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Zinc in PDB 1bs4: Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol

Enzymatic activity of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol

All present enzymatic activity of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol:
3.5.1.31;

Protein crystallography data

The structure of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol, PDB code: 1bs4 was solved by A.Becker, I.Schlichting, W.Kabsch, D.Groche, S.Schultz, A.F.V.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.700, 63.300, 86.800, 90.00, 120.60, 90.00
R / Rfree (%) 19.3 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol (pdb code 1bs4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol, PDB code: 1bs4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1bs4

Go back to Zinc Binding Sites List in 1bs4
Zinc binding site 1 out of 3 in the Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:19.8
occ:1.00
O A:HOH8068 1.8 18.7 1.0
NE2 A:HIS136 2.0 16.9 1.0
NE2 A:HIS132 2.1 12.9 1.0
SG A:CYS90 2.3 19.4 1.0
CD2 A:HIS136 3.0 17.0 1.0
CD2 A:HIS132 3.0 16.0 1.0
CE1 A:HIS136 3.0 18.0 1.0
CE1 A:HIS132 3.1 15.8 1.0
CB A:CYS90 3.3 18.4 1.0
O A:HOH8006 3.6 16.5 1.0
NE2 A:GLN50 3.7 18.0 1.0
OE1 A:GLN50 3.8 20.6 1.0
O A:HOH8004 3.9 24.6 1.0
CA A:CYS90 3.9 19.5 1.0
CD A:GLN50 3.9 19.8 1.0
OE2 A:GLU133 4.0 18.5 1.0
ND1 A:HIS136 4.1 17.5 1.0
CG A:HIS136 4.1 16.5 1.0
ND1 A:HIS132 4.2 14.9 1.0
CG A:HIS132 4.2 15.3 1.0
O A:HOH8007 4.5 15.0 1.0
OE1 A:GLU133 4.5 17.0 1.0
CD A:GLU133 4.6 17.7 1.0
O A:GLY89 4.6 17.2 1.0
N A:LEU91 4.6 19.6 1.0
C A:CYS90 4.7 19.2 1.0
C14 A:2PE170 4.9 35.5 1.0
C15 A:2PE170 4.9 38.3 1.0

Zinc binding site 2 out of 3 in 1bs4

Go back to Zinc Binding Sites List in 1bs4
Zinc binding site 2 out of 3 in the Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:16.8
occ:1.00
O B:HOH9254 1.9 14.0 1.0
NE2 B:HIS632 2.0 14.8 1.0
NE2 B:HIS636 2.1 16.6 1.0
SG B:CYS590 2.3 14.1 1.0
CD2 B:HIS632 3.0 14.0 1.0
CE1 B:HIS636 3.0 15.7 1.0
CE1 B:HIS632 3.1 15.7 1.0
CD2 B:HIS636 3.1 15.3 1.0
CB B:CYS590 3.3 14.2 1.0
O B:HOH9006 3.5 13.5 1.0
NE2 B:GLN550 3.7 15.4 1.0
O B:HOH9004 3.8 14.2 1.0
OE1 B:GLN550 3.9 16.3 1.0
CA B:CYS590 3.9 15.8 1.0
CD B:GLN550 4.0 16.6 1.0
OE2 B:GLU633 4.0 12.4 1.0
CG B:HIS632 4.1 15.3 1.0
ND1 B:HIS636 4.1 14.2 1.0
ND1 B:HIS632 4.1 14.7 1.0
CG B:HIS636 4.2 14.2 1.0
O B:HOH9007 4.4 13.6 1.0
OE1 B:GLU633 4.4 14.5 1.0
CD B:GLU633 4.5 13.4 1.0
O B:GLY589 4.6 15.7 1.0
N B:LEU591 4.7 15.7 1.0
C B:CYS590 4.7 15.7 1.0
O16 B:2PE2 4.9 41.5 1.0
C15 B:2PE2 5.0 42.9 1.0

Zinc binding site 3 out of 3 in 1bs4

Go back to Zinc Binding Sites List in 1bs4
Zinc binding site 3 out of 3 in the Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Peptide Deformylase As ZN2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:20.6
occ:1.00
O C:HOH9255 2.0 13.4 1.0
NE2 C:HIS1132 2.1 17.5 1.0
NE2 C:HIS1136 2.1 18.1 1.0
SG C:CYS1090 2.2 17.5 1.0
CD2 C:HIS1132 3.0 17.5 1.0
CD2 C:HIS1136 3.0 16.4 1.0
CE1 C:HIS1136 3.1 17.8 1.0
CE1 C:HIS1132 3.1 18.6 1.0
CB C:CYS1090 3.3 17.6 1.0
O C:HOH7 3.5 22.7 1.0
NE2 C:GLN1050 3.7 17.2 1.0
OE1 C:GLN1050 3.8 17.9 1.0
O C:HOH7004 3.8 20.4 1.0
CD C:GLN1050 3.9 16.7 1.0
CA C:CYS1090 3.9 19.0 1.0
OE2 C:GLU1133 4.1 16.1 1.0
CG C:HIS1132 4.2 17.3 1.0
ND1 C:HIS1136 4.2 16.1 1.0
CG C:HIS1136 4.2 16.3 1.0
ND1 C:HIS1132 4.2 17.3 1.0
O C:HOH7007 4.4 17.3 1.0
OE1 C:GLU1133 4.4 15.5 1.0
O C:GLY1089 4.6 21.5 1.0
CD C:GLU1133 4.6 14.4 1.0
N C:LEU1091 4.7 19.8 1.0
C12 C:2PE3 4.8 44.3 1.0
C C:CYS1090 4.8 18.8 1.0
C11 C:2PE3 4.8 45.3 1.0

Reference:

A.Becker, I.Schlichting, W.Kabsch, D.Groche, S.Schultz, A.F.Wagner. Iron Center, Substrate Recognition and Mechanism of Peptide Deformylase. Nat.Struct.Biol. V. 5 1053 1998.
ISSN: ISSN 1072-8368
PubMed: 9846875
DOI: 10.1038/4162
Page generated: Wed Dec 16 02:45:59 2020

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