Zinc in PDB 1ud9: Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii

The structure of Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii, PDB code: 1ud9 was solved by E.Tanabe, Y.Yasutake, Y.Tanaka, M.Yao, K.Tsumoto, I.Kumagai, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.400, 75.440, 88.140, 90.00, 98.83, 90.00
R / Rfree (%)	20.2 / 23.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii (pdb code 1ud9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii, PDB code: 1ud9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.4 occ:1.00 O A:HOH1414 2.0 23.3 1.0 N A:ALA1 2.1 22.9 1.0 O A:HOH1413 2.2 18.4 1.0 CA A:ALA1 3.1 21.4 1.0 C A:ALA1 3.3 21.1 1.0 O A:ALA1 3.5 22.4 1.0 ZN A:ZN502 3.6 28.5 1.0 OD2 A:ASP92 4.0 30.6 1.0 N A:HIS2 4.1 20.6 1.0 O A:ALA91 4.1 35.3 1.0 CB A:ALA1 4.4 21.6 1.0 O A:ASP60 4.4 22.6 1.0 CD A:PRO62 4.5 26.4 1.0 OD2 A:ASP90 4.8 30.6 1.0 CB A:HIS2 4.8 21.2 1.0 CG A:PRO62 4.8 24.1 1.0 CA A:HIS2 5.0 19.8 1.0

Zinc binding site 2 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.5 occ:1.00 OD2 A:ASP92 1.9 30.6 1.0 O A:HOH1414 2.0 23.3 1.0 OD1 A:ASP90 2.2 32.9 1.0 OD2 A:ASP90 2.8 30.6 1.0 CG A:ASP92 2.8 35.6 1.0 CG A:ASP90 2.9 31.9 1.0 OD1 A:ASP92 3.2 34.1 1.0 ZN A:ZN501 3.6 27.4 1.0 O A:ALA1 4.2 22.4 1.0 CB A:ASP92 4.2 35.1 1.0 CB A:ASP90 4.4 30.3 1.0 O A:ALA91 4.5 35.3 1.0 CA A:ASP92 4.5 36.2 1.0 C A:ALA91 4.5 34.5 1.0 N A:ASP92 4.5 35.5 1.0 N A:ALA91 4.7 30.5 1.0 N A:ALA1 4.8 22.9 1.0 C A:ALA1 4.9 21.1 1.0

Zinc binding site 3 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.3 occ:1.00 OXT A:SER245 2.0 25.2 1.0 OE1 A:GLU167 2.1 24.0 1.0 O A:HOH1415 2.2 22.2 1.0 C A:SER245 2.7 24.4 1.0 O A:SER245 2.8 26.1 1.0 CD A:GLU167 2.8 27.8 1.0 OE2 A:GLU167 2.9 26.9 1.0 O A:HOH1125 3.9 27.1 1.0 OG1 A:THR152 4.0 22.8 1.0 CG2 A:THR152 4.1 24.9 1.0 CA A:SER245 4.1 23.8 1.0 CG A:GLU167 4.2 28.0 1.0 OG A:SER245 4.4 25.5 1.0 CB A:THR152 4.4 25.0 1.0 N A:SER245 4.6 20.9 1.0 CD A:LYS243 4.7 27.5 1.0 CB A:GLU167 4.8 27.7 1.0 CB A:SER245 4.8 25.3 1.0 O A:HOH1322 4.8 44.6 1.0 CB A:ALA195 4.9 20.1 1.0

Zinc binding site 4 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:25.9 occ:1.00 O A:HOH1437 1.5 21.8 1.0 OE2 A:GLU159 1.9 32.0 1.0 OE1 D:GLU58 2.0 31.0 1.0 CD A:GLU159 2.7 35.7 1.0 OE1 A:GLU159 2.9 38.1 1.0 CD D:GLU58 3.0 29.4 1.0 OE2 D:GLU58 3.2 25.5 1.0 ZN D:ZN504 3.3 24.7 1.0 CG A:GLU159 4.1 31.8 1.0 CG D:GLU58 4.3 26.9 1.0 O D:HOH1436 4.6 34.2 1.0 NE2 D:HIS2 4.7 20.9 1.0

Zinc binding site 5 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:33.2 occ:1.00 OE2 A:GLU191 2.1 26.8 1.0 OE2 D:GLU86 2.1 30.5 1.0 O A:HOH1417 2.2 25.6 1.0 OE1 D:GLU86 2.5 29.5 1.0 CD D:GLU86 2.6 27.7 1.0 CD A:GLU191 2.8 29.2 1.0 OE1 A:GLU191 2.9 29.2 1.0 O A:HOH1416 4.0 25.1 1.0 CG D:GLU86 4.1 30.7 1.0 CG A:GLU191 4.2 26.9 1.0 CG1 D:VAL4 4.5 18.5 1.0 O D:HOH1378 4.6 40.3 1.0 CG D:LYS57 4.7 29.4 1.0

Zinc binding site 6 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:29.5 occ:1.00 OE1 A:GLU58 1.9 33.4 1.0 O A:HOH1136 1.9 35.1 1.0 NE2 A:HIS2 2.1 22.4 1.0 CD A:GLU58 2.7 30.8 1.0 OE2 A:GLU58 2.8 35.7 1.0 CE1 A:HIS2 3.0 24.1 1.0 CD2 A:HIS2 3.0 21.8 1.0 CG2 A:VAL4 4.0 20.5 1.0 ND1 A:HIS2 4.1 22.3 1.0 CG A:GLU58 4.1 30.1 1.0 CG A:HIS2 4.2 21.5 1.0 O A:HOH1372 4.4 43.5 1.0 CB A:GLU58 4.6 27.4 1.0

Zinc binding site 7 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn515 b:56.6 occ:1.00 OD2 A:ASP203 2.1 30.4 1.0 O A:HOH1255 2.4 47.0 1.0 CG A:ASP203 3.0 28.7 1.0 O A:HOH1443 3.1 36.4 1.0 OD1 A:ASP203 3.3 28.0 1.0 O A:HOH1289 4.0 32.0 1.0 OE2 A:GLU199 4.2 48.2 1.0 CB A:ASP203 4.4 25.7 1.0 O A:LYS20 4.6 27.8 1.0 O A:GLU199 4.8 25.0 1.0

Zinc binding site 8 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn516 b:61.1 occ:1.00 OD2 A:ASP197 2.4 30.5 1.0 OD1 A:ASP197 2.7 26.2 1.0 CG A:ASP197 2.8 27.1 1.0 OE1 A:GLU199 3.3 47.9 1.0 O A:ASP151 4.0 25.8 1.0 CB A:GLU199 4.0 33.1 1.0 CB A:ASP197 4.2 24.3 1.0 CD A:GLU199 4.2 44.4 1.0 CB A:ASP151 4.3 31.9 1.0 CG A:GLU199 4.7 41.8 1.0 O A:HOH1315 4.7 37.2 1.0 CA A:ASP197 4.8 21.9 1.0 C A:ASP151 4.9 27.6 1.0 N A:GLU199 4.9 25.4 1.0 CA A:ASP151 5.0 30.4 1.0

Zinc binding site 9 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn508 b:17.7 occ:1.00 NE2 B:HIS2 2.0 15.9 1.0 OE1 B:GLU58 2.0 18.9 1.0 N C:ALA1 2.0 15.4 1.0 O C:HOH1421 2.1 17.5 1.0 CD B:GLU58 2.8 20.9 1.0 OE2 B:GLU58 2.9 26.2 1.0 CE1 B:HIS2 3.0 17.6 1.0 CA C:ALA1 3.0 16.2 1.0 CD2 B:HIS2 3.0 15.3 1.0 C C:ALA1 3.4 17.1 1.0 O C:ALA1 3.5 15.8 1.0 CG2 B:VAL4 3.9 16.6 1.0 O C:HOH1108 3.9 29.8 1.0 OD2 C:ASP92 4.0 32.5 1.0 ND1 B:HIS2 4.1 16.7 1.0 CG B:HIS2 4.1 15.0 1.0 CG B:GLU58 4.3 18.2 1.0 N C:HIS2 4.3 14.4 1.0 O C:ALA91 4.3 20.4 1.0 O C:HOH1196 4.4 32.1 1.0 CB C:ALA1 4.4 16.1 1.0 CB B:GLU58 4.7 17.3 1.0 C C:ALA91 5.0 20.1 1.0

Zinc binding site 10 out of 23 in the Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii


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 Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn510 b:23.1 occ:1.00 OD2 B:ASP92 2.0 22.1 1.0 OD2 C:ASP90 2.1 23.9 1.0 OD1 B:ASP90 2.2 23.2 1.0 OD2 B:ASP90 2.4 22.9 1.0 CG B:ASP90 2.5 22.3 1.0 CG C:ASP90 2.7 22.0 1.0 OD1 C:ASP90 2.8 26.3 1.0 CG B:ASP92 2.9 27.2 1.0 OD1 B:ASP92 3.2 25.6 1.0 O C:HOH1351 3.9 40.9 1.0 CE1 C:HIS2 4.0 21.6 1.0 CB B:ASP90 4.0 17.5 1.0 CG2 C:ILE88 4.1 18.0 1.0 CB C:ASP90 4.2 20.1 1.0 O C:HOH1020 4.2 20.9 1.0 CB B:ASP92 4.2 26.8 1.0 ND1 C:HIS2 4.3 18.7 1.0 O B:ALA1 4.5 20.9 1.0 ND1 B:HIS2 4.6 16.7 1.0 N B:ASP92 4.6 23.2 1.0 CA B:ASP92 4.6 25.2 1.0 NZ B:LYS98 4.6 37.6 1.0 N B:ALA91 4.7 18.6 1.0 C B:ALA91 4.7 21.7 1.0 CA B:ASP90 4.7 17.9 1.0 C B:ASP90 4.8 17.8 1.0 O B:ALA91 4.8 24.6 1.0 CB B:HIS2 5.0 14.9 1.0

E.Tanabe, Y.Yasutake, Y.Tanaka, M.Yao, K.Tsumoto, I.Kumagai, I.Tanaka. Crystal Structure of Proliferating Cell Nuclear Antigen (Pcna) Homolog From Sulfolobus Tokodaii To Be Published.