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Zinc in PDB 1n5n: Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 1n5n was solved by A.Kreusch, G.Spraggon, C.C.Lee, H.Klock, D.Mcmullan, K.Ng, T.Shin, J.Vincent, I.Warner, C.Ericson, S.A.Lesley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.87 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.612, 73.562, 75.995, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 1n5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 1n5n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1n5n

Go back to Zinc Binding Sites List in 1n5n
Zinc binding site 1 out of 2 in the Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa


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 Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:15.6
occ:1.00
NE2 A:HIS134 2.0 12.4 1.0
NE2 A:HIS138 2.0 13.0 1.0
O A:HOH402 2.2 8.9 1.0
SG A:CYS92 2.3 15.6 1.0
CD2 A:HIS134 2.9 16.4 1.0
CE1 A:HIS138 3.0 19.7 1.0
CD2 A:HIS138 3.0 13.1 1.0
CE1 A:HIS134 3.0 16.0 1.0
CB A:CYS92 3.3 14.3 1.0
O A:HOH409 3.5 20.3 1.0
NE2 A:GLN51 3.6 12.8 1.0
CA A:CYS92 3.7 10.6 1.0
CD A:GLN51 4.0 15.0 1.0
CG A:HIS134 4.1 13.6 1.0
OE1 A:GLN51 4.1 16.9 1.0
ND1 A:HIS134 4.1 17.6 1.0
ND1 A:HIS138 4.2 13.8 1.0
N A:LEU93 4.2 11.8 1.0
CG A:HIS138 4.2 10.4 1.0
OE2 A:GLU135 4.2 17.8 1.0
C A:CYS92 4.4 14.3 1.0
O A:HOH410 4.5 11.2 1.0
O A:GLY91 4.5 16.2 1.0
OE1 A:GLU135 4.5 17.0 1.0
CD A:GLU135 4.7 24.3 1.0
N A:SER94 4.8 14.7 1.0
N A:CYS92 4.9 12.4 1.0

Zinc binding site 2 out of 2 in 1n5n

Go back to Zinc Binding Sites List in 1n5n
Zinc binding site 2 out of 2 in the Crystal Structure of Peptide Deformylase From Pseudomonas Aeruginosa


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 Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.3
occ:1.00
NE2 B:HIS138 2.0 12.6 1.0
NE2 B:HIS134 2.0 12.1 1.0
O B:HOH403 2.2 14.3 1.0
SG B:CYS92 2.3 16.6 1.0
CD2 B:HIS134 2.9 15.4 1.0
CD2 B:HIS138 3.0 13.2 1.0
CE1 B:HIS138 3.0 14.9 1.0
CE1 B:HIS134 3.1 13.2 1.0
CB B:CYS92 3.3 14.4 1.0
O B:HOH421 3.5 15.5 1.0
O B:HOH506 3.7 27.3 1.0
NE2 B:GLN51 3.7 14.3 1.0
CA B:CYS92 3.7 12.0 1.0
OE1 B:GLN51 4.0 16.7 1.0
CD B:GLN51 4.0 18.0 1.0
CG B:HIS134 4.1 15.7 1.0
ND1 B:HIS138 4.1 12.0 1.0
OE2 B:GLU135 4.1 17.6 1.0
CG B:HIS138 4.1 11.2 1.0
ND1 B:HIS134 4.2 14.1 1.0
N B:LEU93 4.3 12.0 1.0
C B:CYS92 4.4 15.4 1.0
O B:HOH405 4.4 14.5 1.0
OE1 B:GLU135 4.5 17.9 1.0
CD B:GLU135 4.6 14.1 1.0
O B:GLY91 4.6 18.0 1.0
C1 B:GOL302 4.9 42.4 1.0
N B:SER94 5.0 16.4 1.0
N B:CYS92 5.0 13.7 1.0
CG B:GLN51 5.0 13.2 1.0

Reference:

A.Kreusch, G.Spraggon, C.C.Lee, H.Klock, D.Mcmullan, K.Ng, T.Shin, J.Vincent, I.Warner, C.Ericson, S.A.Lesley. Structure Analysis of Peptide Deformylases From Streptococcus Pneumoniae,Staphylococcus Aureus, Thermotoga Maritima, and Pseudomonas Aeruginosa: Snapshots of the Oxygen Sensitivity of Peptide Deformylase J.Mol.Biol. V. 330 309 2003.
ISSN: ISSN 0022-2836
PubMed: 12823970
DOI: 10.1016/S0022-2836(03)00596-5
Page generated: Thu Oct 29 07:28:36 2020
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