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Calcium in PDB 3auj: Structure of Diol Dehydratase Complexed with Glycerol

Enzymatic activity of Structure of Diol Dehydratase Complexed with Glycerol

All present enzymatic activity of Structure of Diol Dehydratase Complexed with Glycerol:
4.2.1.28;

Protein crystallography data

The structure of Structure of Diol Dehydratase Complexed with Glycerol, PDB code: 3auj was solved by M.Yamanishi, K.Kinoshita, M.Fukuoka, T.Shibata, T.Tobimatsu, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.34 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.610, 196.800, 77.360, 90.00, 95.03, 90.00
R / Rfree (%) 18.6 / 19.1

Other elements in 3auj:

The structure of Structure of Diol Dehydratase Complexed with Glycerol also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Diol Dehydratase Complexed with Glycerol (pdb code 3auj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Diol Dehydratase Complexed with Glycerol, PDB code: 3auj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3auj

Go back to Calcium Binding Sites List in 3auj
Calcium binding site 1 out of 2 in the Structure of Diol Dehydratase Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Diol Dehydratase Complexed with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1603

b:20.6
occ:1.00
OE1 A:GLU221 2.2 20.9 1.0
O A:SER362 2.4 21.3 1.0
OE1 A:GLU170 2.4 20.3 1.0
OE1 A:GLN296 2.4 15.8 1.0
O2 A:GOL1602 2.4 20.6 1.0
OE1 A:GLN141 2.4 20.3 1.0
O1 A:GOL1602 2.6 15.9 1.0
C2 A:GOL1602 3.3 23.2 1.0
CD A:GLU221 3.3 19.9 1.0
CD A:GLU170 3.3 20.5 1.0
C1 A:GOL1602 3.3 19.8 1.0
CD A:GLN296 3.4 17.0 1.0
C A:SER362 3.4 19.5 1.0
CD A:GLN141 3.5 21.5 1.0
OE2 A:GLU170 3.6 19.2 1.0
OE2 A:GLU221 3.7 19.4 1.0
NE2 A:GLN296 3.8 17.8 1.0
NE2 A:GLN141 4.0 20.0 1.0
CB A:SER362 4.0 20.4 1.0
NE2 A:HIS143 4.0 22.5 1.0
OD2 A:ASP335 4.1 23.9 1.0
OG A:SER362 4.2 23.5 1.0
CA A:SER362 4.3 21.2 1.0
NE2 A:GLN200 4.3 22.4 1.0
N A:GLY363 4.4 20.1 1.0
CA A:GLY363 4.5 19.0 1.0
CD2 A:HIS143 4.5 21.6 1.0
CG A:GLU221 4.5 21.5 1.0
CG A:GLU170 4.6 20.1 1.0
C3 A:GOL1602 4.6 26.9 1.0
CG A:GLN296 4.7 16.8 1.0
CB A:GLU170 4.8 20.4 1.0
CG A:GLN141 4.8 19.8 1.0

Calcium binding site 2 out of 2 in 3auj

Go back to Calcium Binding Sites List in 3auj
Calcium binding site 2 out of 2 in the Structure of Diol Dehydratase Complexed with Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Diol Dehydratase Complexed with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca2603

b:21.6
occ:1.00
OE1 L:GLU221 2.2 25.0 1.0
OE1 L:GLU170 2.4 21.2 1.0
O L:SER362 2.4 20.5 1.0
O2 L:GOL2602 2.4 24.0 1.0
OE1 L:GLN296 2.4 17.6 1.0
OE1 L:GLN141 2.4 20.4 1.0
O1 L:GOL2602 2.5 20.4 1.0
C2 L:GOL2602 3.2 25.9 1.0
CD L:GLU221 3.2 24.6 1.0
C1 L:GOL2602 3.3 21.9 1.0
CD L:GLU170 3.3 21.1 1.0
CD L:GLN296 3.4 19.4 1.0
C L:SER362 3.4 20.3 1.0
CD L:GLN141 3.5 19.7 1.0
OE2 L:GLU170 3.6 21.1 1.0
OE2 L:GLU221 3.7 24.4 1.0
NE2 L:GLN296 3.7 19.3 1.0
NE2 L:GLN141 4.0 16.5 1.0
CB L:SER362 4.0 20.1 1.0
NE2 L:GLN200 4.1 19.7 1.0
NE2 L:HIS143 4.1 17.7 1.0
OD2 L:ASP335 4.1 20.6 1.0
CA L:SER362 4.2 20.4 1.0
OG L:SER362 4.3 23.9 1.0
N L:GLY363 4.3 19.9 1.0
CA L:GLY363 4.5 20.1 1.0
CG L:GLU221 4.5 26.2 1.0
CD2 L:HIS143 4.6 18.5 1.0
C3 L:GOL2602 4.6 28.6 1.0
CG L:GLU170 4.6 20.3 1.0
CG L:GLN296 4.7 20.0 1.0
CG L:GLN141 4.8 19.3 1.0
CB L:GLU170 4.8 20.0 1.0

Reference:

M.Yamanishi, K.Kinoshita, M.Fukuoka, T.Saito, A.Tanokuchi, Y.Ikeda, H.Obayashi, K.Mori, N.Shibata, T.Tobimatsu, T.Toraya. Redesign of Coenzyme B(12) Dependent Diol Dehydratase to Be Resistant to the Mechanism-Based Inactivation By Glycerol and Act on Longer Chain 1,2-Diols Febs J. V. 279 793 2012.
ISSN: ISSN 1742-464X
PubMed: 22221669
DOI: 10.1111/J.1742-4658.2012.08470.X
Page generated: Sat Jul 13 08:00:16 2024

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