Zinc in PDB 3ovg: The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound

The structure of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound, PDB code: 3ovg was solved by Z.Zhang, D.Kumaran, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.75 / 2.06
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	89.256, 89.186, 96.059, 98.95, 92.89, 119.86
R / Rfree (%)	17.2 / 21

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

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound (pdb code 3ovg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound, PDB code: 3ovg:
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 The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn362 b:34.0 occ:1.00 OD1 A:ASP272 2.2 16.4 1.0 NE2 A:HIS26 2.3 18.7 1.0 O A:HOH1198 2.4 25.3 1.0 OQ2 A:KCX153 2.4 28.9 1.0 NE2 A:HIS24 2.4 19.8 1.0 O A:HOH1197 2.5 24.7 1.0 CG A:ASP272 3.2 18.7 1.0 CE1 A:HIS26 3.2 18.6 1.0 CD2 A:HIS24 3.3 19.5 1.0 CD2 A:HIS26 3.3 18.5 1.0 CE1 A:HIS24 3.4 23.2 1.0 OD2 A:ASP272 3.5 19.2 1.0 CX A:KCX153 3.6 28.4 1.0 ZN A:ZN363 3.7 46.7 1.0 OQ1 A:KCX153 4.0 27.2 1.0 O A:HOH1039 4.1 28.8 1.0 ND1 A:HIS26 4.3 17.6 1.0 CB A:ASP272 4.4 18.1 1.0 CG A:HIS26 4.4 16.3 1.0 CG A:HIS24 4.4 20.1 1.0 ND1 A:HIS24 4.5 20.6 1.0 NZ A:KCX153 4.6 22.2 1.0 CE1 A:HIS214 4.7 21.4 1.0 CA A:ASP272 4.8 16.5 1.0 NE2 A:HIS214 4.9 22.8 1.0 NZ A:LYS29 4.9 19.1 1.0 O A:HOH946 4.9 26.2 1.0

Zinc binding site 2 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn363 b:46.7 occ:1.00 OQ1 A:KCX153 2.2 27.2 1.0 NE2 A:HIS214 2.4 22.8 1.0 ND1 A:HIS186 2.4 23.1 1.0 O A:HOH1198 2.5 25.3 1.0 CX A:KCX153 3.0 28.4 1.0 OQ2 A:KCX153 3.2 28.9 1.0 CE1 A:HIS214 3.3 21.4 1.0 CD2 A:HIS214 3.4 21.5 1.0 CG A:HIS186 3.4 20.9 1.0 CE1 A:HIS186 3.4 21.6 1.0 CB A:HIS186 3.6 18.6 1.0 ZN A:ZN362 3.7 34.0 1.0 CE1 A:HIS24 3.8 23.2 1.0 NE2 A:HIS24 4.0 19.8 1.0 CE1 A:HIS100 4.1 24.3 1.0 ND1 A:HIS214 4.4 19.9 1.0 NZ A:KCX153 4.4 22.2 1.0 NE2 A:HIS100 4.4 23.7 1.0 CG A:HIS214 4.5 19.3 1.0 NE2 A:HIS186 4.5 21.7 1.0 CD2 A:HIS186 4.5 20.8 1.0 OD2 A:ASP272 4.6 19.2 1.0 O A:HOH1197 4.6 24.7 1.0 CA A:HIS186 4.6 16.4 1.0 O A:HOH605 4.8 27.8 1.0 CE A:KCX153 4.8 20.7 1.0 O A:HOH1039 5.0 28.8 1.0 OD1 A:ASP272 5.0 16.4 1.0 ND1 A:HIS24 5.0 20.6 1.0

Zinc binding site 3 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn362 b:51.0 occ:1.00 OQ1 B:KCX153 2.2 30.2 1.0 NE2 B:HIS214 2.4 21.8 1.0 O B:HOH1190 2.5 23.8 1.0 ND1 B:HIS186 2.5 22.3 1.0 CX B:KCX153 3.0 28.0 1.0 OQ2 B:KCX153 3.1 24.6 1.0 CE1 B:HIS214 3.3 22.0 1.0 CD2 B:HIS214 3.4 20.9 1.0 CG B:HIS186 3.5 19.4 1.0 CE1 B:HIS186 3.5 20.9 1.0 ZN B:ZN363 3.6 33.0 1.0 CB B:HIS186 3.6 18.4 1.0 NE2 B:HIS24 3.7 22.7 1.0 CE1 B:HIS24 4.1 17.6 1.0 CE1 B:HIS100 4.1 24.2 1.0 NE2 B:HIS100 4.2 27.6 1.0 NZ B:KCX153 4.4 23.4 1.0 OD2 B:ASP272 4.4 20.8 1.0 ND1 B:HIS214 4.4 22.4 1.0 O B:HOH1191 4.5 22.4 1.0 CG B:HIS214 4.5 19.9 1.0 CD2 B:HIS186 4.6 20.7 1.0 NE2 B:HIS186 4.6 19.5 1.0 CA B:HIS186 4.7 15.8 1.0 O B:HOH1072 4.8 23.1 1.0 CE B:KCX153 4.8 22.0 1.0 CD2 B:HIS24 4.9 17.7 1.0 OD1 B:ASP272 5.0 20.1 1.0

Zinc binding site 4 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn363 b:33.0 occ:1.00 NE2 B:HIS26 2.2 19.8 1.0 OQ2 B:KCX153 2.2 24.6 1.0 OD1 B:ASP272 2.3 20.1 1.0 CE1 B:HIS24 2.3 17.6 1.0 O B:HOH1191 2.3 22.4 1.0 O B:HOH1190 2.5 23.8 1.0 CE1 B:HIS26 2.9 20.1 1.0 CG B:ASP272 3.2 21.2 1.0 NE2 B:HIS24 3.2 22.7 1.0 ND1 B:HIS24 3.3 18.7 1.0 CD2 B:HIS26 3.3 18.3 1.0 CX B:KCX153 3.4 28.0 1.0 OD2 B:ASP272 3.5 20.8 1.0 ZN B:ZN362 3.6 51.0 1.0 OQ1 B:KCX153 3.9 30.2 1.0 O B:HOH1038 4.1 33.1 1.0 ND1 B:HIS26 4.1 18.1 1.0 CG B:HIS26 4.4 15.9 1.0 CD2 B:HIS24 4.4 17.7 1.0 CG B:HIS24 4.4 19.2 1.0 CB B:ASP272 4.5 19.6 1.0 NZ B:KCX153 4.5 23.4 1.0 CE1 B:HIS214 4.8 22.0 1.0 NE2 B:HIS214 4.9 21.8 1.0 CA B:ASP272 4.9 16.4 1.0 O B:HOH995 4.9 28.1 1.0 O B:MSE67 4.9 19.6 1.0 NZ B:LYS29 5.0 21.1 1.0

Zinc binding site 5 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn362 b:33.1 occ:1.00 NE2 C:HIS26 2.2 17.6 1.0 OD1 C:ASP272 2.3 18.7 1.0 OQ1 C:KCX153 2.4 25.3 1.0 NE2 C:HIS24 2.4 21.0 1.0 O C:HOH1193 2.4 23.8 1.0 O C:HOH1192 2.4 25.6 1.0 CE1 C:HIS26 3.1 18.1 1.0 CG C:ASP272 3.1 19.6 1.0 CD2 C:HIS24 3.1 17.4 1.0 CX C:KCX153 3.2 29.5 1.0 CD2 C:HIS26 3.3 18.8 1.0 OD2 C:ASP272 3.4 22.4 1.0 CE1 C:HIS24 3.5 20.7 1.0 OQ2 C:KCX153 3.7 24.6 1.0 ZN C:ZN363 3.7 51.6 1.0 ND1 C:HIS26 4.2 18.3 1.0 O C:HOH968 4.2 27.0 1.0 CG C:HIS24 4.4 20.0 1.0 CG C:HIS26 4.4 17.7 1.0 CB C:ASP272 4.4 15.9 1.0 ND1 C:HIS24 4.5 18.5 1.0 NZ C:KCX153 4.5 25.4 1.0 CE1 C:HIS214 4.7 20.5 1.0 O C:HOH1194 4.7 29.3 1.0 NE2 C:HIS214 4.8 19.8 1.0 NZ C:LYS29 4.8 19.8 1.0 CA C:ASP272 4.8 16.4 1.0 O C:MSE67 4.9 18.2 1.0

Zinc binding site 6 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn363 b:51.6 occ:1.00 NE2 C:HIS214 2.2 19.8 1.0 OQ2 C:KCX153 2.3 24.6 1.0 O C:HOH1192 2.4 25.6 1.0 ND1 C:HIS186 2.4 22.5 1.0 CD2 C:HIS214 3.2 20.0 1.0 CE1 C:HIS214 3.2 20.5 1.0 CX C:KCX153 3.3 29.5 1.0 CG C:HIS186 3.4 20.3 1.0 CE1 C:HIS186 3.4 23.3 1.0 OQ1 C:KCX153 3.5 25.3 1.0 CB C:HIS186 3.6 18.0 1.0 ZN C:ZN362 3.7 33.1 1.0 CE1 C:HIS24 3.8 20.7 1.0 NE2 C:HIS24 4.0 21.0 1.0 CE1 C:HIS100 4.3 24.5 1.0 ND1 C:HIS214 4.3 20.4 1.0 OD2 C:ASP272 4.3 22.4 1.0 CG C:HIS214 4.3 18.9 1.0 NE2 C:HIS100 4.5 25.6 1.0 NE2 C:HIS186 4.5 20.6 1.0 CD2 C:HIS186 4.5 22.7 1.0 NZ C:KCX153 4.6 25.4 1.0 CA C:HIS186 4.6 17.6 1.0 O C:HOH1193 4.8 23.8 1.0 CE C:KCX153 4.9 21.9 1.0 CG C:ASP272 5.0 19.6 1.0

Zinc binding site 7 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn362 b:49.9 occ:1.00 OQ2 D:KCX153 2.2 26.6 1.0 ND1 D:HIS186 2.4 23.8 1.0 NE2 D:HIS214 2.4 19.7 1.0 O D:HOH1195 2.4 23.4 1.0 CX D:KCX153 3.1 29.0 1.0 CD2 D:HIS214 3.3 20.7 1.0 CE1 D:HIS186 3.3 22.4 1.0 OQ1 D:KCX153 3.3 27.1 1.0 CE1 D:HIS214 3.3 21.2 1.0 CG D:HIS186 3.4 20.6 1.0 CB D:HIS186 3.6 20.5 1.0 ZN D:ZN363 3.7 35.0 1.0 CE1 D:HIS24 3.8 23.1 1.0 NE2 D:HIS24 4.1 21.4 1.0 CE1 D:HIS100 4.2 26.8 1.0 OD2 D:ASP272 4.4 18.5 1.0 NE2 D:HIS186 4.4 18.6 1.0 NZ D:KCX153 4.4 24.1 1.0 ND1 D:HIS214 4.4 20.7 1.0 CG D:HIS214 4.4 18.9 1.0 CD2 D:HIS186 4.5 21.1 1.0 NE2 D:HIS100 4.5 27.8 1.0 CA D:HIS186 4.7 16.5 1.0 CE D:KCX153 4.8 18.3 1.0

Zinc binding site 8 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn363 b:35.0 occ:1.00 OD1 D:ASP272 2.2 15.1 1.0 NE2 D:HIS26 2.3 16.4 1.0 NE2 D:HIS24 2.3 21.4 1.0 OQ1 D:KCX153 2.5 27.1 1.0 O D:HOH1195 2.5 23.4 1.0 CG D:ASP272 3.1 18.8 1.0 CE1 D:HIS26 3.2 18.1 1.0 CD2 D:HIS24 3.2 19.2 1.0 CX D:KCX153 3.3 29.0 1.0 CD2 D:HIS26 3.3 18.6 1.0 OD2 D:ASP272 3.3 18.5 1.0 CE1 D:HIS24 3.4 23.1 1.0 ZN D:ZN362 3.7 49.9 1.0 OQ2 D:KCX153 3.8 26.6 1.0 O D:HOH697 4.2 28.3 1.0 ND1 D:HIS26 4.3 18.2 1.0 CB D:ASP272 4.4 17.0 1.0 CG D:HIS24 4.4 17.6 1.0 CG D:HIS26 4.4 17.0 1.0 ND1 D:HIS24 4.4 18.6 1.0 NZ D:KCX153 4.5 24.1 1.0 CE1 D:HIS214 4.8 21.2 1.0 NE2 D:HIS214 4.8 19.7 1.0 CA D:ASP272 4.8 16.4 1.0 O D:MSE67 4.8 22.1 1.0 NZ D:LYS29 4.9 21.9 1.0 O D:HOH1099 5.0 30.1 1.0

Zinc binding site 9 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn362 b:55.4 occ:1.00 OQ1 E:KCX153 2.2 28.5 1.0 ND1 E:HIS186 2.4 23.0 1.0 NE2 E:HIS214 2.4 23.1 1.0 O E:HOH1199 2.6 23.8 1.0 CX E:KCX153 3.1 27.2 1.0 CG E:HIS186 3.3 22.6 1.0 CE1 E:HIS214 3.3 21.6 1.0 CD2 E:HIS214 3.3 21.1 1.0 CE1 E:HIS186 3.4 21.2 1.0 OQ2 E:KCX153 3.4 23.4 1.0 CB E:HIS186 3.5 20.2 1.0 ZN E:ZN363 3.7 34.3 1.0 CE1 E:HIS24 3.8 20.7 1.0 CE1 E:HIS100 4.0 23.6 1.0 NE2 E:HIS24 4.1 19.2 1.0 NE2 E:HIS100 4.2 25.6 1.0 O E:HOH1204 4.4 32.6 1.0 ND1 E:HIS214 4.4 21.8 1.0 NZ E:KCX153 4.4 22.5 1.0 CD2 E:HIS186 4.4 21.2 1.0 CG E:HIS214 4.5 20.0 1.0 NE2 E:HIS186 4.5 20.3 1.0 CA E:HIS186 4.5 19.3 1.0 CE E:KCX153 4.7 19.4 1.0 OD2 E:ASP272 4.7 20.9 1.0 O E:HOH1201 4.7 20.8 1.0 O E:HOH471 4.8 25.7 1.0 ND1 E:HIS24 5.0 20.8 1.0

Zinc binding site 10 out of 12 in the The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn363 b:34.3 occ:1.00 OD1 E:ASP272 2.2 17.5 1.0 NE2 E:HIS24 2.3 19.2 1.0 NE2 E:HIS26 2.3 19.4 1.0 O E:HOH1201 2.4 20.8 1.0 OQ2 E:KCX153 2.4 23.4 1.0 O E:HOH1199 2.4 23.8 1.0 CG E:ASP272 3.1 21.1 1.0 CD2 E:HIS24 3.2 17.6 1.0 CE1 E:HIS26 3.2 19.0 1.0 CE1 E:HIS24 3.3 20.7 1.0 CD2 E:HIS26 3.3 17.1 1.0 CX E:KCX153 3.5 27.2 1.0 OD2 E:ASP272 3.6 20.9 1.0 ZN E:ZN362 3.7 55.4 1.0 OQ1 E:KCX153 3.8 28.5 1.0 O E:HOH378 4.3 27.4 1.0 ND1 E:HIS26 4.3 17.4 1.0 CG E:HIS24 4.3 19.4 1.0 ND1 E:HIS24 4.3 20.8 1.0 CB E:ASP272 4.4 17.4 1.0 CG E:HIS26 4.4 16.6 1.0 NZ E:KCX153 4.6 22.5 1.0 CE1 E:HIS214 4.7 21.6 1.0 CA E:ASP272 4.8 17.0 1.0 NE2 E:HIS214 4.8 23.1 1.0 O E:MSE67 4.8 19.8 1.0 O E:HOH1202 4.8 26.3 1.0

Z.Zhang, D.Kumaran, S.K.Burley, S.Swaminathan. The Crystal Structure of An Amidohydrolase From Mycoplasma Synoviae with Zn Ion Bound To Be Published.