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

Protein crystallography data

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

Other elements in 4p9d:

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

Chlorine Binding Sites:

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 4p9d

Go back to Chlorine Binding Sites List in 4p9d
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 4p9d

Go back to Chlorine Binding Sites List in 4p9d
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 4p9d

Go back to Chlorine Binding Sites List in 4p9d
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

Reference:

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
Page generated: Fri Jul 11 20:22:28 2025

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