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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

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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: Sat Oct 26 12:17:50 2024

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