Zinc in PDB 4tqt: Crystal Structure of Dihydropyrimidinase From Brucella Suis

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Brucella Suis:
3.5.2.2;

The structure of Crystal Structure of Dihydropyrimidinase From Brucella Suis, PDB code: 4tqt was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.24 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.690, 88.830, 221.240, 90.00, 91.17, 90.00
R / Rfree (%)	13.5 / 18.2

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Brucella Suis (pdb code 4tqt). 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 Dihydropyrimidinase From Brucella Suis, PDB code: 4tqt:
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 Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.7 occ:1.00 OQ1 A:KCX151 2.0 42.8 1.0 NE2 A:HIS63 2.2 40.0 1.0 NE2 A:HIS61 2.2 36.5 1.0 OD1 A:ASP317 2.4 52.1 1.0 CX A:KCX151 3.0 36.1 1.0 CD2 A:HIS61 3.1 32.9 1.0 CE1 A:HIS63 3.1 33.7 1.0 CD2 A:HIS63 3.1 36.6 1.0 CE1 A:HIS61 3.2 35.3 1.0 CG A:ASP317 3.2 48.7 1.0 OQ2 A:KCX151 3.3 36.1 1.0 ZN A:ZN502 3.4 50.5 1.0 O A:HOH606 3.5 53.9 1.0 OD2 A:ASP317 3.6 54.9 1.0 ND1 A:HIS63 4.2 35.9 1.0 CG A:HIS61 4.3 33.0 1.0 CG A:HIS63 4.3 39.1 1.0 ND1 A:HIS61 4.3 31.4 1.0 NZ A:KCX151 4.3 36.4 1.0 CB A:ASP317 4.4 41.4 1.0 CD2 A:HIS240 4.5 31.4 1.0 CE1 A:PHE95 4.6 34.7 1.0 NE2 A:HIS240 4.7 31.3 1.0 CD1 A:PHE95 4.8 34.6 1.0 CA A:ASP317 4.8 34.6 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:50.5 occ:1.00 ND1 A:HIS184 2.3 42.7 1.0 OQ2 A:KCX151 2.3 36.1 1.0 NE2 A:HIS240 2.4 31.3 1.0 O A:HOH606 3.0 53.9 1.0 CE1 A:HIS184 3.1 42.2 1.0 CD2 A:HIS240 3.1 31.4 1.0 CX A:KCX151 3.2 36.1 1.0 ZN A:ZN501 3.4 47.7 1.0 CG A:HIS184 3.4 31.8 1.0 OQ1 A:KCX151 3.5 42.8 1.0 CE1 A:HIS240 3.5 30.9 1.0 CB A:HIS184 3.8 30.3 1.0 O A:SER290 3.9 40.3 1.0 NE2 A:HIS184 4.3 37.9 1.0 OD2 A:ASP317 4.4 54.9 1.0 CG A:HIS240 4.4 31.9 1.0 CE1 A:PHE153 4.4 35.6 1.0 CD2 A:HIS184 4.4 37.1 1.0 CG2 A:VAL239 4.4 24.3 1.0 NE2 A:HIS61 4.5 36.5 1.0 OH A:TYR156 4.5 56.1 1.0 ND1 A:HIS240 4.5 32.2 1.0 NZ A:KCX151 4.5 36.4 1.0 CE1 A:HIS61 4.6 35.3 1.0 CE2 A:TYR156 4.8 49.0 1.0 CA A:HIS184 4.8 30.3 1.0 CD1 A:PHE153 4.9 29.6 1.0 OD1 A:ASP317 4.9 52.1 1.0 CG A:ASP317 4.9 48.7 1.0 C A:SER290 5.0 38.5 1.0 CE A:KCX151 5.0 32.3 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:44.8 occ:1.00 NE2 B:HIS61 2.2 28.7 1.0 NE2 B:HIS63 2.2 34.9 1.0 OQ1 B:KCX151 2.2 42.8 1.0 OD1 B:ASP317 2.6 46.7 1.0 O B:HOH611 3.1 56.1 1.0 CX B:KCX151 3.1 36.1 1.0 CE1 B:HIS61 3.2 30.1 1.0 CD2 B:HIS61 3.2 26.3 1.0 CD2 B:HIS63 3.2 32.2 1.0 CE1 B:HIS63 3.2 35.4 1.0 ZN B:ZN501 3.2 48.7 1.0 CG B:ASP317 3.3 42.1 1.0 OQ2 B:KCX151 3.3 32.4 1.0 OD2 B:ASP317 3.6 50.7 1.0 ND1 B:HIS61 4.3 32.3 1.0 ND1 B:HIS63 4.3 35.5 1.0 NZ B:KCX151 4.3 34.1 1.0 CG B:HIS63 4.3 33.3 1.0 CG B:HIS61 4.3 25.2 1.0 CB B:ASP317 4.4 30.2 1.0 CD2 B:HIS240 4.5 29.0 1.0 CE1 B:PHE95 4.6 31.7 1.0 NE2 B:HIS240 4.6 29.9 1.0 CD1 B:PHE95 4.8 26.5 1.0 CA B:ASP317 4.8 29.7 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:48.7 occ:1.00 OQ2 B:KCX151 2.2 32.4 1.0 ND1 B:HIS184 2.4 30.9 1.0 NE2 B:HIS240 2.5 29.9 1.0 O B:HOH611 2.8 56.1 1.0 CX B:KCX151 3.2 36.1 1.0 CE1 B:HIS184 3.2 29.0 1.0 ZN B:ZN500 3.2 44.8 1.0 CD2 B:HIS240 3.3 29.0 1.0 OQ1 B:KCX151 3.4 42.8 1.0 CG B:HIS184 3.4 30.8 1.0 CE1 B:HIS240 3.5 32.4 1.0 CB B:HIS184 3.8 23.3 1.0 O B:SER290 4.0 36.1 1.0 NE2 B:HIS184 4.4 31.9 1.0 CE2 B:PHE153 4.4 38.0 1.0 OD2 B:ASP317 4.4 50.7 1.0 NZ B:KCX151 4.5 34.1 1.0 CG B:HIS240 4.5 31.8 1.0 CG2 B:VAL239 4.5 23.9 1.0 CD2 B:HIS184 4.5 39.5 1.0 NE2 B:HIS61 4.5 28.7 1.0 CE1 B:HIS61 4.6 30.1 1.0 ND1 B:HIS240 4.6 31.7 1.0 OH B:TYR156 4.6 52.7 1.0 CA B:HIS184 4.8 24.7 1.0 CE2 B:TYR156 4.8 40.1 1.0 CD2 B:PHE153 4.9 29.6 1.0 OD1 B:ASP317 4.9 46.7 1.0 CE B:KCX151 5.0 33.6 1.0 CG B:ASP317 5.0 42.1 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:51.5 occ:1.00 OQ2 C:KCX151 2.1 43.4 1.0 NE2 C:HIS63 2.2 37.8 1.0 NE2 C:HIS61 2.2 36.6 1.0 OD1 C:ASP317 2.4 53.5 1.0 CE1 C:HIS63 3.1 39.4 1.0 CD2 C:HIS61 3.1 33.6 1.0 CG C:ASP317 3.1 49.0 1.0 CD2 C:HIS63 3.2 38.5 1.0 CX C:KCX151 3.2 42.4 1.0 ZN C:ZN501 3.2 53.8 1.0 CE1 C:HIS61 3.3 41.3 1.0 O C:HOH602 3.3 47.9 1.0 OD2 C:ASP317 3.5 54.0 1.0 OQ1 C:KCX151 3.6 48.7 1.0 ND1 C:HIS63 4.2 41.1 1.0 CG C:HIS63 4.3 37.3 1.0 CB C:ASP317 4.3 38.5 1.0 CG C:HIS61 4.3 34.1 1.0 ND1 C:HIS61 4.3 37.5 1.0 NZ C:KCX151 4.4 35.7 1.0 CD2 C:HIS240 4.6 34.5 1.0 CA C:ASP317 4.7 38.0 1.0 CE1 C:PHE95 4.7 34.4 1.0 CD1 C:PHE95 4.8 34.4 1.0 NE2 C:HIS240 4.9 30.2 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:53.8 occ:1.00 OQ1 C:KCX151 2.2 48.7 1.0 ND1 C:HIS184 2.3 39.0 1.0 NE2 C:HIS240 2.5 30.2 1.0 O C:HOH602 3.0 47.9 1.0 CX C:KCX151 3.1 42.4 1.0 CE1 C:HIS184 3.1 32.6 1.0 CD2 C:HIS240 3.2 34.5 1.0 OQ2 C:KCX151 3.2 43.4 1.0 ZN C:ZN500 3.2 51.5 1.0 CG C:HIS184 3.4 34.3 1.0 CE1 C:HIS240 3.7 35.8 1.0 CB C:HIS184 3.8 25.5 1.0 O C:SER290 4.0 41.7 1.0 OD2 C:ASP317 4.3 54.0 1.0 NE2 C:HIS184 4.3 30.6 1.0 OH C:TYR156 4.3 53.3 1.0 NE2 C:HIS61 4.4 36.6 1.0 CE2 C:PHE153 4.4 41.4 1.0 NZ C:KCX151 4.4 35.7 1.0 CG C:HIS240 4.5 35.5 1.0 CD2 C:HIS184 4.5 38.6 1.0 CG2 C:VAL239 4.5 32.0 1.0 CE1 C:HIS61 4.5 41.3 1.0 ND1 C:HIS240 4.7 38.4 1.0 CE2 C:TYR156 4.8 42.8 1.0 OD1 C:ASP317 4.8 53.5 1.0 CG C:ASP317 4.9 49.0 1.0 CA C:HIS184 4.9 27.0 1.0 CD2 C:PHE153 4.9 33.6 1.0 CE C:KCX151 5.0 35.9 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:46.0 occ:1.00 NE2 D:HIS63 2.2 38.8 1.0 NE2 D:HIS61 2.2 29.6 1.0 OQ2 D:KCX151 2.2 37.3 1.0 OD1 D:ASP317 2.4 50.4 1.0 CD2 D:HIS63 3.2 40.1 1.0 CE1 D:HIS63 3.2 42.1 1.0 CX D:KCX151 3.2 40.3 1.0 CE1 D:HIS61 3.2 33.8 1.0 CG D:ASP317 3.2 44.3 1.0 CD2 D:HIS61 3.2 27.2 1.0 ZN D:ZN501 3.3 50.8 1.0 OQ1 D:KCX151 3.5 44.9 1.0 OD2 D:ASP317 3.5 52.8 1.0 O D:HOH609 3.7 57.4 1.0 ND1 D:HIS63 4.3 41.9 1.0 CG D:HIS63 4.3 41.0 1.0 ND1 D:HIS61 4.3 32.3 1.0 CG D:HIS61 4.3 28.1 1.0 CB D:ASP317 4.3 37.4 1.0 NZ D:KCX151 4.4 39.1 1.0 CD2 D:HIS240 4.5 28.9 1.0 CE1 D:PHE95 4.6 32.5 1.0 NE2 D:HIS240 4.7 29.2 1.0 CA D:ASP317 4.8 29.9 1.0 CD1 D:PHE95 4.8 36.5 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:50.8 occ:1.00 OQ1 D:KCX151 2.2 44.9 1.0 ND1 D:HIS184 2.3 35.6 1.0 NE2 D:HIS240 2.5 29.2 1.0 O D:HOH609 3.1 57.4 1.0 CE1 D:HIS184 3.2 32.9 1.0 CX D:KCX151 3.2 40.3 1.0 CD2 D:HIS240 3.2 28.9 1.0 ZN D:ZN500 3.3 46.0 1.0 CG D:HIS184 3.3 39.0 1.0 OQ2 D:KCX151 3.4 37.3 1.0 CE1 D:HIS240 3.6 30.2 1.0 CB D:HIS184 3.6 23.3 1.0 O D:SER290 4.1 40.2 1.0 NE2 D:HIS184 4.3 37.0 1.0 CE2 D:PHE153 4.4 34.3 1.0 CD2 D:HIS184 4.4 40.0 1.0 CG2 D:VAL239 4.4 22.9 1.0 CG D:HIS240 4.5 26.7 1.0 OD2 D:ASP317 4.5 52.8 1.0 NZ D:KCX151 4.5 39.1 1.0 OH D:TYR156 4.5 56.6 1.0 NE2 D:HIS61 4.5 29.6 1.0 ND1 D:HIS240 4.6 26.5 1.0 CE1 D:HIS61 4.6 33.8 1.0 CE2 D:TYR156 4.7 45.1 1.0 CA D:HIS184 4.7 26.9 1.0 CD2 D:PHE153 4.8 31.1 1.0 OD1 D:ASP317 4.9 50.4 1.0 CE D:KCX151 5.0 33.2 1.0 CG D:ASP317 5.0 44.3 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn500 b:45.9 occ:1.00 NE2 E:HIS61 2.1 36.9 1.0 OQ1 E:KCX151 2.2 38.1 1.0 OD1 E:ASP317 2.3 44.5 1.0 NE2 E:HIS63 2.3 35.5 1.0 CD2 E:HIS61 3.1 34.0 1.0 CX E:KCX151 3.1 30.1 1.0 CG E:ASP317 3.1 42.8 1.0 CE1 E:HIS61 3.1 32.8 1.0 CD2 E:HIS63 3.1 31.0 1.0 OQ2 E:KCX151 3.3 32.9 1.0 CE1 E:HIS63 3.3 32.5 1.0 ZN E:ZN501 3.4 51.2 1.0 OD2 E:ASP317 3.4 54.6 1.0 O E:HOH630 3.5 51.2 1.0 ND1 E:HIS61 4.2 29.0 1.0 CG E:HIS61 4.2 31.6 1.0 CB E:ASP317 4.2 28.6 1.0 CG E:HIS63 4.3 34.5 1.0 NZ E:KCX151 4.3 33.0 1.0 ND1 E:HIS63 4.4 32.5 1.0 CD2 E:HIS240 4.5 27.4 1.0 CE1 E:PHE95 4.6 34.9 1.0 CA E:ASP317 4.7 30.3 1.0 NE2 E:HIS240 4.7 30.0 1.0 CD1 E:PHE95 4.8 36.1 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Dihydropyrimidinase From Brucella Suis


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 Dihydropyrimidinase From Brucella Suis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:51.2 occ:1.00 OQ2 E:KCX151 2.2 32.9 1.0 ND1 E:HIS184 2.3 34.0 1.0 NE2 E:HIS240 2.4 30.0 1.0 O E:HOH630 3.1 51.2 1.0 CE1 E:HIS184 3.2 33.5 1.0 CX E:KCX151 3.2 30.1 1.0 CD2 E:HIS240 3.2 27.4 1.0 CG E:HIS184 3.4 32.7 1.0 ZN E:ZN500 3.4 45.9 1.0 OQ1 E:KCX151 3.5 38.1 1.0 CE1 E:HIS240 3.5 28.9 1.0 CB E:HIS184 3.7 29.5 1.0 O E:SER290 4.0 37.7 1.0 OH E:TYR156 4.2 56.6 1.0 NE2 E:HIS184 4.3 34.1 1.0 OD2 E:ASP317 4.4 54.6 1.0 CE2 E:PHE153 4.4 32.9 1.0 CD2 E:HIS184 4.4 33.9 1.0 CG E:HIS240 4.5 28.2 1.0 NZ E:KCX151 4.5 33.0 1.0 CG2 E:VAL239 4.5 23.2 1.0 NE2 E:HIS61 4.5 36.9 1.0 ND1 E:HIS240 4.6 30.3 1.0 CE1 E:HIS61 4.6 32.8 1.0 CE2 E:TYR156 4.6 38.7 1.0 CA E:HIS184 4.8 31.2 1.0 CD2 E:PHE153 4.9 27.9 1.0 CE E:KCX151 4.9 30.9 1.0 OD1 E:ASP317 4.9 44.5 1.0 CZ E:TYR156 4.9 48.1 1.0 CG E:ASP317 5.0 42.8 1.0

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), J.Abendroth, D.R.Davies, D.Lorimer, T.E.Edwards. Crystal Structure of Dihydropyrimidinase From Brucella Suis To Be Published.