Zinc in PDB 4ld2: Crystal Structure of NE0047 in Complex with Cytidine

The structure of Crystal Structure of NE0047 in Complex with Cytidine, PDB code: 4ld2 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)	27.53 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.210, 74.550, 110.110, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 21.8

The binding sites of Zinc atom in the Crystal Structure of NE0047 in Complex with Cytidine (pdb code 4ld2). 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 NE0047 in Complex with Cytidine, PDB code: 4ld2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of NE0047 in Complex with Cytidine


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 NE0047 in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:11.3 occ:1.00 ND1 A:HIS77 2.1 8.0 1.0 O A:HOH301 2.2 11.5 1.0 SG A:CYS115 2.3 9.4 1.0 SG A:CYS112 2.4 9.3 1.0 CE1 A:HIS77 3.0 9.0 1.0 CG A:HIS77 3.1 8.4 1.0 CB A:CYS115 3.2 7.0 1.0 CB A:CYS112 3.4 10.7 1.0 CB A:HIS77 3.5 8.7 1.0 N A:CYS115 3.9 7.7 1.0 N A:CYS112 3.9 10.4 1.0 OE2 A:GLU79 3.9 17.2 1.0 CE A:MET114 4.0 7.0 1.0 OE1 A:GLU79 4.1 12.3 1.0 N3 A:CTN202 4.1 19.8 1.0 CA A:CYS115 4.1 7.6 1.0 NE2 A:HIS77 4.2 8.8 1.0 CA A:CYS112 4.2 10.0 1.0 CD2 A:HIS77 4.2 8.4 1.0 CD A:GLU79 4.2 11.8 1.0 C2 A:CTN202 4.7 21.1 1.0 O2 A:CTN202 4.7 18.5 1.0 C A:CYS112 4.7 10.5 1.0 O A:CYS112 4.7 9.8 1.0 C4 A:CTN202 4.7 20.7 1.0 O A:HOH306 4.7 16.6 1.0 N4 A:CTN202 4.8 21.3 1.0 CB A:MET114 4.8 7.0 1.0 C A:MET114 4.9 7.8 1.0 CA A:HIS77 5.0 8.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of NE0047 in Complex with Cytidine


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 NE0047 in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:9.6 occ:1.00 ND1 B:HIS77 2.1 7.7 1.0 O B:HOH301 2.2 10.9 1.0 SG B:CYS115 2.3 8.9 1.0 SG B:CYS112 2.4 9.1 1.0 CE1 B:HIS77 3.0 8.1 1.0 CG B:HIS77 3.1 6.2 1.0 CB B:CYS115 3.2 8.5 1.0 CB B:CYS112 3.4 10.5 1.0 CB B:HIS77 3.5 5.9 1.0 O2 B:EDO203 3.9 26.5 1.0 N B:CYS112 3.9 9.2 1.0 N B:CYS115 3.9 7.3 1.0 OE2 B:GLU79 3.9 11.5 1.0 CE B:MET114 4.0 7.8 1.0 OE1 B:GLU79 4.1 9.4 1.0 NE2 B:HIS77 4.1 9.1 1.0 CA B:CYS115 4.2 8.0 1.0 CA B:CYS112 4.2 9.1 1.0 CD B:GLU79 4.2 9.3 1.0 CD2 B:HIS77 4.2 7.3 1.0 O B:CYS112 4.7 8.5 1.0 C B:CYS112 4.7 9.5 1.0 CB B:MET114 4.8 5.9 1.0 O B:HOH324 4.9 31.4 1.0 O B:HOH326 4.9 19.9 1.0 C B:MET114 5.0 8.4 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