Zinc in PDB 4lcn: Crytsal Structure of NE0047 in Complex with 2'-Deoxy-Guanosine

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

Resolution Low / High (Å)	34.76 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.020, 73.310, 109.590, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.7

The binding sites of Zinc atom in the Crytsal Structure of NE0047 in Complex with 2'-Deoxy-Guanosine (pdb code 4lcn). 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'-Deoxy-Guanosine, PDB code: 4lcn:
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'-Deoxy-Guanosine


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'-Deoxy-Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.5 occ:1.00 O A:HOH362 2.1 19.8 1.0 ND1 A:HIS77 2.1 16.4 1.0 SG A:CYS112 2.3 17.9 1.0 SG A:CYS115 2.4 17.8 1.0 CE1 A:HIS77 3.0 17.9 1.0 CB A:CYS115 3.1 16.3 1.0 CG A:HIS77 3.1 15.7 1.0 CB A:CYS112 3.5 18.5 1.0 CB A:HIS77 3.5 13.9 1.0 N A:CYS112 3.9 16.6 1.0 N A:CYS115 3.9 14.8 1.0 OE2 A:GLU79 3.9 20.9 1.0 CE A:MET114 3.9 13.6 1.0 CA A:CYS115 4.1 14.9 1.0 CA A:CYS112 4.2 16.3 1.0 NE2 A:HIS77 4.2 16.9 1.0 N3 A:GNG202 4.2 34.0 1.0 C4 A:GNG202 4.2 36.5 1.0 CD2 A:HIS77 4.3 16.3 1.0 OE1 A:GLU79 4.3 17.4 1.0 C2 A:GNG202 4.4 35.8 1.0 CD A:GLU79 4.4 17.1 1.0 C5 A:GNG202 4.4 34.3 1.0 O A:CYS112 4.5 15.3 1.0 C A:CYS112 4.6 17.3 1.0 CB A:MET114 4.6 13.9 1.0 C6 A:GNG202 4.6 29.9 1.0 N1 A:GNG202 4.6 31.4 1.0 N9 A:GNG202 4.7 37.1 1.0 O4' A:GNG202 4.9 54.2 1.0 C A:MET114 4.9 15.5 1.0 N2 A:GNG202 5.0 35.7 1.0 C A:PRO111 5.0 15.7 1.0

Zinc binding site 2 out of 2 in the Crytsal Structure of NE0047 in Complex with 2'-Deoxy-Guanosine


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'-Deoxy-Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:17.3 occ:1.00 ND1 B:HIS77 2.0 12.2 1.0 O B:HOH303 2.1 17.5 1.0 SG B:CYS115 2.3 14.9 1.0 SG B:CYS112 2.4 14.4 1.0 CE1 B:HIS77 3.0 13.1 1.0 CG B:HIS77 3.1 12.1 1.0 CB B:CYS115 3.1 12.5 1.0 CB B:CYS112 3.4 14.4 1.0 CB B:HIS77 3.5 12.4 1.0 O2 B:EDO203 3.8 32.7 1.0 N B:CYS112 3.9 13.2 1.0 N B:CYS115 3.9 11.6 1.0 OE2 B:GLU79 3.9 17.3 1.0 CE B:MET114 4.0 12.1 1.0 OE1 B:GLU79 4.0 15.8 1.0 CA B:CYS115 4.1 13.0 1.0 NE2 B:HIS77 4.1 14.7 1.0 CA B:CYS112 4.2 14.2 1.0 CD2 B:HIS77 4.2 13.2 1.0 CD B:GLU79 4.2 15.6 1.0 C B:CYS112 4.7 13.6 1.0 O B:CYS112 4.7 12.7 1.0 CB B:MET114 4.7 12.0 1.0 O B:HOH322 4.8 27.5 1.0 O B:HOH314 4.9 23.5 1.0 O B:HOH317 4.9 15.3 1.0 O B:HOH304 4.9 21.0 1.0 CA B:HIS77 5.0 12.8 1.0 NE1 A:TRP121 5.0 17.9 1.0 C B:MET114 5.0 12.6 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