Chlorine in PDB 4p9d: Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.

The structure of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp., PDB code: 4p9d was solved by A.Marx, A.Alian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.02 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.900, 79.020, 126.520, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.8

The structure of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Zinc	(Zn)	6 atoms

The binding sites of Chlorine atom in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. (pdb code 4p9d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp., PDB code: 4p9d:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:31.2 occ:1.00 O A:SER79 2.9 39.2 1.0 O D:MET76 2.9 33.2 1.0 O D:SER79 2.9 38.0 1.0 O A:MET76 3.0 33.6 1.0 O D:GLU81 3.0 40.2 1.0 O A:GLU81 3.1 39.5 1.0 C D:SER79 3.6 37.3 1.0 C A:SER79 3.7 38.9 1.0 O A:ALA77 3.8 34.8 1.0 N A:GLU81 3.8 41.1 1.0 C A:GLU81 3.8 40.4 1.0 N D:GLU81 3.9 39.9 1.0 C D:GLU81 4.0 40.4 1.0 C D:MET76 4.1 33.1 1.0 C A:MET76 4.2 32.9 1.0 CA A:SER80 4.2 40.2 1.0 N D:SER80 4.2 38.1 1.0 O D:ALA77 4.2 33.3 1.0 CA D:SER80 4.3 38.5 1.0 CA D:SER79 4.3 36.5 1.0 C A:ALA77 4.3 34.2 1.0 C D:SER80 4.3 39.4 1.0 C A:SER80 4.3 40.8 1.0 N D:SER79 4.4 35.3 1.0 CB D:SER79 4.4 36.1 1.0 CA A:GLU81 4.4 41.2 1.0 N A:SER80 4.4 39.4 1.0 CA A:ALA77 4.4 33.7 1.0 C D:ALA77 4.5 33.2 1.0 CA A:SER79 4.5 38.4 1.0 CA D:ALA77 4.6 32.9 1.0 N A:SER79 4.6 37.2 1.0 CA D:GLU81 4.6 40.4 1.0 CB A:SER79 4.6 38.5 1.0 N A:SER82 4.7 39.5 1.0 N A:ALA77 4.8 33.2 1.0 N D:ALA77 4.8 32.9 1.0 OG A:SER79 4.9 38.2 1.0 N D:SER82 4.9 40.8 1.0 CA A:SER82 5.0 38.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl205 b:27.2 occ:1.00 O B:MET76 2.8 33.1 1.0 O C:GLU81 2.9 36.5 1.0 O B:SER79 2.9 38.1 1.0 O C:SER79 2.9 35.4 1.0 O B:GLU81 2.9 38.2 1.0 O C:MET76 3.0 29.8 1.0 C B:SER79 3.5 37.6 1.0 O C:ALA77 3.9 29.5 1.0 C C:GLU81 3.9 36.7 1.0 O B:ALA77 3.9 32.4 1.0 C C:SER79 3.9 34.6 1.0 C B:MET76 4.0 33.1 1.0 C B:GLU81 4.0 38.3 1.0 N B:GLU81 4.0 38.5 1.0 N B:SER80 4.1 38.2 1.0 CA B:SER80 4.1 38.5 1.0 C C:MET76 4.1 29.5 1.0 N C:GLU81 4.2 35.8 1.0 C B:SER80 4.3 38.5 1.0 CA B:SER79 4.3 37.0 1.0 C B:ALA77 4.3 32.9 1.0 CA B:ALA77 4.4 32.9 1.0 C C:ALA77 4.4 29.8 1.0 CA C:ALA77 4.4 29.7 1.0 CB B:SER79 4.4 37.3 1.0 N B:SER79 4.4 35.9 1.0 C C:SER80 4.4 35.2 1.0 CA C:SER80 4.5 35.4 1.0 N C:SER80 4.6 35.5 1.0 N B:ALA77 4.7 33.1 1.0 CA B:GLU81 4.7 38.7 1.0 CA C:GLU81 4.7 36.7 1.0 N C:ALA77 4.7 29.5 1.0 N C:SER82 4.8 36.7 1.0 OG B:SER79 4.8 37.8 1.0 CA C:SER82 4.8 36.7 1.0 N C:SER79 4.8 32.6 1.0 CA C:SER79 4.9 33.9 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl205 b:28.1 occ:1.00 O E:SER79 2.9 41.8 1.0 O F:MET76 2.9 32.7 1.0 O F:SER79 2.9 41.2 1.0 O E:MET76 3.0 41.1 1.0 O F:GLU81 3.1 43.8 1.0 O E:GLU81 3.2 42.1 1.0 C F:SER79 3.6 40.9 1.0 C E:SER80 3.9 42.7 1.0 OG F:SER79 3.9 40.4 1.0 C F:GLU81 4.0 43.7 1.0 O E:SER80 4.0 42.9 1.0 C E:SER79 4.0 41.4 1.0 CA E:SER80 4.0 42.4 1.0 C F:MET76 4.0 32.5 1.0 N F:GLU81 4.1 44.2 1.0 C E:GLU81 4.1 42.8 1.0 CA F:SER80 4.1 43.7 1.0 C F:SER80 4.1 44.3 1.0 N F:SER80 4.1 42.4 1.0 O F:ALA77 4.2 35.1 1.0 C E:MET76 4.2 40.7 1.0 N E:GLU81 4.3 42.8 1.0 CA F:ALA77 4.4 34.3 1.0 O E:ALA77 4.4 39.0 1.0 C F:ALA77 4.4 34.8 1.0 N E:SER80 4.5 42.1 1.0 CA F:SER79 4.5 39.8 1.0 N F:SER79 4.6 38.0 1.0 CA F:GLU81 4.6 44.4 1.0 CA E:ALA77 4.6 40.1 1.0 N F:ALA77 4.7 33.7 1.0 O F:SER80 4.7 45.3 1.0 C E:ALA77 4.8 39.6 1.0 N F:SER82 4.8 42.7 1.0 CA E:GLU81 4.8 43.4 1.0 CB F:SER79 4.9 39.7 1.0 N E:ALA77 4.9 40.5 1.0 CA F:SER82 5.0 41.1 1.0 N E:SER82 5.0 42.5 1.0 CA E:SER82 5.0 42.6 1.0

A.Marx, A.Alian. The First Crystal Structure of A Dttp Bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.617720