Zinc in PDB 5c2o: Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp

The structure of Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp, PDB code: 5c2o was solved by Y.H.Li, Z.Q.Gao, H.F.Hou, Y.H.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.19 / 2.35
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	112.455, 112.455, 112.455, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.2

The structure of Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp (pdb code 5c2o). 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 Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp, PDB code: 5c2o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp


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 Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:55.7 occ:1.00 SG A:CYS54 2.4 44.6 1.0 CD2 A:HIS59 2.4 47.5 1.0 SG A:CYS66 2.4 43.3 1.0 SG A:CYS24 2.4 44.5 1.0 CG A:HIS59 3.2 51.0 1.0 CB A:CYS54 3.3 45.3 1.0 CB A:CYS24 3.3 44.1 1.0 CB A:CYS66 3.4 44.3 1.0 CB A:HIS59 3.5 47.9 1.0 NE2 A:HIS59 3.5 53.3 1.0 CA A:HIS59 3.8 49.3 1.0 CA A:CYS24 4.2 46.3 1.0 O A:HOH825 4.4 49.9 1.0 ND1 A:HIS59 4.4 53.0 1.0 O A:HOH822 4.5 43.9 1.0 CE1 A:HIS59 4.6 54.7 1.0 CD A:ARG26 4.6 49.3 1.0 N A:GLU60 4.7 48.3 1.0 CA A:CYS54 4.7 47.5 1.0 CB A:ARG68 4.7 42.9 1.0 N A:HIS59 4.8 47.9 1.0 CA A:CYS66 4.8 51.6 1.0 C A:HIS59 4.8 49.9 1.0 CG2 A:THR69 4.9 43.6 1.0 C A:CYS24 4.9 46.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp


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 Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:68.7 occ:1.00 ND1 A:HIS71 2.2 49.2 1.0 SG A:CYS99 2.3 46.0 1.0 O A:HOH812 2.4 44.0 1.0 SG A:CYS102 2.4 47.4 1.0 CE1 A:HIS71 3.1 45.0 1.0 CG A:HIS71 3.2 50.0 1.0 CB A:CYS102 3.3 45.6 1.0 CB A:CYS99 3.4 45.1 1.0 CB A:HIS71 3.5 40.8 1.0 N A:CYS99 3.8 41.0 1.0 O A:HOH838 4.1 48.6 1.0 CA A:CYS99 4.2 44.1 1.0 OE1 A:GLU73 4.2 45.2 1.0 N A:CYS102 4.2 39.3 1.0 NE2 A:HIS71 4.3 54.6 1.0 CD2 A:HIS71 4.3 48.7 1.0 CA A:CYS102 4.3 43.0 1.0 OE2 A:GLU73 4.4 57.8 1.0 CD A:GLU73 4.5 53.0 1.0 C A:CYS99 4.8 42.1 1.0 O A:CYS99 4.8 41.6 1.0 C A:PRO98 4.9 44.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp


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 Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:63.3 occ:1.00 SG B:CYS66 2.3 53.2 1.0 SG B:CYS54 2.4 56.8 1.0 ND1 B:HIS59 2.4 61.3 1.0 SG B:CYS24 2.5 53.1 1.0 CG B:HIS59 3.3 62.6 1.0 CB B:CYS54 3.3 53.0 1.0 CB B:CYS24 3.3 50.3 1.0 CB B:CYS66 3.3 60.0 1.0 CE1 B:HIS59 3.4 63.5 1.0 CB B:HIS59 3.5 53.4 1.0 CA B:HIS59 3.8 54.7 1.0 CA B:CYS24 4.3 53.3 1.0 NE2 B:HIS59 4.5 66.8 1.0 CD2 B:HIS59 4.5 63.3 1.0 CD B:ARG26 4.6 66.7 1.0 N B:GLU60 4.6 58.3 1.0 CA B:CYS54 4.7 54.3 1.0 N B:HIS59 4.7 51.5 1.0 CA B:CYS66 4.7 59.2 1.0 C B:HIS59 4.8 58.4 1.0 CB B:ARG68 4.8 48.2 1.0 C B:CYS24 4.9 56.4 1.0 CG2 B:THR69 5.0 43.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp


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 Streptococcus Mutans Deoxycytidylate Deaminase Complexed with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:67.5 occ:1.00 ND1 B:HIS71 2.1 50.1 1.0 O B:HOH802 2.3 43.0 1.0 SG B:CYS99 2.4 44.6 1.0 SG B:CYS102 2.5 48.1 1.0 CE1 B:HIS71 3.0 45.7 1.0 CG B:HIS71 3.2 50.1 1.0 CB B:CYS102 3.2 42.4 1.0 CB B:CYS99 3.5 36.3 1.0 CB B:HIS71 3.5 44.3 1.0 N B:CYS99 3.8 47.2 1.0 O B:HOH831 3.8 50.5 1.0 O B:HOH850 4.0 43.5 1.0 OE2 B:GLU73 4.1 57.1 1.0 CA B:CYS99 4.1 43.8 1.0 N B:CYS102 4.2 45.2 1.0 NE2 B:HIS71 4.2 55.7 1.0 CA B:CYS102 4.3 42.4 1.0 CD2 B:HIS71 4.3 51.7 1.0 OE1 B:GLU73 4.3 51.7 1.0 CD B:GLU73 4.4 52.1 1.0 O B:CYS99 4.6 44.0 1.0 C B:CYS99 4.7 43.6 1.0 C B:PRO98 4.8 48.2 1.0 CA B:PRO98 5.0 50.8 1.0

Y.Li, Z.Guo, L.Jin, D.Wang, Z.Gao, X.Su, H.Hou, Y.Dong. Mechanism of the Allosteric Regulation of Streptococcus Mutans 2'-Deoxycytidylate Deaminase Acta Crystallogr.,Sect.D V. 72 883 2016.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798316009153