Zinc in PDB 6ck7: Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin:
3.5.1.88;

The structure of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin, PDB code: 6ck7 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.39 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.650, 132.060, 90.380, 90.00, 103.64, 90.00
R / Rfree (%)	18.2 / 20.8

The binding sites of Zinc atom in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin (pdb code 6ck7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin, PDB code: 6ck7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


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 A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.8 occ:1.00 NE2 A:HIS133 2.0 17.4 1.0 NE2 A:HIS137 2.1 14.6 1.0 O4 A:BB2202 2.1 21.0 1.0 O2 A:BB2202 2.1 23.4 1.0 SG A:CYS91 2.3 18.3 1.0 C3 A:BB2202 2.8 23.7 1.0 N1 A:BB2202 3.0 23.5 1.0 CD2 A:HIS133 3.0 19.8 1.0 CE1 A:HIS133 3.0 20.6 1.0 CD2 A:HIS137 3.0 20.4 1.0 CE1 A:HIS137 3.1 19.9 1.0 NE2 A:GLN51 3.3 19.2 1.0 CB A:CYS91 3.4 16.1 1.0 O A:HOH376 3.6 20.8 1.0 CD A:GLN51 3.8 20.1 1.0 CA A:CYS91 3.8 18.4 1.0 OE1 A:GLN51 3.9 19.5 1.0 N A:LEU92 4.1 15.1 1.0 ND1 A:HIS133 4.1 19.0 1.0 CG A:HIS133 4.2 18.3 1.0 C5 A:BB2202 4.2 18.9 1.0 CG A:HIS137 4.2 16.5 1.0 ND1 A:HIS137 4.2 20.3 1.0 C A:CYS91 4.4 17.4 1.0 C6 A:BB2202 4.5 17.6 1.0 O A:HOH356 4.6 20.2 1.0 N A:SER93 4.8 18.1 1.0 CG A:GLN51 4.9 19.1 1.0 C7 A:BB2202 5.0 21.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


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 A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:18.7 occ:1.00 NE2 B:HIS133 2.0 16.9 1.0 O4 B:BB2202 2.1 18.6 1.0 NE2 B:HIS137 2.1 16.9 1.0 O2 B:BB2202 2.3 23.3 1.0 SG B:CYS91 2.4 18.6 1.0 C3 B:BB2202 2.9 21.4 1.0 CD2 B:HIS133 3.0 17.4 1.0 CE1 B:HIS133 3.0 19.4 1.0 CD2 B:HIS137 3.0 22.4 1.0 N1 B:BB2202 3.1 23.5 1.0 CE1 B:HIS137 3.2 20.1 1.0 NE2 B:GLN51 3.3 19.8 1.0 CB B:CYS91 3.4 15.9 1.0 O B:HOH364 3.6 20.5 1.0 CD B:GLN51 3.8 21.5 1.0 CA B:CYS91 3.8 13.4 1.0 OE1 B:GLN51 3.9 20.5 1.0 N B:LEU92 4.1 14.3 1.0 ND1 B:HIS133 4.1 19.0 1.0 CG B:HIS133 4.1 16.9 1.0 CG B:HIS137 4.2 16.6 1.0 C5 B:BB2202 4.2 19.5 1.0 ND1 B:HIS137 4.3 18.7 1.0 C B:CYS91 4.4 14.7 1.0 C6 B:BB2202 4.5 18.4 1.0 O B:HOH367 4.6 17.9 1.0 N B:SER93 4.8 19.2 1.0 CG B:GLN51 4.9 17.6 1.0 C7 B:BB2202 5.0 21.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:21.1 occ:1.00 NE2 C:HIS133 2.0 19.0 1.0 O4 C:BB2202 2.1 23.1 1.0 NE2 C:HIS137 2.1 23.0 1.0 O2 C:BB2202 2.3 23.9 1.0 SG C:CYS91 2.3 18.7 1.0 C3 C:BB2202 2.8 23.2 1.0 CE1 C:HIS133 3.0 18.6 1.0 CD2 C:HIS133 3.0 22.0 1.0 CD2 C:HIS137 3.0 21.6 1.0 N1 C:BB2202 3.0 24.1 1.0 CE1 C:HIS137 3.1 24.0 1.0 NE2 C:GLN51 3.3 19.7 1.0 CB C:CYS91 3.5 17.8 1.0 O C:HOH368 3.6 23.2 1.0 CD C:GLN51 3.8 22.5 1.0 CA C:CYS91 3.9 19.0 1.0 OE1 C:GLN51 3.9 22.8 1.0 N C:LEU92 4.1 15.1 1.0 ND1 C:HIS133 4.1 22.4 1.0 CG C:HIS133 4.1 21.0 1.0 C5 C:BB2202 4.2 20.4 1.0 CG C:HIS137 4.2 21.0 1.0 ND1 C:HIS137 4.2 24.9 1.0 C C:CYS91 4.4 17.8 1.0 C6 C:BB2202 4.5 17.9 1.0 O C:HOH359 4.6 23.9 1.0 N C:SER93 4.8 18.5 1.0 C7 C:BB2202 4.9 22.9 1.0 CG C:GLN51 4.9 19.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:20.9 occ:1.00 NE2 D:HIS133 2.0 19.8 1.0 NE2 D:HIS137 2.1 21.1 1.0 O4 D:BB2202 2.1 22.1 1.0 SG D:CYS91 2.3 19.3 1.0 O2 D:BB2202 2.4 26.5 1.0 C3 D:BB2202 2.9 24.6 1.0 CE1 D:HIS133 3.0 19.7 1.0 CD2 D:HIS133 3.0 18.9 1.0 CD2 D:HIS137 3.1 22.4 1.0 CE1 D:HIS137 3.1 20.0 1.0 N1 D:BB2202 3.1 24.9 1.0 NE2 D:GLN51 3.3 21.8 1.0 CB D:CYS91 3.4 18.4 1.0 O D:HOH378 3.6 21.0 1.0 CD D:GLN51 3.8 21.0 1.0 CA D:CYS91 3.8 18.2 1.0 OE1 D:GLN51 3.9 24.6 1.0 N D:LEU92 4.0 16.8 1.0 ND1 D:HIS133 4.1 21.1 1.0 CG D:HIS133 4.2 17.9 1.0 ND1 D:HIS137 4.2 20.8 1.0 CG D:HIS137 4.2 19.9 1.0 C5 D:BB2202 4.2 22.5 1.0 C D:CYS91 4.4 16.6 1.0 C6 D:BB2202 4.5 20.0 1.0 O D:HOH369 4.6 21.1 1.0 N D:SER93 4.8 20.8 1.0 CG D:GLN51 4.9 18.0 1.0 C7 D:BB2202 4.9 21.6 1.0

T.E.Edwards, P.S.Horanyi, D.D.Lorimer. Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin To Be Published.