Atomistry » Calcium » PDB 5yjd-5z4p » 5ysh
Atomistry »
  Calcium »
    PDB 5yjd-5z4p »
      5ysh »

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: Wed Jul 9 12:04:07 2025

Last articles

Mg in 3CMQ
Mg in 3CLY
Mg in 3CK5
Mg in 3CLC
Mg in 3CKG
Mg in 3CKE
Mg in 3CK4
Mg in 3CJO
Mg in 3CJ8
Mg in 3CIK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy