Zinc in PDB 4p9c: Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump

The structure of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump, PDB code: 4p9c 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)	99.99 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.050, 147.210, 100.470, 90.00, 95.62, 90.00
R / Rfree (%)	23.1 / 26.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump (pdb code 4p9c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump, PDB code: 4p9c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:34.4 occ:1.00 ND1 A:HIS67 2.1 30.0 1.0 O4 A:DU203 2.2 35.6 1.0 SG A:CYS95 2.3 39.0 1.0 SG A:CYS98 2.3 32.9 1.0 C4 A:DU203 2.8 34.6 1.0 CG A:HIS67 3.0 30.9 1.0 CE1 A:HIS67 3.1 28.3 1.0 CB A:CYS98 3.2 33.5 1.0 OE2 A:GLU69 3.3 34.3 1.0 N3 A:DU203 3.3 34.7 1.0 CB A:HIS67 3.3 27.8 1.0 CB A:CYS95 3.4 33.4 1.0 N A:CYS95 3.7 33.0 1.0 C5 A:DU203 3.8 33.0 1.0 CD2 A:HIS67 4.1 32.1 1.0 CA A:CYS95 4.1 34.0 1.0 NE2 A:HIS67 4.2 31.6 1.0 CD A:GLU69 4.2 38.8 1.0 N A:CYS98 4.4 33.9 1.0 CA A:CYS98 4.4 33.5 1.0 C2 A:DU203 4.4 34.2 1.0 O A:CYS95 4.7 33.9 1.0 C A:CYS95 4.8 33.6 1.0 CA A:HIS67 4.8 27.6 1.0 CB A:GLU69 4.8 27.8 1.0 C6 A:DU203 4.8 34.7 1.0 C A:PRO94 4.8 32.2 1.0 OE1 A:GLU69 4.9 42.8 1.0 CG A:GLU69 4.9 31.4 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:31.4 occ:1.00 O B:HOH335 2.0 30.0 1.0 ND1 B:HIS67 2.1 20.1 1.0 SG B:CYS98 2.3 33.7 1.0 SG B:CYS95 2.3 28.1 1.0 CG B:HIS67 3.0 24.3 1.0 CE1 B:HIS67 3.1 19.4 1.0 CB B:CYS98 3.2 30.9 1.0 O4 B:DU203 3.2 35.6 1.0 CB B:HIS67 3.3 22.4 1.0 CB B:CYS95 3.5 25.4 1.0 OE1 B:GLU69 3.7 37.6 1.0 C4 B:DU203 3.7 34.6 1.0 N B:CYS95 3.8 25.1 1.0 CD B:GLU69 3.9 40.9 1.0 CG B:GLU69 4.0 31.7 1.0 N3 B:DU203 4.0 34.7 1.0 CD2 B:HIS67 4.1 24.5 1.0 NE2 B:HIS67 4.2 23.6 1.0 CA B:CYS95 4.2 26.0 1.0 CA B:CYS98 4.3 30.3 1.0 N B:CYS98 4.3 30.2 1.0 C5 B:DU203 4.5 33.0 1.0 OE2 B:GLU69 4.6 42.4 1.0 O B:CYS95 4.7 27.9 1.0 CA B:HIS67 4.8 22.6 1.0 C B:CYS95 4.8 26.9 1.0 C B:PRO94 4.9 24.4 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:29.2 occ:1.00 ND1 C:HIS67 2.0 23.6 1.0 SG C:CYS95 2.3 29.3 1.0 SG C:CYS98 2.3 29.3 1.0 O4 C:DU203 2.4 35.6 1.0 CE1 C:HIS67 2.9 25.4 1.0 C4 C:DU203 3.0 34.6 1.0 CG C:HIS67 3.1 26.7 1.0 CB C:CYS98 3.2 29.9 1.0 OE2 C:GLU69 3.4 32.0 1.0 CB C:HIS67 3.5 22.8 1.0 CB C:CYS95 3.5 26.7 1.0 C5 C:DU203 3.6 33.0 1.0 N3 C:DU203 3.7 34.7 1.0 N C:CYS95 3.8 26.5 1.0 NE2 C:HIS67 4.1 27.2 1.0 CD2 C:HIS67 4.1 26.7 1.0 CA C:CYS95 4.2 27.6 1.0 N C:CYS98 4.4 30.4 1.0 CA C:CYS98 4.4 30.1 1.0 CD C:GLU69 4.4 37.5 1.0 C6 C:DU203 4.7 34.7 1.0 O C:CYS95 4.7 29.2 1.0 C2 C:DU203 4.8 34.2 1.0 C C:CYS95 4.8 28.5 1.0 C C:PRO94 4.9 26.3 1.0 CA C:HIS67 5.0 23.1 1.0 CB C:GLU69 5.0 30.1 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:35.5 occ:1.00 ND1 D:HIS67 2.0 29.3 1.0 SG D:CYS98 2.2 36.5 1.0 SG D:CYS95 2.2 32.8 1.0 O4 D:DU203 2.6 35.6 1.0 CE1 D:HIS67 2.9 27.9 1.0 CB D:CYS98 3.1 36.0 1.0 CG D:HIS67 3.1 30.5 1.0 CB D:CYS95 3.3 32.2 1.0 C4 D:DU203 3.4 34.6 1.0 OE2 D:GLU69 3.4 37.6 1.0 CB D:HIS67 3.5 28.4 1.0 N D:CYS95 3.7 32.1 1.0 N3 D:DU203 3.8 34.7 1.0 NE2 D:HIS67 4.0 28.9 1.0 CA D:CYS95 4.1 33.2 1.0 N D:CYS98 4.1 35.9 1.0 CD2 D:HIS67 4.2 29.9 1.0 CA D:CYS98 4.2 35.3 1.0 C5 D:DU203 4.3 33.0 1.0 CD D:GLU69 4.3 41.0 1.0 O D:CYS95 4.4 35.1 1.0 C D:CYS95 4.6 34.2 1.0 CB D:GLU69 4.7 31.2 1.0 C D:PRO94 4.9 32.1 1.0 CG D:GLU69 4.9 34.1 1.0 C2 D:DU203 5.0 34.2 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:29.4 occ:1.00 ND1 E:HIS67 2.1 30.0 1.0 SG E:CYS98 2.2 29.7 1.0 SG E:CYS95 2.3 33.9 1.0 O4 E:DU203 2.5 35.6 1.0 CG E:HIS67 3.0 30.8 1.0 CE1 E:HIS67 3.0 29.8 1.0 C4 E:DU203 3.1 34.6 1.0 CB E:CYS98 3.2 31.8 1.0 CB E:HIS67 3.4 27.7 1.0 OE2 E:GLU69 3.4 34.6 1.0 CB E:CYS95 3.5 29.6 1.0 N3 E:DU203 3.8 34.7 1.0 C5 E:DU203 3.8 33.0 1.0 N E:CYS95 3.9 28.6 1.0 NE2 E:HIS67 4.1 32.7 1.0 CD2 E:HIS67 4.1 29.9 1.0 CA E:CYS95 4.3 30.7 1.0 N E:CYS98 4.3 31.8 1.0 CA E:CYS98 4.3 31.5 1.0 CD E:GLU69 4.4 35.8 1.0 O E:CYS95 4.7 32.0 1.0 O E:HOH312 4.7 31.7 1.0 C E:CYS95 4.9 31.4 1.0 C2 E:DU203 4.9 34.2 1.0 CA E:HIS67 4.9 27.2 1.0 C6 E:DU203 4.9 34.7 1.0 CB E:GLU69 4.9 29.6 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


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 Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:32.8 occ:1.00 ND1 F:HIS67 2.2 27.7 1.0 SG F:CYS98 2.3 35.8 1.0 SG F:CYS95 2.3 25.6 1.0 O4 F:DU203 2.5 35.6 1.0 CB F:CYS98 3.1 32.3 1.0 OE2 F:GLU69 3.1 32.8 1.0 C4 F:DU203 3.2 34.6 1.0 CE1 F:HIS67 3.2 27.6 1.0 CG F:HIS67 3.2 27.9 1.0 CB F:CYS95 3.5 25.8 1.0 CB F:HIS67 3.5 25.7 1.0 N F:CYS95 3.7 25.5 1.0 N3 F:DU203 3.7 34.7 1.0 C5 F:DU203 4.0 33.0 1.0 CD F:GLU69 4.0 37.0 1.0 CA F:CYS95 4.1 26.2 1.0 N F:CYS98 4.2 30.5 1.0 CA F:CYS98 4.3 31.1 1.0 NE2 F:HIS67 4.3 27.9 1.0 CD2 F:HIS67 4.3 29.7 1.0 O F:HOH337 4.4 32.6 1.0 O F:CYS95 4.5 28.0 1.0 CB F:GLU69 4.7 28.9 1.0 C F:CYS95 4.7 27.1 1.0 C F:PRO94 4.7 24.9 1.0 CG F:GLU69 4.8 31.9 1.0 OE1 F:GLU69 4.8 40.7 1.0 CA F:PRO94 4.8 24.0 1.0 C2 F:DU203 4.9 34.2 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:38.0 occ:1.00 ND1 G:HIS67 2.1 29.0 1.0 SG G:CYS98 2.2 31.6 1.0 O G:HOH323 2.2 30.0 1.0 SG G:CYS95 2.4 32.0 1.0 CG G:HIS67 2.9 30.4 1.0 CE1 G:HIS67 3.1 27.0 1.0 OE2 G:GLU69 3.1 39.7 1.0 CB G:HIS67 3.2 30.1 1.0 CB G:CYS98 3.2 28.2 1.0 O4 G:DU203 3.5 35.6 1.0 CB G:CYS95 3.6 29.6 1.0 C4 G:DU203 3.8 34.6 1.0 N G:CYS95 4.0 30.5 1.0 N3 G:DU203 4.0 34.7 1.0 CD2 G:HIS67 4.0 30.4 1.0 NE2 G:HIS67 4.1 28.3 1.0 CD G:GLU69 4.3 40.0 1.0 CA G:CYS98 4.4 27.2 1.0 CA G:CYS95 4.4 30.4 1.0 N G:CYS98 4.4 27.5 1.0 C5 G:DU203 4.7 33.0 1.0 CA G:HIS67 4.7 29.2 1.0 CB G:GLU69 4.8 31.4 1.0 O G:CYS95 4.8 30.9 1.0 C2 G:DU203 4.9 34.2 1.0 C G:CYS95 5.0 30.3 1.0 CG G:GLU69 5.0 34.9 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:40.7 occ:1.00 O H:HOH322 2.1 30.0 1.0 ND1 H:HIS67 2.2 36.6 1.0 SG H:CYS98 2.4 39.2 1.0 SG H:CYS95 2.4 37.3 1.0 CG H:HIS67 3.0 33.6 1.0 O4 H:DU203 3.1 35.6 1.0 CE1 H:HIS67 3.1 34.9 1.0 OE2 H:GLU69 3.2 35.5 1.0 CB H:CYS98 3.2 32.5 1.0 CB H:HIS67 3.3 33.1 1.0 C4 H:DU203 3.6 34.6 1.0 CB H:CYS95 3.8 33.7 1.0 N3 H:DU203 3.9 34.7 1.0 N H:CYS95 4.1 34.1 1.0 CD2 H:HIS67 4.1 32.8 1.0 NE2 H:HIS67 4.2 29.9 1.0 CD H:GLU69 4.2 38.6 1.0 CA H:CYS98 4.3 32.4 1.0 N H:CYS98 4.4 32.9 1.0 C5 H:DU203 4.5 33.0 1.0 CA H:CYS95 4.6 34.1 1.0 CB H:GLU69 4.8 34.8 1.0 CA H:HIS67 4.8 33.2 1.0 C2 H:DU203 4.9 34.2 1.0 CG H:GLU69 5.0 36.7 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:39.1 occ:1.00 O I:HOH321 2.1 30.0 1.0 ND1 I:HIS67 2.2 36.8 1.0 SG I:CYS98 2.3 36.7 1.0 SG I:CYS95 2.3 38.8 1.0 OE2 I:GLU69 3.0 40.7 1.0 CE1 I:HIS67 3.1 36.8 1.0 CG I:HIS67 3.1 36.4 1.0 CB I:CYS98 3.1 36.9 1.0 O4 I:DU203 3.2 35.6 1.0 CB I:HIS67 3.4 35.8 1.0 CB I:CYS95 3.4 38.3 1.0 C4 I:DU203 3.6 34.6 1.0 N I:CYS95 3.7 39.1 1.0 N3 I:DU203 4.0 34.7 1.0 CD I:GLU69 4.1 42.4 1.0 CA I:CYS95 4.1 39.1 1.0 NE2 I:HIS67 4.2 38.4 1.0 CD2 I:HIS67 4.2 38.1 1.0 CA I:CYS98 4.3 36.6 1.0 C5 I:DU203 4.3 33.0 1.0 N I:CYS98 4.4 38.0 1.0 O I:CYS95 4.5 38.8 1.0 C I:CYS95 4.7 39.6 1.0 C I:PRO94 4.8 38.8 1.0 OE1 I:GLU69 4.8 45.0 1.0 CB I:GLU69 4.9 34.7 1.0 CG I:GLU69 4.9 37.5 1.0 C2 I:DU203 4.9 34.2 1.0 CA I:HIS67 4.9 34.8 1.0 CA I:PRO94 5.0 39.4 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dcmp and Dump within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:34.4 occ:1.00 ND1 J:HIS67 2.1 30.4 1.0 O J:HOH322 2.2 30.0 1.0 SG J:CYS95 2.3 29.1 1.0 SG J:CYS98 2.4 33.4 1.0 OE1 J:GLU69 2.7 39.9 1.0 CG J:HIS67 2.9 30.4 1.0 CE1 J:HIS67 3.1 30.5 1.0 CB J:HIS67 3.2 29.5 1.0 CB J:CYS98 3.3 32.5 1.0 O4 J:DU203 3.3 35.6 1.0 CB J:CYS95 3.6 30.3 1.0 C4 J:DU203 3.7 34.6 1.0 N3 J:DU203 3.8 34.7 1.0 CD J:GLU69 3.8 39.2 1.0 N J:CYS95 3.9 31.9 1.0 CD2 J:HIS67 4.1 31.5 1.0 NE2 J:HIS67 4.2 32.6 1.0 CA J:CYS95 4.3 31.2 1.0 OE2 J:GLU69 4.3 36.6 1.0 N J:CYS98 4.4 33.1 1.0 CA J:CYS98 4.4 31.8 1.0 C5 J:DU203 4.5 33.0 1.0 CA J:HIS67 4.7 29.0 1.0 C2 J:DU203 4.7 34.2 1.0 O J:CYS95 4.8 30.9 1.0 CG J:GLU69 4.9 34.8 1.0 C J:CYS95 4.9 32.1 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