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Zinc in PDB 3vus: Escherichia Coli Pgab N-Terminal Domain

Protein crystallography data

The structure of Escherichia Coli Pgab N-Terminal Domain, PDB code: 3vus was solved by T.Nishiyama, H.Noguchi, H.Yoshida, S.-Y.Park, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.559, 53.114, 144.170, 90.00, 95.25, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 3vus:

The structure of Escherichia Coli Pgab N-Terminal Domain also contains other interesting chemical elements:

Mercury (Hg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Pgab N-Terminal Domain (pdb code 3vus). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Escherichia Coli Pgab N-Terminal Domain, PDB code: 3vus:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3vus

Go back to Zinc Binding Sites List in 3vus
Zinc binding site 1 out of 2 in the Escherichia Coli Pgab N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Pgab N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.2
occ:1.00
O A:ACT402 2.0 30.0 1.0
OXT A:ACT402 2.1 30.2 1.0
NE2 A:HIS184 2.1 19.9 1.0
OD1 A:ASP115 2.1 24.1 1.0
NE2 A:HIS189 2.2 23.6 1.0
C A:ACT402 2.2 38.1 1.0
CD2 A:HIS184 3.1 21.5 1.0
CE1 A:HIS189 3.1 25.5 1.0
CD2 A:HIS189 3.2 23.3 1.0
CE1 A:HIS184 3.2 22.5 1.0
CG A:ASP115 3.2 27.9 1.0
OD2 A:ASP115 3.6 27.6 1.0
CH3 A:ACT402 3.8 21.1 1.0
NE2 A:HIS55 4.2 25.6 1.0
CB A:ASP114 4.3 23.8 1.0
ND1 A:HIS189 4.3 27.6 1.0
CG A:HIS184 4.3 20.7 1.0
ND1 A:HIS184 4.3 20.8 1.0
CG A:HIS189 4.3 24.8 1.0
CD2 A:HIS55 4.5 26.2 1.0
CB A:ASP115 4.6 24.0 1.0
OD2 A:ASP114 4.8 27.0 1.0
CA A:PRO251 4.8 20.4 1.0
N A:ASP115 4.8 23.1 1.0
N A:TYR252 4.8 22.1 1.0
CA A:ASP115 4.9 21.5 1.0
CG A:ASP114 4.9 24.8 1.0

Zinc binding site 2 out of 2 in 3vus

Go back to Zinc Binding Sites List in 3vus
Zinc binding site 2 out of 2 in the Escherichia Coli Pgab N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Pgab N-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:24.8
occ:1.00
OXT B:ACT402 1.4 14.9 0.8
O B:ACT402 2.1 25.9 0.8
C B:ACT402 2.2 24.9 0.8
OD1 B:ASP115 2.2 19.2 1.0
NE2 B:HIS189 2.2 32.1 1.0
NE2 B:HIS184 2.2 19.5 1.0
O B:HOH584 3.1 11.3 0.2
CD2 B:HIS184 3.2 23.5 1.0
CE1 B:HIS189 3.2 27.8 1.0
CG B:ASP115 3.3 25.8 1.0
CD2 B:HIS189 3.3 23.1 1.0
CE1 B:HIS184 3.3 21.6 1.0
NE2 B:HIS55 3.3 27.7 1.0
OD2 B:ASP115 3.6 26.5 1.0
CH3 B:ACT402 3.7 16.1 0.8
CD2 B:HIS55 3.9 25.3 1.0
CB B:ASP114 3.9 19.1 1.0
ND1 B:HIS184 4.4 20.2 1.0
CG B:HIS184 4.4 20.1 1.0
OD2 B:ASP114 4.4 25.1 1.0
ND1 B:HIS189 4.4 28.5 1.0
CG B:HIS189 4.5 27.8 1.0
CE1 B:HIS55 4.5 21.4 1.0
CG B:ASP114 4.6 24.1 1.0
CB B:ASP115 4.7 23.3 1.0
CA B:PRO251 4.8 18.9 1.0
N B:ASP115 4.8 19.5 1.0
N B:TYR252 4.9 22.3 1.0

Reference:

T.Nishiyama, H.Noguchi, H.Yoshida, S.Y.Park, J.R.Tame. The Structure of the Deacetylase Domain of Escherichia Coli Pgab, An Enzyme Required For Biofilm Formation: A Circularly Permuted Member of the Carbohydrate Esterase 4 Family Acta Crystallogr.,Sect.D V. 69 44 2013.
ISSN: ISSN 0907-4449
PubMed: 23275162
DOI: 10.1107/S0907444912042059
Page generated: Wed Dec 16 04:56:39 2020

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