Zinc in PDB 4je8: Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser

All present enzymatic activity of Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser:
3.5.1.88;

The structure of Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser, PDB code: 4je8 was solved by S.Fieulaine, T.Meinnel, C.Giglione, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.68 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.550, 74.710, 109.760, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 25.1

The binding sites of Zinc atom in the Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser (pdb code 4je8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser, PDB code: 4je8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser


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 Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:35.3 occ:1.00 NE2 A:HIS157 2.1 14.6 1.0 NE2 A:HIS153 2.3 17.0 1.0 O A:HOH301 2.4 29.6 1.0 SG A:CYS111 2.5 13.9 1.0 CD2 A:HIS153 2.9 13.8 1.0 CE1 A:HIS157 3.1 10.1 1.0 CD2 A:HIS157 3.2 17.2 1.0 CE1 A:HIS153 3.4 18.8 1.0 CB A:CYS111 3.5 12.8 1.0 NE2 A:GLN54 3.6 13.1 1.0 OE2 A:GLU112 3.7 19.0 1.0 O A:HOH326 3.7 33.4 1.0 OE1 A:GLU154 3.9 19.0 1.0 CA A:CYS111 3.9 13.5 1.0 CD A:GLN54 4.0 13.6 1.0 OE1 A:GLN54 4.1 18.8 1.0 CG A:HIS153 4.1 17.1 1.0 ND1 A:HIS157 4.2 9.2 1.0 CG A:HIS157 4.3 16.0 1.0 O A:HOH306 4.4 22.1 1.0 ND1 A:HIS153 4.4 19.3 1.0 N A:GLU112 4.5 14.4 1.0 C A:CYS111 4.7 14.7 1.0 CD A:GLU112 4.7 19.8 1.0 CD A:GLU154 4.8 19.9 1.0 N D:MET1 4.8 38.5 1.0 CA D:MET1 4.8 37.5 1.0 O A:GLY110 4.9 16.9 1.0 OE2 A:GLU154 4.9 19.3 1.0 O A:HIS153 4.9 14.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser


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 Human-Like Mitochondrial Peptide Deformylase in Complex with Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:36.7 occ:1.00 SG B:CYS111 2.1 22.4 1.0 NE2 B:HIS153 2.1 14.5 1.0 NE2 B:HIS157 2.2 17.4 1.0 O B:HOH301 2.5 36.0 1.0 CD2 B:HIS153 2.9 17.8 1.0 CD2 B:HIS157 3.1 12.7 1.0 CE1 B:HIS157 3.2 14.7 1.0 CE1 B:HIS153 3.3 21.1 1.0 CB B:CYS111 3.3 19.8 1.0 OE1 B:GLU112 3.5 34.3 1.0 O B:HOH318 3.7 27.1 1.0 NE2 B:GLN54 3.9 18.2 1.0 CA B:CYS111 4.0 21.6 1.0 OE1 B:GLN54 4.1 24.5 1.0 CG B:HIS153 4.1 19.9 1.0 CD B:GLN54 4.2 20.1 1.0 ND1 B:HIS153 4.3 21.3 1.0 ND1 B:HIS157 4.3 22.6 1.0 CG B:HIS157 4.3 21.9 1.0 N E:MET1 4.3 41.6 1.0 OE1 B:GLU154 4.4 40.4 1.0 O B:HOH372 4.5 30.6 1.0 N B:GLU112 4.5 23.5 1.0 CA E:MET1 4.5 41.9 1.0 CD B:GLU112 4.6 31.7 1.0 OE2 B:GLU154 4.6 39.5 1.0 C B:CYS111 4.8 22.7 1.0 O B:GLY110 4.8 20.6 1.0 OE2 B:GLU112 4.8 37.8 1.0 O B:HIS153 4.9 18.9 1.0 CD B:GLU154 4.9 38.7 1.0

S.Fieulaine, M.Desmadril, T.Meinnel, C.Giglione. Understanding the Highly Efficient Catalysis of Prokaryotic Peptide Deformylases By Shedding Light on the Determinants Specifying the Low Activity of the Human Counterpart. Acta Crystallogr.,Sect.D V. 70 242 2014.
ISSN: ISSN 0907-4449
PubMed: 24531459
DOI: 10.1107/S1399004713026461