Atomistry » Zinc » PDB 1r22-1rad » 1vpy
Atomistry »
  Zinc »
    PDB 1r22-1rad »
      1vpy »

Zinc in PDB 1vpy: Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution

Protein crystallography data

The structure of Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution, PDB code: 1vpy was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.52 / 2.52
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 114.079, 114.079, 52.307, 90.00, 90.00, 120.00
R / Rfree (%) 22.5 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution (pdb code 1vpy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution, PDB code: 1vpy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1vpy

Go back to Zinc Binding Sites List in 1vpy
Zinc binding site 1 out of 4 in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn278

b:45.0
occ:0.50
NE2 A:HIS216 2.3 34.2 1.0
OE1 A:GLN257 3.1 46.8 1.0
CE1 A:HIS216 3.3 34.5 1.0
CD2 A:HIS216 3.3 33.8 1.0
CD A:GLN257 3.8 45.3 1.0
NE2 A:GLN257 3.8 46.4 1.0
O A:TYR217 4.0 34.7 1.0
ND1 A:HIS216 4.4 34.4 1.0
CG A:HIS216 4.5 34.0 1.0
ND2 A:ASN254 4.5 39.7 1.0
CG A:GLU253 4.6 41.8 1.0

Zinc binding site 2 out of 4 in 1vpy

Go back to Zinc Binding Sites List in 1vpy
Zinc binding site 2 out of 4 in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn279

b:42.2
occ:1.00
NE2 A:HIS-2 2.1 43.0 1.0
NE2 A:HIS0 2.1 46.4 1.0
CD2 A:HIS0 2.9 47.6 1.0
CD2 A:HIS-2 2.9 43.4 1.0
CE1 A:HIS-2 3.1 43.9 1.0
CE1 A:HIS0 3.2 46.6 1.0
CG A:HIS-2 4.1 45.6 1.0
CG A:HIS0 4.1 48.0 1.0
ND1 A:HIS-2 4.1 44.9 1.0
ND1 A:HIS0 4.2 47.0 1.0

Zinc binding site 3 out of 4 in 1vpy

Go back to Zinc Binding Sites List in 1vpy
Zinc binding site 3 out of 4 in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn280

b:72.0
occ:1.00
NE2 A:HIS128 2.1 55.5 1.0
CD2 A:HIS128 2.8 49.4 1.0
CE1 A:HIS128 3.2 51.0 1.0
CG A:HIS128 4.0 46.5 1.0
ND1 A:HIS128 4.2 49.1 1.0
OE2 A:GLU83 4.2 49.6 1.0
OE1 A:GLU83 4.6 49.3 1.0
CD A:GLU83 4.8 48.9 1.0
CD1 A:TRP129 4.8 41.6 1.0

Zinc binding site 4 out of 4 in 1vpy

Go back to Zinc Binding Sites List in 1vpy
Zinc binding site 4 out of 4 in the Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A DUF72 Family Protein (EF0366) From Enterococcus Faecalis V583 at 2.52 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn281

b:69.2
occ:0.50
OE1 A:GLU25 2.5 44.9 1.0
NE2 A:HIS29 2.5 46.7 1.0
CE1 A:HIS29 2.8 47.2 1.0
O A:HOH337 2.9 38.1 1.0
CD A:GLU25 3.3 44.5 1.0
OE2 A:GLU25 3.4 44.5 1.0
O A:HOH334 3.4 38.3 1.0
O A:HOH333 3.4 41.3 1.0
CD2 A:HIS29 3.7 46.2 1.0
ND1 A:HIS29 4.0 47.0 1.0
CG A:HIS29 4.4 45.5 1.0
CG A:GLU25 4.7 43.0 1.0
O A:GLU25 5.0 42.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Fri Sep 25 23:55:39 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy