Zinc in PDB 4lcp: Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine

The structure of Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine, PDB code: 4lcp was solved by A.Bitra, A.Biswas, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.95 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.212, 74.012, 110.322, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 22.3

The binding sites of Zinc atom in the Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine (pdb code 4lcp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine, PDB code: 4lcp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:20.6 occ:1.00 ND1 A:HIS77 2.0 16.9 1.0 O A:HOH302 2.2 20.3 1.0 SG A:CYS112 2.3 18.2 1.0 SG A:CYS115 2.3 18.3 1.0 CE1 A:HIS77 2.9 17.5 1.0 CG A:HIS77 3.1 17.3 1.0 CB A:CYS115 3.1 15.3 1.0 CB A:CYS112 3.4 17.4 1.0 CB A:HIS77 3.5 15.6 1.0 N A:CYS112 3.8 18.0 1.0 OE2 A:GLU79 3.9 22.0 1.0 N A:CYS115 3.9 16.6 1.0 CE A:MET114 4.0 16.6 1.0 NE2 A:HIS77 4.1 17.8 1.0 CA A:CYS115 4.1 17.0 1.0 OE1 A:GLU79 4.1 20.2 1.0 CA A:CYS112 4.1 17.7 1.0 CD2 A:HIS77 4.2 17.5 1.0 CD A:GLU79 4.2 21.6 1.0 N3 A:6AP202 4.4 57.0 0.9 C4 A:6AP202 4.5 52.3 0.9 C2 A:6AP202 4.6 49.8 0.9 C A:CYS112 4.7 17.6 1.0 O A:CYS112 4.7 17.3 1.0 CB A:MET114 4.8 15.6 1.0 C5 A:6AP202 4.8 60.8 0.9 N1 A:6AP202 4.9 53.4 0.9 N9 A:6AP202 4.9 46.9 0.9 NE1 B:TRP121 5.0 20.0 1.0 C A:PRO111 5.0 19.6 1.0 C A:MET114 5.0 16.9 1.0

Zinc binding site 2 out of 2 in the Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crytsal Structure of NE0047 in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:20.2 occ:1.00 O B:HOH315 2.1 17.9 1.0 ND1 B:HIS77 2.2 14.8 1.0 SG B:CYS115 2.3 16.2 1.0 SG B:CYS112 2.3 15.2 1.0 CE1 B:HIS77 3.1 13.9 1.0 CG B:HIS77 3.1 15.0 1.0 CB B:CYS115 3.2 16.2 1.0 CB B:CYS112 3.4 16.0 1.0 CB B:HIS77 3.5 15.4 1.0 OE2 B:GLU79 3.8 18.6 1.0 N B:CYS115 3.9 15.6 1.0 N B:CYS112 3.9 16.6 1.0 CE B:MET114 3.9 13.7 1.0 OE1 B:GLU79 4.1 16.3 1.0 CA B:CYS115 4.1 16.3 1.0 CA B:CYS112 4.2 14.9 1.0 CD B:GLU79 4.2 16.9 1.0 NE2 B:HIS77 4.3 15.0 1.0 CD2 B:HIS77 4.3 15.3 1.0 C B:CYS112 4.7 16.3 1.0 CB B:MET114 4.7 14.9 1.0 O B:CYS112 4.8 15.2 1.0 NE1 A:TRP121 4.9 21.9 1.0 C B:MET114 4.9 15.6 1.0 CA B:HIS77 5.0 15.4 1.0

A.Bitra, A.Biswas, R.Anand. Structural Basis of the Substrate Specificity of Cytidine Deaminase Superfamily Guanine Deaminase Biochemistry V. 52 8106 2013.
ISSN: ISSN 0006-2960
PubMed: 24083949
DOI: 10.1021/BI400818E