Zinc in PDB 6jf8: K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii

All present enzymatic activity of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii:
3.5.1.88;

The structure of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf8 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)	49.99 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.158, 40.034, 111.051, 90.00, 90.02, 90.00
R / Rfree (%)	17.2 / 21.1

The binding sites of Zinc atom in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii (pdb code 6jf8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:23.5 occ:1.00 O1 A:LHY202 1.9 30.4 1.0 NE2 A:HIS145 2.1 18.9 1.0 NE2 A:HIS149 2.1 19.9 1.0 SG A:CYS103 2.3 23.4 1.0 O2 A:LHY202 2.4 55.9 1.0 C1 A:LHY202 2.7 32.0 1.0 N2 A:LHY202 2.8 24.9 1.0 CE1 A:HIS145 3.1 20.6 1.0 CD2 A:HIS145 3.1 17.6 1.0 CD2 A:HIS149 3.1 19.3 1.0 CE1 A:HIS149 3.1 19.7 1.0 CB A:CYS103 3.3 25.8 1.0 NE2 A:GLN55 3.5 16.7 1.0 O A:HOH338 3.5 22.9 1.0 CA A:CYS103 3.7 25.8 1.0 N A:LHY202 3.9 32.7 1.0 CD A:GLN55 4.1 19.6 1.0 ND1 A:HIS145 4.2 20.3 1.0 CG A:HIS145 4.2 17.4 1.0 N A:LEU104 4.2 22.6 1.0 ND1 A:HIS149 4.2 19.4 1.0 CG A:HIS149 4.2 16.0 1.0 CA A:LHY202 4.3 33.1 1.0 OE1 A:GLN55 4.4 20.1 1.0 C A:CYS103 4.4 27.3 1.0 O A:HOH331 4.4 20.7 1.0 O A:GLY102 4.7 28.2 1.0 N A:SER105 4.9 23.1 1.0 OE2 A:GLU146 4.9 22.2 1.0 N A:CYS103 5.0 27.1 1.0

Zinc binding site 2 out of 4 in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:20.9 occ:1.00 NE2 B:HIS145 2.0 15.4 1.0 NE2 B:HIS149 2.1 15.5 1.0 O1 B:LHY202 2.2 25.6 1.0 O2 B:LHY202 2.2 51.3 1.0 SG B:CYS103 2.3 20.8 1.0 N2 B:LHY202 2.9 24.1 1.0 C1 B:LHY202 2.9 28.3 1.0 CD2 B:HIS145 3.0 18.1 1.0 CE1 B:HIS145 3.0 20.4 1.0 CE1 B:HIS149 3.1 16.2 1.0 CD2 B:HIS149 3.1 17.0 1.0 CB B:CYS103 3.3 21.3 1.0 NE2 B:GLN55 3.4 19.0 1.0 O B:HOH326 3.5 20.7 1.0 CA B:CYS103 3.7 19.8 1.0 CD B:GLN55 4.0 17.8 1.0 N B:LHY202 4.1 28.8 1.0 CG B:HIS145 4.1 17.2 1.0 ND1 B:HIS145 4.2 19.9 1.0 ND1 B:HIS149 4.2 14.3 1.0 OE1 B:GLN55 4.2 17.7 1.0 CG B:HIS149 4.3 14.8 1.0 N B:LEU104 4.3 21.7 1.0 CA B:LHY202 4.4 29.5 1.0 C B:CYS103 4.5 21.4 1.0 O B:HOH323 4.5 20.2 1.0 O B:GLY102 4.6 22.3 1.0 OE1 B:GLU146 4.9 19.9 1.0 OE2 B:GLU146 4.9 22.7 1.0 N B:SER105 4.9 23.6 1.0 N B:CYS103 4.9 22.7 1.0

Zinc binding site 3 out of 4 in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.0 occ:1.00 O1 C:LHY202 1.9 28.8 1.0 NE2 C:HIS145 2.1 21.1 1.0 NE2 C:HIS149 2.1 20.6 1.0 SG C:CYS103 2.3 21.8 1.0 O2 C:LHY202 2.6 53.1 1.0 C1 C:LHY202 2.7 30.6 1.0 N2 C:LHY202 2.8 23.6 1.0 CD2 C:HIS145 3.1 18.5 1.0 CE1 C:HIS145 3.1 22.3 1.0 CD2 C:HIS149 3.1 18.8 1.0 CE1 C:HIS149 3.1 18.8 1.0 CB C:CYS103 3.3 24.8 1.0 NE2 C:GLN55 3.4 18.8 1.0 O C:HOH341 3.5 23.7 1.0 CA C:CYS103 3.7 25.1 1.0 N C:LHY202 3.9 32.4 1.0 CD C:GLN55 4.1 20.3 1.0 ND1 C:HIS145 4.2 21.0 1.0 N C:LEU104 4.2 23.4 1.0 CG C:HIS145 4.2 18.6 1.0 ND1 C:HIS149 4.2 17.4 1.0 CG C:HIS149 4.2 15.9 1.0 CA C:LHY202 4.3 31.8 1.0 C C:CYS103 4.4 27.0 1.0 OE1 C:GLN55 4.4 19.0 1.0 O C:HOH340 4.5 19.9 1.0 O C:GLY102 4.7 29.2 1.0 OE2 C:GLU146 4.9 22.0 1.0 N C:SER105 4.9 22.3 1.0 N C:CYS103 4.9 27.3 1.0 OE1 C:GLU146 5.0 21.1 1.0

Zinc binding site 4 out of 4 in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:21.2 occ:1.00 O2 D:LHY202 1.7 39.8 1.0 NE2 D:HIS145 2.0 16.5 1.0 NE2 D:HIS149 2.1 15.9 1.0 O1 D:LHY202 2.1 26.5 1.0 SG D:CYS103 2.3 20.5 1.0 N2 D:LHY202 2.9 24.2 1.0 C1 D:LHY202 3.0 26.8 1.0 CD2 D:HIS145 3.0 18.2 1.0 CE1 D:HIS149 3.0 16.8 1.0 CE1 D:HIS145 3.1 20.0 1.0 CD2 D:HIS149 3.2 17.4 1.0 CB D:CYS103 3.4 20.5 1.0 NE2 D:GLN55 3.5 19.2 1.0 O D:HOH325 3.5 19.8 1.0 CA D:CYS103 3.7 19.7 1.0 CD D:GLN55 4.0 17.0 1.0 N D:LHY202 4.1 31.9 1.0 CG D:HIS145 4.2 17.7 1.0 ND1 D:HIS149 4.2 15.4 1.0 ND1 D:HIS145 4.2 19.8 1.0 CG D:HIS149 4.2 15.0 1.0 OE1 D:GLN55 4.2 17.2 1.0 N D:LEU104 4.3 21.7 1.0 CA D:LHY202 4.4 30.8 1.0 C D:CYS103 4.4 20.9 1.0 O D:HOH320 4.5 20.5 1.0 O D:GLY102 4.6 22.9 1.0 OE1 D:GLU146 4.8 19.6 1.0 OE2 D:GLU146 4.9 22.7 1.0 N D:CYS103 4.9 22.3 1.0 N D:SER105 4.9 23.7 1.0

I.H.Lee, T.H.Ho, L.W.Kang. K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii To Be Published.