Zinc in PDB 6jev: K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii

Enzymatic activity of K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii

All present enzymatic activity of K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii:
3.5.1.88;

Protein crystallography data

The structure of K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii, PDB code: 6jev was solved by I.H.Lee, T.H.Ho, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.58 / 1.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 40.062, 40.062, 188.271, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii (pdb code 6jev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii, PDB code: 6jev:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6jev

Go back to Zinc Binding Sites List in 6jev
Zinc binding site 1 out of 2 in the K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:19.1
occ:1.00
O21 A:K2U202 2.0 27.2 1.0
NE2 A:HIS138 2.0 15.5 1.0
NE2 A:HIS134 2.1 17.9 1.0
SG A:CYS92 2.3 18.3 1.0
C1 A:K2U202 2.8 44.2 1.0
CD2 A:HIS134 3.0 19.6 1.0
CD2 A:HIS138 3.0 14.8 1.0
CE1 A:HIS138 3.1 16.6 1.0
CE1 A:HIS134 3.1 22.4 1.0
CB A:CYS92 3.3 20.0 1.0
O22 A:K2U202 3.5 32.7 1.0
O A:HOH310 3.5 20.1 1.0
NE2 A:GLN51 3.8 17.9 1.0
CA A:CYS92 3.9 19.1 1.0
OE1 A:GLN51 3.9 16.1 1.0
C2 A:K2U202 4.0 55.1 1.0
CD A:GLN51 4.0 17.8 1.0
OE2 A:GLU135 4.1 21.6 1.0
CG A:HIS134 4.1 17.9 1.0
CG A:HIS138 4.1 15.6 1.0
ND1 A:HIS138 4.2 17.1 1.0
ND1 A:HIS134 4.2 19.3 1.0
O A:HOH309 4.4 16.2 1.0
C3 A:K2U202 4.4 57.3 1.0
OE1 A:GLU135 4.5 20.3 1.0
CD A:GLU135 4.6 19.6 1.0
N A:LEU93 4.6 19.7 1.0
O A:GLY91 4.6 21.2 1.0
C A:CYS92 4.6 19.6 1.0
C4 A:K2U202 4.8 54.6 1.0

Zinc binding site 2 out of 2 in 6jev

Go back to Zinc Binding Sites List in 6jev
Zinc binding site 2 out of 2 in the K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of K2U Bound Crystal Structure of Class I Type A Peptide Deformylase From Acinetobacter Baumanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:19.4
occ:1.00
O21 B:K2U202 2.1 31.3 1.0
NE2 B:HIS134 2.1 19.2 1.0
NE2 B:HIS138 2.1 17.3 1.0
SG B:CYS92 2.3 18.8 1.0
C1 B:K2U202 3.0 41.2 1.0
CD2 B:HIS134 3.0 20.2 1.0
CD2 B:HIS138 3.1 15.4 1.0
CE1 B:HIS138 3.1 16.1 1.0
CE1 B:HIS134 3.1 23.5 1.0
CB B:CYS92 3.3 19.1 1.0
O B:HOH310 3.4 21.1 1.0
O22 B:K2U202 3.6 33.8 1.0
NE2 B:GLN51 3.8 16.4 1.0
CA B:CYS92 3.9 18.8 1.0
OE1 B:GLN51 3.9 15.8 1.0
CD B:GLN51 4.0 17.8 1.0
OE2 B:GLU135 4.1 22.2 1.0
C2 B:K2U202 4.1 52.8 1.0
CG B:HIS134 4.2 18.7 1.0
ND1 B:HIS134 4.2 19.9 1.0
ND1 B:HIS138 4.2 17.7 1.0
CG B:HIS138 4.2 16.2 1.0
O B:HOH308 4.4 18.0 1.0
OE1 B:GLU135 4.5 21.2 1.0
C3 B:K2U202 4.6 55.6 1.0
CD B:GLU135 4.6 19.7 1.0
N B:LEU93 4.6 20.2 1.0
C B:CYS92 4.7 20.5 1.0
O B:GLY91 4.7 20.6 1.0
C4 B:K2U202 4.7 51.9 1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K2U Bound Crystal Peptide Deformylase From Acinetobacter Baumanii To Be Published.
Page generated: Wed Dec 16 12:04:18 2020

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