
CD G:GLU170 3.4 34.0 1.0
C G:SER362 3.4 28.9 1.0
C1 G:PGO604 3.4 46.0 1.0
CD G:GLN141 3.6 35.1 1.0
NE2 G:GLN296 3.6 24.0 1.0
OE2 G:GLU221 3.8 28.6 1.0
OE2 G:GLU170 3.8 31.4 1.0
CB G:SER362 3.9 25.4 1.0
OG G:SER362 4.0 30.1 1.0
NE2 G:HIS143 4.1 26.2 1.0
OD2 G:ASP335 4.1 30.9 1.0
OE1 G:GLN141 4.1 39.9 1.0
CA G:SER362 4.2 25.0 1.0
NE2 G:GLN200 4.3 33.7 1.0
N G:GLY363 4.4 29.5 1.0
CA G:GLY363 4.5 28.1 1.0
CD2 G:HIS143 4.5 27.5 1.0
CG G:GLU221 4.6 25.9 1.0
CG G:GLN296 4.6 22.7 1.0
CG G:GLU170 4.7 31.3 1.0
C3 G:PGO604 4.8 53.8 1.0
CB G:GLU170 4.8 28.7 1.0
CG G:GLN141 4.8 30.9 1.0

Calcium binding site 4 out of 4 in 5ysh

Go back to Calcium Binding Sites List in 5ysh
Calcium binding site 4 out of 4 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-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 - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca601

b:32.3
occ:1.00
 O J:SER362 2.3 42.0 1.0
OE2 J:GLU221 2.4 45.3 1.0
OE1 J:GLN296 2.4 36.3 1.0
OE1 J:GLN141 2.4 43.5 1.0
OE1 J:GLU170 2.4 42.9 1.0
O1 J:PGO604 2.5 54.0 1.0
O2 J:PGO604 2.5 35.9 1.0
CD J:GLN296 3.4 37.9 1.0
CD J:GLU170 3.4 49.8 1.0
CD J:GLU221 3.4 43.5 1.0
C1 J:PGO604 3.4 64.3 1.0
C2 J:PGO604 3.4 59.7 1.0
C J:SER362 3.5 40.2 1.0
CD J:GLN141 3.6 41.1 1.0
OE2 J:GLU170 3.7 51.1 1.0
NE2 J:GLN296 3.8 36.7 1.0
OE1 J:GLU221 3.8 37.7 1.0
CB J:SER362 4.0 34.5 1.0
NE2 J:HIS143 4.0 39.4 1.0
OG J:SER362 4.2 34.2 1.0
OD2 J:ASP335 4.2 43.5 1.0
NE2 J:GLN200 4.2 43.0 1.0
CA J:SER362 4.3 34.4 1.0
NE2 J:GLN141 4.3 39.3 1.0
N J:GLY363 4.4 32.7 1.0
CD2 J:HIS143 4.5 37.0 1.0
CA J:GLY363 4.5 33.3 1.0
CG J:GLU221 4.6 44.6 1.0
CG J:GLU170 4.7 44.5 1.0
CG J:GLN296 4.7 34.8 1.0
CG J:GLN141 4.7 39.9 1.0
C3 J:PGO604 4.8 61.9 1.0
CB J:GLU170 4.8 39.1 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 15:34:41 2024

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