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Zinc in PDB 4uej: Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.

Enzymatic activity of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.

All present enzymatic activity of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.:
1.1.1.251;

Protein crystallography data

The structure of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol., PDB code: 4uej was solved by R.Benavente, M.Esteban-Torres, G.W.Kohring, A.Cortes-Cabrera, F.Gago, I.Acebron, B.De Las Rivas, R.Munoz, J.M.Mancheno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.672 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.311, 78.810, 68.244, 90.00, 94.75, 90.00
R / Rfree (%) 18.5 / 22.81

Zinc Binding Sites:

The binding sites of Zinc atom in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. (pdb code 4uej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol., PDB code: 4uej:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4uej

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Zinc binding site 1 out of 5 in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1347

b:17.9
occ:1.00
 SG A:CYS95 2.3 18.7 1.0
SG A:CYS92 2.3 21.5 1.0
SG A:CYS89 2.3 20.9 1.0
SG A:CYS103 2.5 21.6 1.0
CB A:CYS103 3.3 18.4 1.0
CB A:CYS95 3.4 19.5 1.0
CB A:CYS92 3.4 22.9 1.0
CB A:CYS89 3.5 20.3 1.0
N A:CYS89 3.6 18.4 1.0
N A:PHE90 3.7 20.4 1.0
N A:CYS92 3.8 22.5 1.0
CA A:CYS89 3.9 19.3 1.0
CA A:CYS103 3.9 20.8 1.0
O A:HOH2105 4.2 46.3 1.0
CA A:CYS92 4.2 23.3 1.0
C A:CYS89 4.2 24.2 1.0
N A:CYS95 4.3 20.5 1.0
N A:THR91 4.3 21.1 1.0
CA A:CYS95 4.4 19.7 1.0
CA A:PHE90 4.6 22.8 1.0
C A:PRO88 4.7 17.6 1.0
O A:CYS92 4.8 22.6 1.0
N A:ALA104 4.8 32.2 1.0
C A:CYS103 4.8 25.9 1.0
C A:CYS92 4.8 29.3 1.0
CB A:PRO88 4.9 22.8 1.0
C A:PHE90 4.9 23.5 1.0
C A:THR91 5.0 23.1 1.0

Zinc binding site 2 out of 5 in 4uej

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Zinc binding site 2 out of 5 in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1348

b:20.8
occ:1.00
 O A:HOH2053 2.0 16.9 1.0
NE2 A:HIS59 2.1 16.4 1.0
O1 A:GOL1350 2.2 21.9 1.0
O2 A:GOL1350 2.2 31.3 1.0
C2 A:GOL1350 2.6 30.9 1.0
SG A:CYS38 2.7 23.0 1.0
C1 A:GOL1350 3.0 26.8 1.0
CD2 A:HIS59 3.0 15.8 1.0
CE1 A:HIS59 3.1 17.2 1.0
CB A:CYS38 3.7 22.2 1.0
OE2 A:GLU60 3.7 17.2 1.0
OG A:SER40 3.8 27.9 1.0
OE1 A:GLU144 3.8 13.2 1.0
C3 A:GOL1350 4.1 31.4 1.0
OE2 A:GLU144 4.1 16.1 1.0
CG A:HIS59 4.2 16.3 1.0
ND1 A:HIS59 4.2 17.2 1.0
CD A:GLU144 4.4 12.0 1.0
CD A:GLU60 4.6 20.2 1.0
CG A:GLU60 4.6 17.1 1.0
O3 A:GOL1350 4.7 34.1 1.0
CB A:SER40 4.8 27.8 1.0

Zinc binding site 3 out of 5 in 4uej

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Zinc binding site 3 out of 5 in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1349

b:18.8
occ:1.00
 ND1 B:HIS267 2.0 20.8 1.0
ND1 A:HIS267 2.0 20.4 1.0
O A:HOH2263 2.2 7.4 1.0
CE1 B:HIS267 2.8 19.5 1.0
CE1 A:HIS267 2.9 20.9 1.0
CG B:HIS267 3.0 21.6 1.0
CG A:HIS267 3.1 19.3 1.0
CB B:HIS267 3.5 16.9 1.0
CB A:HIS267 3.6 18.6 1.0
NE2 B:HIS267 4.0 18.8 1.0
NE2 A:HIS267 4.0 20.0 1.0
CD2 B:HIS267 4.1 19.1 1.0
CD2 A:HIS267 4.2 19.0 1.0
CA B:HIS267 4.5 15.2 1.0
CA A:HIS267 4.6 21.1 1.0

Zinc binding site 4 out of 5 in 4uej

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Zinc binding site 4 out of 5 in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1347

b:16.5
occ:1.00
 SG B:CYS92 2.3 18.8 1.0
SG B:CYS95 2.3 17.6 1.0
SG B:CYS89 2.4 16.9 1.0
SG B:CYS103 2.4 21.7 1.0
CB B:CYS103 3.3 22.1 1.0
CB B:CYS95 3.3 20.2 1.0
CB B:CYS92 3.4 20.7 1.0
CB B:CYS89 3.5 16.5 1.0
N B:CYS89 3.6 19.4 1.0
N B:CYS92 3.8 19.4 1.0
N B:PHE90 3.8 16.0 1.0
CA B:CYS103 3.8 22.3 1.0
CA B:CYS89 3.9 17.0 1.0
CA B:CYS92 4.2 20.5 1.0
N B:ALA104 4.2 34.5 1.0
C B:CYS89 4.2 17.4 1.0
N B:CYS95 4.3 18.7 1.0
N B:THR91 4.3 17.5 1.0
CA B:CYS95 4.3 17.8 1.0
C B:CYS103 4.4 26.0 1.0
CA B:PHE90 4.7 19.2 1.0
C B:PRO88 4.7 14.4 1.0
CB B:PRO88 4.7 24.9 1.0
O B:CYS92 4.8 20.5 1.0
C B:CYS92 4.8 21.1 1.0
C B:THR91 4.9 19.8 1.0
N B:LYS105 4.9 30.7 1.0
C B:PHE90 4.9 22.7 1.0
CA B:PRO88 5.0 12.8 1.0

Zinc binding site 5 out of 5 in 4uej

Go back to Zinc Binding Sites List in 4uej
Zinc binding site 5 out of 5 in the Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Closed State of Galactitol-1-Phosphate 5-Dehydrogenase From E. Coli in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1348

b:19.3
occ:1.00
 O B:HOH2052 2.0 13.2 1.0
NE2 B:HIS59 2.1 11.2 1.0
O2 B:GOL1349 2.2 29.4 1.0
O1 B:GOL1349 2.2 20.4 1.0
SG B:CYS38 2.7 18.5 1.0
C2 B:GOL1349 2.7 35.7 1.0
C1 B:GOL1349 3.0 25.3 1.0
CD2 B:HIS59 3.0 12.8 1.0
CE1 B:HIS59 3.1 12.8 1.0
CB B:CYS38 3.6 13.4 1.0
OG B:SER40 3.8 22.0 1.0
OE2 B:GLU60 3.8 15.2 1.0
OE1 B:GLU144 3.9 11.2 1.0
O B:HOH2057 4.1 38.2 1.0
OE2 B:GLU144 4.1 14.1 1.0
C3 B:GOL1349 4.2 40.2 1.0
CG B:HIS59 4.2 9.7 1.0
ND1 B:HIS59 4.2 11.9 1.0
CD B:GLU144 4.4 13.2 1.0
CD B:GLU60 4.6 15.8 1.0
CG B:GLU60 4.7 9.6 1.0
CD1 B:ILE172 4.8 9.3 0.5
CB B:SER40 4.8 20.0 1.0
O3 B:GOL1349 4.8 46.3 1.0

Reference:

R.Benavente, M.Esteban-Torres, G.W.Kohring, A.Cortes-Cabrera, P.A.Sanchez-Murcia, F.Gago, I.Acebron, B.De Las Rivas, R.Munoz, J.M.Mancheno. Enantioselective Oxidation of Galactitol 1-Phosphate By Galactitol-1-Phosphate 5-Dehydrogenase From Escherichia Coli Acta Crystallogr.,Sect.D V. 71 1540 2015.
ISSN: ISSN 0907-4449
PubMed: 26143925
DOI: 10.1107/S1399004715009281
Page generated: Sun Oct 27 08:59:12 2024

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