Atomistry » Zinc » PDB 3qla-3qym » 3qu1
Atomistry »
  Zinc »
    PDB 3qla-3qym »
      3qu1 »

Zinc in PDB 3qu1: Peptide Deformylase From Vibrio Cholerae

Enzymatic activity of Peptide Deformylase From Vibrio Cholerae

All present enzymatic activity of Peptide Deformylase From Vibrio Cholerae:
3.5.1.88;

Protein crystallography data

The structure of Peptide Deformylase From Vibrio Cholerae, PDB code: 3qu1 was solved by J.Osipiuk, R.Mulligan, L.Papazisi, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.20 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.296, 74.296, 127.219, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.4

Other elements in 3qu1:

The structure of Peptide Deformylase From Vibrio Cholerae also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Peptide Deformylase From Vibrio Cholerae (pdb code 3qu1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Peptide Deformylase From Vibrio Cholerae, PDB code: 3qu1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 1 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.7
occ:1.00
O A:HOH219 2.0 22.6 1.0
NE2 A:HIS137 2.0 20.0 1.0
NE2 A:HIS133 2.1 19.9 1.0
SG A:CYS91 2.3 20.1 1.0
CE1 A:HIS137 3.0 20.4 1.0
CD2 A:HIS133 3.0 21.3 1.0
CD2 A:HIS137 3.1 20.6 1.0
CE1 A:HIS133 3.1 24.2 1.0
CB A:CYS91 3.3 19.7 1.0
ZN A:ZN505 3.5 25.5 1.0
O A:HOH177 3.5 21.4 1.0
NE2 A:GLN51 3.6 20.1 1.0
OXT B:ARG168 3.7 31.0 1.0
OE1 A:GLN51 3.9 18.3 1.0
CA A:CYS91 3.9 19.0 1.0
CD A:GLN51 4.0 22.6 1.0
ND1 A:HIS137 4.1 21.3 1.0
CG A:HIS133 4.2 22.9 1.0
CG A:HIS137 4.2 21.9 1.0
ND1 A:HIS133 4.2 22.0 1.0
OE1 A:GLU134 4.2 23.4 1.0
O A:HOH174 4.3 23.1 1.0
OE2 A:GLU134 4.4 24.4 1.0
N A:LEU92 4.4 19.4 1.0
C A:CYS91 4.6 20.2 1.0
CD A:GLU134 4.6 23.3 1.0
O A:GLY90 4.7 23.1 1.0
C B:ARG168 4.9 31.5 1.0

Zinc binding site 2 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 2 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:20.9
occ:1.00
OD2 A:ASP96 1.9 21.0 1.0
OH B:TYR98 1.9 19.4 1.0
O B:HOH215 1.9 22.5 1.0
ND1 A:HIS162 2.0 20.6 1.0
CG A:ASP96 2.8 21.1 1.0
CE1 A:HIS162 2.9 27.9 1.0
CZ B:TYR98 3.0 18.7 1.0
OD1 A:ASP96 3.0 20.8 1.0
CG A:HIS162 3.1 21.9 1.0
CE2 B:TYR98 3.3 18.9 1.0
ZN A:ZN507 3.4 27.7 0.7
CB A:HIS162 3.5 22.4 1.0
O B:HOH267 3.7 42.8 1.0
O B:HOH226 3.7 28.3 1.0
NH2 A:ARG168 3.7 22.4 1.0
OD1 B:ASP96 4.0 20.5 1.0
O A:HOH257 4.1 24.7 1.0
NE2 A:HIS162 4.1 23.5 1.0
CA A:HIS162 4.1 22.1 1.0
CA B:ASP96 4.2 20.0 1.0
CB A:ASP96 4.2 21.5 1.0
CD2 A:HIS162 4.2 24.6 1.0
CE1 B:TYR98 4.2 20.1 1.0
NE A:ARG168 4.4 42.7 1.0
CZ A:ARG168 4.6 36.1 1.0
N B:ASP96 4.6 18.7 1.0
CG B:ASP96 4.7 20.2 1.0
CD2 B:TYR98 4.7 18.6 1.0
O B:HOH216 4.8 22.8 1.0
CB B:ASP96 4.9 19.1 1.0
C B:ASP96 5.0 20.6 1.0

Zinc binding site 3 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 3 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:25.5
occ:1.00
OE2 A:GLU134 1.9 24.4 1.0
O A:HOH219 1.9 22.6 1.0
OXT B:ARG168 2.0 31.0 1.0
O A:GLY46 2.1 20.4 1.0
CD A:GLU134 2.7 23.3 1.0
C B:ARG168 2.8 31.5 1.0
OE1 A:GLU134 2.9 23.4 1.0
C A:GLY46 2.9 21.0 1.0
O B:ARG168 3.0 33.3 1.0
ZN A:ZN501 3.5 20.7 1.0
CA A:GLY46 3.5 22.9 1.0
O A:HOH226 3.8 30.8 1.0
NE2 A:HIS133 3.8 19.9 1.0
N A:LEU47 3.9 21.2 1.0
CD2 A:HIS133 3.9 21.3 1.0
N A:GLY46 3.9 23.9 1.0
OE1 A:GLN51 4.1 18.3 1.0
CG A:GLU134 4.1 21.3 1.0
CA A:LEU47 4.2 20.3 1.0
CA B:ARG168 4.2 29.5 1.0
CD1 A:LEU92 4.7 22.6 1.0
NE2 A:HIS137 4.7 20.0 1.0
NE2 A:GLN51 4.8 20.1 1.0
CE1 A:HIS133 4.8 24.2 1.0
CD A:GLN51 4.9 22.6 1.0
CG A:LEU92 4.9 25.2 1.0
CD2 A:HIS137 4.9 20.6 1.0
N B:ARG168 4.9 30.1 1.0
CG A:HIS133 4.9 22.9 1.0
N A:LEU92 5.0 19.4 1.0

Zinc binding site 4 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 4 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:27.7
occ:0.70
O B:HOH215 2.0 22.5 1.0
OD1 B:ASP96 2.1 20.5 1.0
OD1 A:ASP96 2.1 20.8 1.0
O A:HOH217 2.2 22.6 1.0
O B:HOH216 2.2 22.8 1.0
O A:HOH257 2.2 24.7 1.0
CG B:ASP96 3.0 20.2 1.0
CG A:ASP96 3.2 21.1 1.0
ZN A:ZN503 3.4 20.9 1.0
ZN B:ZN502 3.4 21.1 1.0
OD2 B:ASP96 3.5 21.9 1.0
OD2 A:ASP96 3.6 21.0 1.0
O B:HOH267 4.1 42.8 1.0
CB B:ASP96 4.2 19.1 1.0
CB A:ASP96 4.4 21.5 1.0
ND1 B:HIS162 4.4 22.1 1.0
ND1 A:HIS162 4.4 20.6 1.0
CA B:ASP96 4.4 20.0 1.0
CE1 A:HIS162 4.4 27.9 1.0
CE1 B:HIS162 4.5 26.2 1.0
CA A:ASP96 4.6 22.0 1.0
N A:ASP96 4.6 21.4 1.0
N B:ASP96 4.6 18.7 1.0
O A:HOH203 4.9 27.1 1.0
OH A:TYR98 4.9 19.9 1.0
OH B:TYR98 4.9 19.4 1.0

Zinc binding site 5 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 5 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:21.1
occ:1.00
OH A:TYR98 1.8 19.9 1.0
O A:HOH217 1.9 22.6 1.0
OD2 B:ASP96 1.9 21.9 1.0
ND1 B:HIS162 2.0 22.1 1.0
CG B:ASP96 2.8 20.2 1.0
CE1 B:HIS162 3.0 26.2 1.0
CZ A:TYR98 3.0 19.6 1.0
OD1 B:ASP96 3.0 20.5 1.0
CG B:HIS162 3.0 22.6 1.0
CE2 A:TYR98 3.4 19.4 1.0
CB B:HIS162 3.4 21.3 1.0
ZN A:ZN507 3.4 27.7 0.7
O A:HOH203 3.6 27.1 1.0
NH2 B:ARG168 3.7 28.6 1.0
O B:HOH216 4.0 22.8 1.0
OD1 A:ASP96 4.0 20.8 1.0
CA B:HIS162 4.1 21.4 1.0
NE2 B:HIS162 4.1 23.1 1.0
CB B:ASP96 4.1 19.1 1.0
CD2 B:HIS162 4.2 20.4 1.0
CE1 A:TYR98 4.2 22.2 1.0
NE B:ARG168 4.4 31.9 1.0
CA A:ASP96 4.5 22.0 1.0
CZ B:ARG168 4.6 34.1 1.0
CD2 A:TYR98 4.7 21.5 1.0
N A:ASP96 4.7 21.4 1.0
O A:HOH257 4.8 24.7 1.0
CG A:ASP96 4.8 21.1 1.0

Zinc binding site 6 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 6 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:20.4
occ:1.00
NE2 B:HIS133 2.0 19.1 1.0
NE2 B:HIS137 2.1 19.4 1.0
O B:HOH223 2.1 24.7 1.0
SG B:CYS91 2.3 19.3 1.0
CD2 B:HIS133 2.9 20.2 1.0
CE1 B:HIS137 3.0 22.1 1.0
CD2 B:HIS137 3.1 19.4 1.0
CE1 B:HIS133 3.1 21.9 1.0
CB B:CYS91 3.3 18.8 1.0
O B:HOH173 3.5 18.7 1.0
ZN B:ZN506 3.5 22.3 0.6
NE2 B:GLN51 3.7 20.6 1.0
O B:HOH318 3.7 42.5 1.0
OE1 B:GLN51 3.9 22.6 1.0
CA B:CYS91 3.9 18.6 1.0
CD B:GLN51 3.9 21.9 1.0
CG B:HIS133 4.1 19.5 1.0
ND1 B:HIS133 4.2 21.3 1.0
ND1 B:HIS137 4.2 19.0 1.0
OE2 B:GLU134 4.2 24.1 1.0
CG B:HIS137 4.2 20.5 1.0
O A:ARG168 4.2 47.6 1.0
OE1 B:GLU134 4.3 22.9 1.0
O B:HOH193 4.4 19.8 1.0
CD B:GLU134 4.6 20.5 1.0
N B:LEU92 4.6 20.6 1.0
C B:CYS91 4.7 19.4 1.0
O B:GLY90 4.7 22.2 1.0

Zinc binding site 7 out of 7 in 3qu1

Go back to Zinc Binding Sites List in 3qu1
Zinc binding site 7 out of 7 in the Peptide Deformylase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Peptide Deformylase From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:22.3
occ:0.60
OE2 B:GLU134 1.7 24.1 1.0
O B:HOH223 1.9 24.7 1.0
O A:ARG168 1.9 47.6 1.0
O B:GLY46 2.3 23.9 1.0
CD B:GLU134 2.7 20.5 1.0
O B:HOH318 2.8 42.5 1.0
C A:ARG168 2.9 47.5 1.0
C B:GLY46 2.9 22.6 1.0
OE1 B:GLU134 3.1 22.9 1.0
OXT A:ARG168 3.3 46.0 1.0
ZN B:ZN504 3.5 20.4 1.0
CA B:GLY46 3.5 22.5 1.0
CD2 B:HIS133 3.8 20.2 1.0
NE2 B:HIS133 3.8 19.1 1.0
N B:GLY46 3.9 22.4 1.0
N B:LEU47 3.9 21.1 1.0
CG B:GLU134 4.1 20.6 1.0
OE1 B:GLN51 4.1 22.6 1.0
O A:HOH262 4.2 51.5 1.0
CA A:ARG168 4.3 46.6 1.0
CA B:LEU47 4.3 21.0 1.0
NE2 B:GLN51 4.8 20.6 1.0
NE2 B:HIS137 4.8 19.4 1.0
CG B:HIS133 4.8 19.5 1.0
CD B:GLN51 4.8 21.9 1.0
CE1 B:HIS133 4.8 21.9 1.0
N A:ARG168 5.0 47.2 1.0
CD2 B:HIS137 5.0 19.4 1.0

Reference:

J.Osipiuk, R.Mulligan, L.Papazisi, W.F.Anderson, A.Joachimiak. Peptide Deformylase From Vibrio Cholerae. To Be Published.
Page generated: Wed Dec 16 04:46:01 2020

Last articles

Zn in 7NN0
Zn in 7NIO
Zn in 7LUP
Zn in 7M1Y
Zn in 7LO4
Zn in 7KWO
Zn in 7KJY
Zn in 7KCQ
Zn in 7KC2
Zn in 7KCB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy