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Zinc in PDB 1zy1: X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser

Enzymatic activity of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser

All present enzymatic activity of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser:
3.5.1.88;

Protein crystallography data

The structure of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser, PDB code: 1zy1 was solved by S.Fieulaine, C.Juillan-Binard, A.Serero, F.Dardel, C.Giglione, T.Meinnel, J.-L.Ferrer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.600, 76.300, 109.300, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser (pdb code 1zy1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser, PDB code: 1zy1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1zy1

Go back to Zinc Binding Sites List in 1zy1
Zinc binding site 1 out of 2 in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn198

b:38.5
occ:1.00
O D:HOH4 2.0 51.8 1.0
NE2 A:HIS153 2.1 40.5 1.0
NE2 A:HIS157 2.2 39.1 1.0
SG A:CYS111 2.2 46.1 1.0
O A:HOH199 2.4 16.4 1.0
CE1 A:HIS157 2.9 40.3 1.0
CD2 A:HIS153 2.9 39.0 1.0
CB A:CYS111 3.1 43.4 1.0
NE2 A:GLN54 3.2 43.8 1.0
CE1 A:HIS153 3.2 39.9 1.0
CD2 A:HIS157 3.3 41.3 1.0
CA A:CYS111 3.5 42.5 1.0
N A:LEU112 3.9 43.2 1.0
CD A:GLN54 3.9 41.9 1.0
ND1 A:HIS157 4.1 40.7 1.0
OE1 A:GLN54 4.1 44.5 1.0
CG A:HIS153 4.1 37.9 1.0
N D:MET1 4.2 42.3 1.0
CA D:MET1 4.2 42.1 1.0
C A:CYS111 4.2 42.8 1.0
ND1 A:HIS153 4.2 38.9 1.0
CG A:HIS157 4.3 40.5 1.0
O A:GLY110 4.7 43.8 1.0
N A:CYS111 4.7 42.9 1.0
OE1 A:GLU154 4.8 38.5 1.0
N A:SER113 5.0 45.3 1.0

Zinc binding site 2 out of 2 in 1zy1

Go back to Zinc Binding Sites List in 1zy1
Zinc binding site 2 out of 2 in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A) in Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn198

b:42.4
occ:1.00
NE2 B:HIS157 2.1 42.8 1.0
NE2 B:HIS153 2.2 41.7 1.0
SG B:CYS111 2.3 47.0 1.0
O B:HOH199 2.4 43.4 1.0
CE1 B:HIS157 2.9 43.0 1.0
CD2 B:HIS153 2.9 40.9 1.0
NE2 B:GLN54 3.0 43.9 1.0
CD2 B:HIS157 3.2 43.6 1.0
CB B:CYS111 3.4 44.8 1.0
CE1 B:HIS153 3.4 42.8 1.0
CD B:GLN54 3.7 43.4 1.0
CA B:CYS111 3.7 44.9 1.0
OE1 B:GLN54 3.8 45.1 1.0
ND1 B:HIS157 4.0 42.7 1.0
N B:LEU112 4.0 46.1 1.0
N E:MET1 4.1 54.7 1.0
CG B:HIS157 4.2 42.9 1.0
CG B:HIS153 4.2 41.5 1.0
ND1 B:HIS153 4.4 44.0 1.0
CA E:MET1 4.4 56.5 1.0
C B:CYS111 4.4 45.4 1.0
OE1 B:GLU154 4.5 44.8 1.0
OE2 B:GLU154 4.9 47.7 1.0
O B:GLY110 4.9 46.9 1.0
CG B:GLN54 4.9 41.0 1.0
N B:CYS111 5.0 45.9 1.0

Reference:

S.Fieulaine, C.Juillan-Binard, A.Serero, F.Dardel, C.Giglione, T.Meinnel, J.-L.Ferrer. The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines For the Design of Inhibitors Specific For the Bacterial Forms J.Biol.Chem. V. 280 42315 2005.
ISSN: ISSN 0021-9258
PubMed: 16192279
DOI: 10.1074/JBC.M507155200
Page generated: Wed Dec 16 03:16:17 2020

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