Zinc 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
Chlorine	(Cl)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn201 b:37.3 occ:1.00 ND1 A:HIS67 2.0 27.9 1.0 O A:HOH304 2.1 52.0 1.0 SG A:CYS95 2.2 40.1 1.0 SG A:CYS98 2.3 33.2 1.0 CE1 A:HIS67 3.0 27.6 1.0 CG A:HIS67 3.1 27.4 1.0 CB A:CYS95 3.3 36.9 1.0 CB A:CYS98 3.3 34.4 1.0 O4 A:TMP204 3.4 45.9 1.0 CB A:HIS67 3.4 27.2 1.0 N A:CYS95 3.6 35.8 1.0 OE1 A:GLU69 3.8 35.8 1.0 C4 A:TMP204 3.9 44.9 1.0 CA A:CYS95 4.0 36.8 1.0 NE2 A:HIS67 4.1 26.3 1.0 CD2 A:HIS67 4.2 27.6 1.0 N A:CYS98 4.3 35.9 1.0 N3 A:TMP204 4.3 45.6 1.0 CA A:CYS98 4.4 34.5 1.0 O A:CYS95 4.5 37.2 1.0 C A:CYS95 4.6 36.8 1.0 C5 A:TMP204 4.6 44.4 1.0 C A:PRO94 4.7 34.9 1.0 CD A:GLU69 4.8 35.2 1.0 CB A:GLU69 4.8 29.4 1.0 C5M A:TMP204 4.9 43.5 1.0 CA A:HIS67 4.9 27.5 1.0 CA A:PRO94 5.0 34.2 1.0

Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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:Zn201 b:37.9 occ:1.00 ND1 B:HIS67 2.0 31.9 1.0 O B:HOH305 2.1 30.0 1.0 SG B:CYS98 2.3 32.1 1.0 SG B:CYS95 2.3 30.0 1.0 CG B:HIS67 3.0 31.7 1.0 CE1 B:HIS67 3.0 32.8 1.0 CB B:CYS98 3.2 32.8 1.0 CB B:HIS67 3.3 30.6 1.0 CB B:CYS95 3.4 30.6 1.0 O4 B:TMP203 3.6 48.5 1.0 N B:CYS95 3.7 31.6 1.0 C4 B:TMP203 4.0 49.4 1.0 OE1 B:GLU69 4.0 38.2 1.0 CD2 B:HIS67 4.1 32.5 1.0 NE2 B:HIS67 4.1 33.3 1.0 CA B:CYS95 4.1 30.8 1.0 N B:CYS98 4.3 33.5 1.0 CA B:CYS98 4.3 32.9 1.0 N3 B:TMP203 4.4 49.5 1.0 CD B:GLU69 4.6 37.4 1.0 CB B:GLU69 4.6 28.6 1.0 C5 B:TMP203 4.7 49.9 1.0 O B:CYS95 4.7 31.2 1.0 C B:CYS95 4.8 31.0 1.0 CA B:HIS67 4.8 30.5 1.0 C B:PRO94 4.9 31.3 1.0 CG B:GLU69 5.0 31.4 1.0

Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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 C:Zn201 b:38.9 occ:1.00 ND1 C:HIS67 2.0 24.8 1.0 O C:HOH307 2.1 30.0 1.0 SG C:CYS95 2.3 36.3 1.0 SG C:CYS98 2.3 33.3 1.0 CE1 C:HIS67 3.0 27.0 1.0 CG C:HIS67 3.0 23.2 1.0 CB C:CYS98 3.2 33.7 1.0 CB C:CYS95 3.3 36.6 1.0 CB C:HIS67 3.4 22.4 1.0 O4 C:TMP204 3.5 70.4 1.0 N C:CYS95 3.6 37.0 1.0 C4 C:TMP204 3.9 68.7 1.0 OE1 C:GLU69 3.9 31.1 1.0 CA C:CYS95 4.0 36.4 1.0 NE2 C:HIS67 4.1 26.7 1.0 CD2 C:HIS67 4.1 25.7 1.0 N3 C:TMP204 4.1 69.2 1.0 N C:CYS98 4.4 34.5 1.0 CA C:CYS98 4.4 33.5 1.0 CD C:GLU69 4.6 32.4 1.0 O C:CYS95 4.7 36.6 1.0 C5 C:TMP204 4.7 67.7 1.0 C C:CYS95 4.7 36.5 1.0 CB C:GLU69 4.7 25.0 1.0 C C:PRO94 4.7 37.5 1.0 CA C:HIS67 4.9 22.5 1.0 CA C:PRO94 4.9 38.0 1.0

Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn binding site number 4 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 D:Zn201 b:41.3 occ:1.00 ND1 D:HIS67 2.0 32.4 1.0 O D:HOH304 2.1 30.0 1.0 SG D:CYS95 2.3 36.3 1.0 SG D:CYS98 2.3 35.7 1.0 CE1 D:HIS67 2.8 33.1 1.0 CG D:HIS67 2.9 31.9 1.0 O4 D:TMP204 3.1 56.6 1.0 CB D:CYS98 3.3 36.5 1.0 CB D:CYS95 3.3 39.0 1.0 CB D:HIS67 3.3 30.8 1.0 N D:CYS95 3.7 39.6 1.0 C4 D:TMP204 3.7 55.7 1.0 NE2 D:HIS67 3.8 33.9 1.0 CD2 D:HIS67 3.8 32.8 1.0 OE1 D:GLU69 4.0 38.1 1.0 CA D:CYS95 4.1 39.1 1.0 N3 D:TMP204 4.2 56.6 1.0 N D:CYS98 4.4 38.9 1.0 CA D:CYS98 4.4 36.8 1.0 C5 D:TMP204 4.5 54.3 1.0 CD D:GLU69 4.7 38.9 1.0 C5M D:TMP204 4.7 52.5 1.0 CB D:GLU69 4.8 31.3 1.0 O D:CYS95 4.8 39.8 1.0 C D:PRO94 4.8 39.9 1.0 C D:CYS95 4.8 39.7 1.0 CA D:HIS67 4.9 30.9 1.0 CG D:GLN70 5.0 32.2 1.0

Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn binding site number 5 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:Zn201 b:47.3 occ:1.00 ND1 E:HIS67 2.0 44.3 1.0 O E:HOH303 2.1 30.0 1.0 SG E:CYS98 2.3 46.9 1.0 SG E:CYS95 2.3 36.9 1.0 CE1 E:HIS67 3.0 45.0 1.0 CG E:HIS67 3.0 44.0 1.0 CB E:CYS98 3.2 42.6 1.0 CB E:HIS67 3.4 44.0 1.0 CB E:CYS95 3.6 37.9 1.0 O4 E:TMP204 3.8 45.7 1.0 OE1 E:GLU69 3.8 48.3 1.0 N E:CYS95 4.0 38.4 1.0 C4 E:TMP204 4.0 46.9 1.0 NE2 E:HIS67 4.1 45.4 1.0 CD2 E:HIS67 4.1 44.6 1.0 N E:CYS98 4.2 41.9 1.0 N3 E:TMP204 4.2 45.1 1.0 CA E:CYS98 4.3 42.5 1.0 CA E:CYS95 4.4 38.1 1.0 CD E:GLU69 4.4 47.9 1.0 CB E:GLU69 4.5 42.0 1.0 C5 E:TMP204 4.8 48.1 1.0 CG E:GLU69 4.8 44.0 1.0 O E:CYS95 4.9 38.1 1.0 CA E:HIS67 4.9 44.0 1.0 C E:CYS95 4.9 38.8 1.0 CG E:GLN70 5.0 40.2 1.0

Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn binding site number 6 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 F:Zn201 b:58.0 occ:1.00 O F:HOH306 2.1 30.0 1.0 ND1 F:HIS67 2.2 30.8 1.0 SG F:CYS98 2.2 43.5 1.0 CB F:CYS95 2.3 40.2 1.0 SG F:CYS95 2.5 42.0 1.0 CE1 F:HIS67 3.0 31.8 1.0 CB F:CYS98 3.2 42.0 1.0 N F:CYS95 3.2 39.7 1.0 CA F:CYS95 3.2 40.0 1.0 CG F:HIS67 3.3 30.9 1.0 O4 F:TMP204 3.3 59.5 1.0 CB F:HIS67 3.7 29.1 1.0 OE1 F:GLU69 3.7 36.0 1.0 C4 F:TMP204 3.8 58.6 1.0 C F:CYS95 4.0 40.2 1.0 O F:CYS95 4.0 40.5 1.0 N F:CYS98 4.1 42.2 1.0 NE2 F:HIS67 4.2 32.2 1.0 N3 F:TMP204 4.2 59.3 1.0 CA F:CYS98 4.3 42.1 1.0 CD2 F:HIS67 4.3 32.1 1.0 C F:PRO94 4.5 38.3 1.0 C5 F:TMP204 4.6 59.3 1.0 CD F:GLU69 4.7 37.7 1.0 C5M F:TMP204 4.9 59.1 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