Zinc in PDB 6k63: The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae

All present enzymatic activity of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae:
3.5.4.5;

The structure of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae, PDB code: 6k63 was solved by W.Liu, F.Shang, J.Lan, Y.Chen, L.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.90 / 2.07
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.748, 151.748, 120.155, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 22.3

The binding sites of Zinc atom in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae (pdb code 6k63). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae, PDB code: 6k63:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.2 occ:1.00 O A:HOH610 2.0 14.7 1.0 ND1 A:HIS102 2.1 11.0 1.0 SG A:CYS132 2.3 11.8 1.0 SG A:CYS129 2.3 12.0 1.0 CE1 A:HIS102 2.9 18.0 1.0 CG A:HIS102 3.1 12.3 1.0 CB A:CYS132 3.2 9.0 1.0 CB A:CYS129 3.6 12.3 1.0 CB A:HIS102 3.6 13.0 1.0 N A:CYS129 3.8 10.7 1.0 N A:CYS132 3.9 12.9 1.0 NE2 A:HIS102 4.0 12.9 1.0 OE1 A:GLU104 4.1 14.2 1.0 CA A:CYS132 4.1 10.1 1.0 CD2 A:HIS102 4.1 13.8 1.0 OE2 A:GLU104 4.2 18.4 1.0 CD2 A:HIS131 4.2 10.2 1.0 CA A:CYS129 4.2 11.3 1.0 O A:HOH516 4.3 28.1 1.0 CD A:GLU104 4.3 18.2 1.0 C2' A:DIO302 4.4 40.9 1.0 O1' A:DIO302 4.6 35.9 1.0 O A:CYS129 4.6 11.2 1.0 C A:CYS129 4.7 11.8 1.0 C A:PRO128 4.8 12.5 1.0 C A:HIS131 4.9 12.9 1.0 CG A:HIS131 4.9 12.2 1.0 CB A:HIS131 4.9 9.1 1.0 CA A:PRO128 5.0 13.0 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:14.7 occ:1.00 ND1 B:HIS102 2.0 10.2 1.0 O B:HOH542 2.0 15.2 1.0 SG B:CYS132 2.3 13.9 1.0 SG B:CYS129 2.4 13.5 1.0 CE1 B:HIS102 2.8 16.0 1.0 CG B:HIS102 3.1 16.3 1.0 CB B:CYS132 3.2 9.3 1.0 CB B:CYS129 3.5 12.9 1.0 CB B:HIS102 3.6 9.6 1.0 N B:CYS129 3.8 9.5 1.0 N B:CYS132 3.8 10.6 1.0 NE2 B:HIS102 3.9 16.3 1.0 O B:HOH434 4.0 24.1 1.0 OE1 B:GLU104 4.1 17.9 1.0 CA B:CYS132 4.1 12.6 1.0 CD2 B:HIS102 4.1 13.7 1.0 CA B:CYS129 4.1 12.9 1.0 OE2 B:GLU104 4.2 23.8 1.0 CD2 B:HIS131 4.2 11.8 1.0 O1 B:DIO303 4.2 36.5 1.0 CD B:GLU104 4.3 18.9 1.0 O B:CYS129 4.6 15.5 1.0 C B:CYS129 4.6 17.9 1.0 C2 B:DIO303 4.8 42.3 1.0 C1 B:DIO303 4.8 31.1 1.0 C B:PRO128 4.8 15.3 1.0 C B:HIS131 4.9 13.5 1.0 CG B:HIS131 4.9 12.8 1.0 CB B:HIS131 4.9 13.9 1.0 O B:HOH573 5.0 17.3 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:14.9 occ:1.00 ND1 C:HIS102 2.0 15.4 1.0 O C:HOH441 2.2 21.2 1.0 SG C:CYS129 2.2 13.3 1.0 SG C:CYS132 2.3 14.7 1.0 CE1 C:HIS102 2.8 21.2 1.0 CG C:HIS102 3.1 14.3 1.0 CB C:CYS132 3.2 11.1 1.0 CB C:CYS129 3.5 12.0 1.0 CB C:HIS102 3.6 11.1 1.0 N C:CYS129 3.7 15.0 1.0 N C:CYS132 3.8 12.2 1.0 OE2 C:GLU104 4.0 17.2 1.0 NE2 C:HIS102 4.0 18.0 1.0 CA C:CYS132 4.1 12.6 1.0 CA C:CYS129 4.1 15.0 1.0 CD2 C:HIS102 4.1 17.5 1.0 C2 D:DIO301 4.2 38.5 1.0 OE1 C:GLU104 4.2 15.8 1.0 CD2 C:HIS131 4.3 12.8 1.0 O C:HOH431 4.3 18.3 1.0 CD C:GLU104 4.3 15.1 1.0 C C:CYS129 4.7 14.0 1.0 O C:CYS129 4.7 13.2 1.0 C2' D:DIO301 4.8 37.2 1.0 C C:PRO128 4.8 14.0 1.0 C C:HIS131 4.9 17.7 1.0 CB C:HIS131 4.9 12.4 1.0 CG C:HIS131 5.0 17.1 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn305 b:16.2 occ:1.00 ND1 D:HIS102 2.0 21.2 1.0 O D:HOH439 2.2 17.4 1.0 SG D:CYS132 2.3 15.1 1.0 SG D:CYS129 2.3 11.0 1.0 CE1 D:HIS102 2.6 28.4 1.0 CG D:HIS102 3.0 23.1 1.0 CB D:CYS132 3.1 10.8 1.0 CB D:CYS129 3.5 14.1 1.0 NE2 D:HIS102 3.6 35.3 1.0 CB D:HIS102 3.7 13.7 1.0 N D:CYS129 3.7 16.1 1.0 CD2 D:HIS102 3.8 32.7 1.0 N D:CYS132 3.9 10.3 1.0 OE2 D:GLU104 3.9 23.6 1.0 O1' D:DIO304 4.0 25.0 1.0 OE1 D:GLU104 4.0 15.7 1.0 CA D:CYS132 4.1 11.4 1.0 CA D:CYS129 4.1 15.1 1.0 CD D:GLU104 4.3 17.6 1.0 CD2 D:HIS131 4.3 20.0 1.0 O D:HOH430 4.3 20.0 1.0 C D:CYS129 4.6 13.2 1.0 O D:CYS129 4.7 11.8 1.0 C1' D:DIO304 4.7 25.6 1.0 C D:PRO128 4.8 17.8 1.0 C D:HIS131 5.0 14.6 1.0 CA D:PRO128 5.0 15.9 1.0 CB D:HIS131 5.0 14.6 1.0

W.Liu, F.Shang, J.Lan, Y.Chen, L.Wang, Y.Xu. The Crystal Structure of Cytidine Deaminase From Klebsiella Pneumoniae To Be Published.