Zinc in PDB 4f3w: Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum

All present enzymatic activity of Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum:
3.5.4.5;

The structure of Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum, PDB code: 4f3w was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.470, 48.710, 53.920, 100.19, 110.42, 98.39
R / Rfree (%)	18 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum (pdb code 4f3w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum, PDB code: 4f3w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum


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 Cytidine Deaminase Cdd From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:16.0 occ:1.00 O A:HOH323 2.0 17.8 1.0 SG A:CYS56 2.3 13.9 1.0 SG A:CYS89 2.3 11.9 1.0 SG A:CYS92 2.4 10.9 1.0 CB A:CYS56 3.1 11.8 1.0 CB A:CYS92 3.2 10.4 1.0 CB A:CYS89 3.4 11.5 1.0 N A:CYS89 3.9 11.5 1.0 O A:HOH326 3.9 21.9 1.0 N A:CYS92 4.0 10.7 1.0 NE A:ARG91 4.0 17.7 1.0 OE1 A:GLU58 4.1 13.0 1.0 OG C:SER50 4.2 15.1 1.0 CA A:CYS89 4.2 11.6 1.0 OE2 A:GLU58 4.2 15.3 1.0 CA A:CYS92 4.2 10.2 1.0 O C:HOH339 4.2 25.4 1.0 CD A:GLU58 4.4 13.4 1.0 O A:CYS89 4.6 11.2 1.0 NH2 A:ARG91 4.6 18.4 1.0 CA A:CYS56 4.6 11.2 1.0 C A:CYS89 4.6 11.3 1.0 CZ A:ARG91 4.8 19.9 1.0 CD A:ARG91 4.9 16.2 1.0 O A:HOH311 4.9 13.5 1.0 CB A:ARG91 5.0 13.3 1.0 O A:HOH366 5.0 38.8 1.0 C A:PRO88 5.0 12.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum


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 Cytidine Deaminase Cdd From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.8 occ:1.00 O B:HOH325 2.1 15.3 1.0 SG B:CYS92 2.3 13.3 1.0 SG B:CYS89 2.3 13.5 1.0 SG B:CYS56 2.4 12.7 1.0 CB B:CYS56 3.2 11.3 1.0 CB B:CYS92 3.2 12.2 1.0 CB B:CYS89 3.5 12.9 1.0 O D:HOH324 3.8 30.0 1.0 N B:CYS89 3.8 12.2 1.0 N B:CYS92 4.0 11.7 1.0 OE2 B:GLU58 4.0 16.4 1.0 NE B:ARG91 4.0 20.1 1.0 CA B:CYS89 4.1 12.7 1.0 CA B:CYS92 4.2 11.2 1.0 OG D:SER50 4.3 16.0 1.0 OE1 B:GLU58 4.3 15.3 1.0 CD B:GLU58 4.3 15.3 1.0 O D:HOH363 4.4 27.0 1.0 O B:CYS89 4.6 12.2 1.0 C B:CYS89 4.6 12.2 1.0 CA B:CYS56 4.6 10.7 1.0 NH2 B:ARG91 4.7 21.4 1.0 CD B:ARG91 4.8 18.6 1.0 O B:HOH307 4.8 11.8 1.0 CZ B:ARG91 4.9 22.7 1.0 CB B:ARG91 4.9 14.7 1.0 C B:PRO88 5.0 12.8 1.0 O D:HOH325 5.0 19.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:16.7 occ:1.00 O C:HOH335 2.2 16.1 1.0 SG C:CYS92 2.3 10.9 1.0 SG C:CYS89 2.3 11.3 1.0 SG C:CYS56 2.4 14.1 1.0 CB C:CYS56 3.2 12.1 1.0 CB C:CYS92 3.2 10.8 1.0 CB C:CYS89 3.4 10.9 1.0 N C:CYS89 3.9 11.0 1.0 O C:HOH334 4.0 27.0 1.0 NE C:ARG91 4.0 18.5 1.0 N C:CYS92 4.0 11.2 1.0 OE2 C:GLU58 4.1 15.9 1.0 CA C:CYS89 4.2 11.3 1.0 OE1 C:GLU58 4.2 14.1 1.0 CA C:CYS92 4.2 10.6 1.0 OG A:SER50 4.3 16.3 1.0 CD C:GLU58 4.3 14.1 1.0 NH1 C:ARG91 4.6 19.8 1.0 O C:CYS89 4.6 10.8 1.0 C C:CYS89 4.6 11.4 1.0 CA C:CYS56 4.7 11.3 1.0 CZ C:ARG91 4.8 20.7 1.0 CD C:ARG91 4.9 17.1 1.0 C C:PRO88 5.0 11.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cytidine Deaminase Cdd From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:14.2 occ:1.00 O D:HOH328 2.1 12.5 1.0 SG D:CYS89 2.3 12.0 1.0 SG D:CYS92 2.3 11.7 1.0 SG D:CYS56 2.4 12.3 1.0 CB D:CYS56 3.2 11.2 1.0 CB D:CYS92 3.2 10.9 1.0 CB D:CYS89 3.5 11.6 1.0 N D:CYS89 3.8 11.5 1.0 OE2 D:GLU58 3.9 13.7 1.0 O B:HOH323 3.9 27.8 1.0 N D:CYS92 4.0 10.8 1.0 NE D:ARG91 4.1 17.6 1.0 OG B:SER50 4.1 15.5 1.0 CA D:CYS89 4.1 11.6 1.0 CA D:CYS92 4.2 10.4 1.0 OE1 D:GLU58 4.3 12.6 1.0 CD D:GLU58 4.3 13.5 1.0 O B:HOH322 4.6 31.2 1.0 O D:CYS89 4.6 10.9 1.0 C D:CYS89 4.6 11.2 1.0 CA D:CYS56 4.7 10.8 1.0 NH2 D:ARG91 4.7 19.5 1.0 CD D:ARG91 4.8 16.5 1.0 C D:PRO88 4.9 12.2 1.0 CZ D:ARG91 4.9 19.8 1.0 O D:HOH307 4.9 12.7 1.0 CB D:ARG91 5.0 13.6 1.0

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003