Zinc in PDB 4dr8: Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus:
3.5.1.88;

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus, PDB code: 4dr8 was solved by D.Lorimer, J.Abendroth, T.Craig, A.Burgin, A.Segall, F.Rohwer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.400, 65.360, 69.030, 80.01, 76.38, 81.71
R / Rfree (%)	16.2 / 19.4

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus (pdb code 4dr8). 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 Synechococcus Elongatus, PDB code: 4dr8:
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 Synechococcus Elongatus


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 Synechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:10.5 occ:1.00 NE2 A:HIS151 2.0 7.8 1.0 NE2 A:HIS155 2.0 7.7 1.0 O2 A:FMT203 2.0 14.3 1.0 SG A:CYS109 2.2 10.2 1.0 C A:FMT203 2.4 10.3 1.0 CD2 A:HIS151 3.0 8.3 1.0 CE1 A:HIS155 3.0 8.0 1.0 CE1 A:HIS151 3.0 8.0 1.0 CD2 A:HIS155 3.0 7.7 1.0 CB A:CYS109 3.3 9.7 1.0 O A:HOH302 3.6 10.4 1.0 O1 A:FMT203 3.6 16.8 1.0 NE2 A:GLN66 3.7 8.6 1.0 CA A:CYS109 3.9 9.9 1.0 OE1 A:GLN66 3.9 9.0 1.0 CD A:GLN66 4.0 9.6 1.0 CG A:HIS151 4.1 7.4 1.0 ND1 A:HIS155 4.1 8.4 1.0 OE2 A:GLU152 4.1 11.2 1.0 ND1 A:HIS151 4.1 8.1 1.0 CG A:HIS155 4.2 8.0 1.0 O A:HOH303 4.4 8.8 1.0 N A:LEU110 4.4 9.4 1.0 OE1 A:GLU152 4.5 10.3 1.0 C A:CYS109 4.6 10.1 1.0 CD A:GLU152 4.6 9.2 1.0 O A:GLY108 4.8 11.8 1.0 O A:HOH483 4.8 30.3 1.0 O A:HOH374 5.0 29.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus


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 Synechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:8.6 occ:1.00 NE2 B:HIS151 2.0 7.1 1.0 O2 B:FMT204 2.0 9.3 1.0 NE2 B:HIS155 2.1 7.2 1.0 SG B:CYS109 2.3 6.9 1.0 C B:FMT204 2.4 12.6 1.0 CD2 B:HIS151 3.0 7.1 1.0 CE1 B:HIS155 3.0 7.3 1.0 CD2 B:HIS155 3.1 7.2 1.0 CE1 B:HIS151 3.1 7.2 1.0 CB B:CYS109 3.3 7.3 1.0 O B:HOH301 3.4 7.5 1.0 O1 B:FMT204 3.7 12.3 1.0 NE2 B:GLN66 3.7 7.1 1.0 OE1 B:GLN66 3.9 6.7 1.0 CA B:CYS109 3.9 7.7 1.0 OE2 B:GLU152 3.9 7.2 1.0 CD B:GLN66 4.0 6.9 1.0 CG B:HIS151 4.1 6.8 1.0 ND1 B:HIS151 4.2 7.4 1.0 ND1 B:HIS155 4.2 7.3 1.0 CG B:HIS155 4.2 7.0 1.0 O B:HOH309 4.3 7.5 1.0 OE1 B:GLU152 4.4 7.1 1.0 CD B:GLU152 4.5 6.7 1.0 N B:LEU110 4.6 8.1 1.0 C B:CYS109 4.7 8.0 1.0 O B:GLY108 4.7 8.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus


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 Synechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:9.7 occ:1.00 NE2 C:HIS151 2.0 7.3 1.0 NE2 C:HIS155 2.0 7.8 1.0 O2 C:FMT203 2.1 13.5 1.0 SG C:CYS109 2.3 8.4 1.0 C C:FMT203 2.4 11.2 1.0 CD2 C:HIS151 3.0 7.5 1.0 CE1 C:HIS155 3.0 7.8 1.0 CE1 C:HIS151 3.0 7.9 1.0 CD2 C:HIS155 3.1 7.7 1.0 CB C:CYS109 3.3 8.6 1.0 O C:HOH308 3.5 9.2 1.0 O1 C:FMT203 3.6 16.4 1.0 NE2 C:GLN66 3.7 9.0 1.0 CA C:CYS109 3.9 8.9 1.0 OE1 C:GLN66 3.9 8.9 1.0 CD C:GLN66 4.0 8.8 1.0 OE2 C:GLU152 4.1 9.1 1.0 ND1 C:HIS151 4.2 7.8 1.0 CG C:HIS151 4.2 7.6 1.0 ND1 C:HIS155 4.2 8.0 1.0 CG C:HIS155 4.2 7.8 1.0 O C:HOH304 4.4 8.2 1.0 OE1 C:GLU152 4.5 7.9 1.0 N C:LEU110 4.5 8.9 1.0 CD C:GLU152 4.6 8.1 1.0 C C:CYS109 4.7 9.0 1.0 O C:GLY108 4.7 10.7 1.0 O C:HOH343 5.0 27.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus


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 Synechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:9.8 occ:1.00 NE2 D:HIS155 2.0 7.5 1.0 NE2 D:HIS151 2.0 7.8 1.0 O2 D:FMT202 2.1 14.4 1.0 SG D:CYS109 2.3 9.4 1.0 C D:FMT202 2.3 10.4 1.0 CD2 D:HIS151 2.9 7.8 1.0 CD2 D:HIS155 3.0 7.6 1.0 CE1 D:HIS151 3.0 8.2 1.0 CE1 D:HIS155 3.0 7.6 1.0 CB D:CYS109 3.3 9.9 1.0 O D:HOH303 3.5 7.9 1.0 O1 D:FMT202 3.6 17.6 1.0 NE2 D:GLN66 3.6 8.2 1.0 CA D:CYS109 3.8 10.2 1.0 OE1 D:GLN66 4.0 7.4 1.0 CD D:GLN66 4.0 7.5 1.0 CG D:HIS151 4.1 7.8 1.0 OE2 D:GLU152 4.1 10.1 1.0 ND1 D:HIS155 4.2 7.5 1.0 CG D:HIS155 4.2 7.2 1.0 ND1 D:HIS151 4.2 7.9 1.0 O D:HOH302 4.4 8.3 1.0 N D:LEU110 4.4 10.0 1.0 C D:CYS109 4.5 10.0 1.0 OE1 D:GLU152 4.6 8.8 1.0 O D:GLY108 4.6 11.8 1.0 CD D:GLU152 4.7 8.7 1.0 N D:CYS109 5.0 10.6 1.0

J.A.Frank, D.Lorimer, M.Youle, P.Witte, T.Craig, J.Abendroth, F.Rohwer, R.A.Edwards, A.M.Segall, A.B.Burgin. Structure and Function of A Cyanophage-Encoded Peptide Deformylase. Isme J V. 7 1150 2013.
ISSN: ISSN 1751-7362
PubMed: 23407310
DOI: 10.1038/ISMEJ.2013.4