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Zinc in PDB 1bs5: Peptide Deformylase As ZN2+ Containing Form

Enzymatic activity of Peptide Deformylase As ZN2+ Containing Form

All present enzymatic activity of Peptide Deformylase As ZN2+ Containing Form:
3.5.1.31;

Protein crystallography data

The structure of Peptide Deformylase As ZN2+ Containing Form, PDB code: 1bs5 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 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.400, 64.100, 84.600, 90.00, 123.20, 90.00
R / Rfree (%) 20.8 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Peptide Deformylase As ZN2+ Containing Form (pdb code 1bs5). 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, PDB code: 1bs5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1bs5

Go back to Zinc Binding Sites List in 1bs5
Zinc binding site 1 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:26.1
occ:1.00
NE2 A:HIS132 2.0 23.3 1.0
SG A:CYS90 2.1 26.3 1.0
NE2 A:HIS136 2.2 17.5 1.0
O A:HOH2034 2.2 20.2 1.0
CD2 A:HIS132 3.0 21.0 1.0
CE1 A:HIS132 3.0 23.0 1.0
CD2 A:HIS136 3.1 17.9 1.0
CE1 A:HIS136 3.1 18.4 1.0
O A:HOH2021 3.1 44.5 1.0
CB A:CYS90 3.3 26.4 1.0
NE2 A:GLN50 3.7 24.0 1.0
CA A:CYS90 3.8 28.8 1.0
OE1 A:GLN50 4.0 26.3 1.0
CD A:GLN50 4.0 26.9 1.0
O A:HOH2024 4.1 35.3 1.0
ND1 A:HIS132 4.1 22.7 1.0
CG A:HIS132 4.1 19.8 1.0
OE2 A:GLU133 4.2 23.1 1.0
ND1 A:HIS136 4.3 15.9 1.0
CG A:HIS136 4.3 18.1 1.0
O A:GLY89 4.5 30.7 1.0
N A:LEU91 4.6 29.6 1.0
C A:CYS90 4.6 29.3 1.0
OE1 A:GLU133 4.6 25.4 1.0
O A:HOH2007 4.7 26.1 1.0
CD A:GLU133 4.8 23.5 1.0
N A:CYS90 5.0 30.5 1.0

Zinc binding site 2 out of 3 in 1bs5

Go back to Zinc Binding Sites List in 1bs5
Zinc binding site 2 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:21.8
occ:1.00
O B:HOH3004 1.8 8.3 1.0
NE2 B:HIS636 2.1 14.9 1.0
NE2 B:HIS632 2.1 22.3 1.0
SG B:CYS590 2.1 22.8 1.0
CD2 B:HIS632 3.0 21.1 1.0
CE1 B:HIS636 3.0 16.6 1.0
CE1 B:HIS632 3.1 21.0 1.0
CD2 B:HIS636 3.1 15.5 1.0
CB B:CYS590 3.3 24.1 1.0
NE2 B:GLN550 3.6 20.1 1.0
O B:HOH60 3.7 15.8 1.0
O B:HOH114 3.7 24.7 1.0
CA B:CYS590 3.8 26.3 1.0
OE1 B:GLN550 4.0 22.8 1.0
CD B:GLN550 4.0 23.3 1.0
ND1 B:HIS636 4.1 12.6 1.0
CG B:HIS632 4.2 20.0 1.0
ND1 B:HIS632 4.2 21.5 1.0
OE2 B:GLU633 4.2 19.6 1.0
CG B:HIS636 4.2 15.1 1.0
O B:HOH4 4.4 6.2 1.0
O B:GLY589 4.6 27.3 1.0
OE1 B:GLU633 4.6 23.4 1.0
N B:LEU591 4.6 26.1 1.0
C B:CYS590 4.7 25.9 1.0
CD B:GLU633 4.8 22.2 1.0

Zinc binding site 3 out of 3 in 1bs5

Go back to Zinc Binding Sites List in 1bs5
Zinc binding site 3 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:22.9
occ:1.00
O C:HOH3005 1.8 22.2 1.0
NE2 C:HIS1136 2.1 13.9 1.0
SG C:CYS1090 2.1 22.4 1.0
NE2 C:HIS1132 2.1 22.5 1.0
CE1 C:HIS1136 3.0 13.7 1.0
CD2 C:HIS1132 3.1 21.4 1.0
CD2 C:HIS1136 3.1 13.0 1.0
CE1 C:HIS1132 3.2 21.9 1.0
CB C:CYS1090 3.3 24.5 1.0
NE2 C:GLN1050 3.6 23.1 1.0
O C:HOH43 3.8 19.0 1.0
CA C:CYS1090 3.8 25.6 1.0
OE1 C:GLN1050 3.8 23.3 1.0
CD C:GLN1050 3.9 24.4 1.0
ND1 C:HIS1136 4.1 12.6 1.0
OE2 C:GLU1133 4.2 20.6 1.0
CG C:HIS1136 4.2 14.8 1.0
CG C:HIS1132 4.2 20.7 1.0
ND1 C:HIS1132 4.3 22.5 1.0
N C:LEU1091 4.6 25.3 1.0
O C:HOH102 4.6 15.6 1.0
O C:GLY1089 4.6 28.5 1.0
C C:CYS1090 4.6 25.5 1.0
OE1 C:GLU1133 4.7 21.4 1.0
CD C:GLU1133 4.8 21.2 1.0
O C:HOH51 4.9 29.2 1.0
CG C:GLN1050 5.0 26.5 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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