Zinc in PDB 3rqz: Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus

The structure of Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus, PDB code: 3rqz was solved by C.Chang, R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	72.838, 72.838, 123.006, 90.00, 90.00, 120.00
R / Rfree (%)	12.3 / 15

The binding sites of Zinc atom in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus (pdb code 3rqz). 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 Metallophosphoesterase From Sphaerobacter Thermophilus, PDB code: 3rqz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:29.8 occ:1.00 OD1 A:ASP8 2.2 21.8 1.0 OD2 A:ASP34 2.2 24.1 1.0 NE2 A:HIS10 2.2 19.7 1.0 NE2 A:HIS149 2.3 22.2 1.0 O A:HOH257 2.5 26.7 1.0 ZN A:ZN302 2.5 50.2 0.3 CE1 A:HIS10 3.1 21.5 1.0 CE1 A:HIS149 3.2 22.8 1.0 CG A:ASP34 3.2 21.0 1.0 CG A:ASP8 3.2 20.8 1.0 CD2 A:HIS10 3.3 18.7 1.0 CD2 A:HIS149 3.3 22.7 1.0 CB A:ASP34 3.5 20.3 1.0 CB A:ASP8 3.8 19.8 1.0 OD2 A:ASP8 4.2 22.7 1.0 CE1 A:HIS114 4.2 20.3 1.0 NE2 A:HIS114 4.3 19.5 1.0 ND1 A:HIS10 4.3 20.7 1.0 ND1 A:HIS149 4.3 24.1 1.0 OD1 A:ASP34 4.3 23.3 1.0 CG A:HIS10 4.4 19.8 1.0 O A:HIS147 4.4 23.0 1.0 CG A:HIS149 4.4 22.6 1.0 CD2 A:HIS62 4.4 24.4 1.0 CA A:ASP8 4.6 19.7 1.0 CA A:HIS147 4.6 21.2 1.0 ND1 A:HIS147 4.7 22.6 1.0 OD1 A:ASN61 4.8 21.4 1.0 C A:HIS147 4.8 21.4 1.0 NE2 A:HIS62 4.9 27.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:50.2 occ:0.30 ND1 A:HIS147 2.3 22.6 1.0 ZN A:ZN301 2.5 29.8 1.0 O A:HOH257 2.6 26.7 1.0 OD2 A:ASP34 2.6 24.1 1.0 OD1 A:ASN61 3.0 21.4 1.0 NE2 A:HIS114 3.0 19.5 1.0 CE1 A:HIS147 3.1 24.7 1.0 O A:HIS147 3.4 23.0 1.0 CG A:HIS147 3.4 22.2 1.0 CA A:HIS147 3.5 21.2 1.0 OD1 A:ASP8 3.5 21.8 1.0 CE1 A:HIS114 3.8 20.3 1.0 CG A:ASP34 3.8 21.0 1.0 CG A:ASN61 3.9 20.6 1.0 C A:HIS147 3.9 21.4 1.0 NE2 A:HIS149 3.9 22.2 1.0 CB A:HIS147 3.9 21.4 1.0 ND2 A:ASN61 4.0 22.3 1.0 CD2 A:HIS114 4.1 17.4 1.0 NE2 A:HIS147 4.3 23.8 1.0 OD1 A:ASP34 4.4 23.3 1.0 CD2 A:HIS62 4.5 24.4 1.0 CD2 A:HIS147 4.5 23.1 1.0 CD2 A:HIS149 4.5 22.7 1.0 NE2 A:HIS10 4.5 19.7 1.0 N A:HIS147 4.6 19.9 1.0 CG A:ASP8 4.7 20.8 1.0 CB A:ASP34 4.8 20.3 1.0 CE1 A:TYR124 4.8 26.6 1.0 CE1 A:HIS149 4.9 22.8 1.0 NE2 A:HIS62 4.9 27.3 1.0 ND1 A:HIS114 5.0 18.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:33.6 occ:1.00 OD1 B:ASP8 2.1 19.3 1.0 OD2 B:ASP34 2.2 25.5 1.0 NE2 B:HIS10 2.2 24.1 1.0 NE2 B:HIS149 2.3 24.8 1.0 O B:HOH316 2.4 39.2 1.0 ZN B:ZN302 2.7 71.9 0.3 CG B:ASP8 3.1 23.9 1.0 CE1 B:HIS10 3.1 26.0 1.0 CE1 B:HIS149 3.2 26.8 1.0 CG B:ASP34 3.2 23.9 1.0 CD2 B:HIS10 3.2 23.7 1.0 CD2 B:HIS149 3.3 26.0 1.0 CB B:ASP34 3.5 21.9 1.0 CB B:ASP8 3.7 23.6 1.0 OD2 B:ASP8 4.1 27.7 1.0 CE1 B:HIS114 4.2 24.1 1.0 ND1 B:HIS10 4.3 25.6 1.0 ND1 B:HIS149 4.3 27.7 1.0 OD1 B:ASP34 4.3 24.4 1.0 CG B:HIS10 4.3 24.5 1.0 NE2 B:HIS114 4.4 23.9 1.0 CG B:HIS149 4.4 27.7 1.0 CA B:ASP8 4.4 23.8 1.0 O B:HIS147 4.4 28.5 1.0 CD2 B:HIS62 4.5 26.4 1.0 CA B:HIS147 4.5 26.0 1.0 ND1 B:HIS147 4.7 28.2 1.0 C B:HIS147 4.8 27.3 1.0 CE2 B:TYR38 4.9 32.0 1.0 NE2 B:HIS62 5.0 29.2 1.0 CA B:ASP34 5.0 22.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:71.9 occ:0.30 ND1 B:HIS147 2.1 28.2 1.0 OD2 B:ASP34 2.5 25.5 1.0 O B:HOH316 2.7 39.2 1.0 ZN B:ZN301 2.7 33.6 1.0 CE1 B:HIS147 2.8 27.9 1.0 NE2 B:HIS114 2.9 23.9 1.0 OD1 B:ASN61 3.0 23.7 1.0 CG B:HIS147 3.2 26.2 1.0 CA B:HIS147 3.4 26.0 1.0 O B:HIS147 3.4 28.5 1.0 OD1 B:ASP8 3.5 19.3 1.0 CE1 B:HIS114 3.6 24.1 1.0 CG B:ASP34 3.7 23.9 1.0 CB B:HIS147 3.7 25.9 1.0 C B:HIS147 3.9 27.3 1.0 CG B:ASN61 3.9 23.1 1.0 NE2 B:HIS147 4.0 27.8 1.0 CD2 B:HIS114 4.0 22.7 1.0 ND2 B:ASN61 4.0 25.8 1.0 NE2 B:HIS149 4.1 24.8 1.0 CD2 B:HIS147 4.2 27.0 1.0 OD1 B:ASP34 4.3 24.4 1.0 CD2 B:HIS62 4.4 26.4 1.0 N B:HIS147 4.5 25.1 1.0 CG B:ASP8 4.7 23.9 1.0 CD2 B:HIS149 4.7 26.0 1.0 NE2 B:HIS10 4.7 24.1 1.0 CB B:ASP34 4.7 21.9 1.0 OD1 C:ASN55 4.8 27.9 1.0 ND1 B:HIS114 4.8 23.7 1.0 CE1 B:TYR124 4.8 34.2 1.0 NE2 B:HIS62 4.9 29.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:30.1 occ:1.00 OD2 C:ASP8 2.1 24.3 1.0 OD2 C:ASP34 2.1 24.0 1.0 NE2 C:HIS10 2.2 20.0 1.0 NE2 C:HIS149 2.3 24.6 1.0 O C:HOH251 2.4 24.1 1.0 ZN C:ZN302 2.4 52.3 0.3 CE1 C:HIS10 3.0 21.0 1.0 CG C:ASP34 3.2 21.4 1.0 CE1 C:HIS149 3.2 24.0 1.0 CG C:ASP8 3.2 22.1 1.0 CD2 C:HIS10 3.3 19.3 1.0 CD2 C:HIS149 3.3 23.3 1.0 CB C:ASP34 3.5 21.4 1.0 CB C:ASP8 3.9 21.8 1.0 OD1 C:ASP8 4.1 24.3 1.0 CE1 C:HIS114 4.2 18.6 1.0 ND1 C:HIS10 4.2 21.6 1.0 O C:HIS147 4.3 23.5 1.0 NE2 C:HIS114 4.3 19.6 1.0 OD1 C:ASP34 4.3 22.1 1.0 ND1 C:HIS149 4.3 24.6 1.0 CG C:HIS10 4.4 20.8 1.0 CG C:HIS149 4.4 25.0 1.0 CD2 C:HIS62 4.5 23.7 1.0 CA C:ASP8 4.5 21.1 1.0 CA C:HIS147 4.6 22.9 1.0 O C:HOH253 4.6 42.0 1.0 ND1 C:HIS147 4.7 22.6 1.0 C C:HIS147 4.9 23.7 1.0 OD1 C:ASN61 4.9 20.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus


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 Metallophosphoesterase From Sphaerobacter Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:52.3 occ:0.30 ND1 C:HIS147 2.3 22.6 1.0 ZN C:ZN301 2.4 30.1 1.0 OD2 C:ASP34 2.6 24.0 1.0 O C:HOH251 3.0 24.1 1.0 NE2 C:HIS114 3.0 19.6 1.0 CE1 C:HIS147 3.1 24.0 1.0 OD1 C:ASN61 3.2 20.3 1.0 O C:HIS147 3.3 23.5 1.0 CA C:HIS147 3.3 22.9 1.0 OD2 C:ASP8 3.4 24.3 1.0 CG C:HIS147 3.4 23.0 1.0 CE1 C:HIS114 3.6 18.6 1.0 C C:HIS147 3.7 23.7 1.0 CG C:ASP34 3.8 21.4 1.0 CB C:HIS147 3.8 22.5 1.0 NE2 C:HIS149 3.8 24.6 1.0 CG C:ASN61 4.1 20.5 1.0 CD2 C:HIS114 4.1 18.4 1.0 ND2 C:ASN61 4.1 22.4 1.0 NE2 C:HIS147 4.3 25.3 1.0 CD2 C:HIS149 4.3 23.3 1.0 N C:HIS147 4.4 23.1 1.0 CG C:ASP8 4.4 22.1 1.0 CD2 C:HIS147 4.4 24.0 1.0 O C:HOH253 4.4 42.0 1.0 OD1 C:ASP34 4.5 22.1 1.0 NE2 C:HIS10 4.5 20.0 1.0 CB C:ASP34 4.7 21.4 1.0 CE1 C:TYR124 4.8 27.5 1.0 ND1 C:HIS114 4.8 18.4 1.0 OD1 C:ASP8 4.8 24.3 1.0 CD2 C:HIS62 4.8 23.7 1.0 CE1 C:HIS149 4.9 24.0 1.0

C.Chang, R.Wu, S.Clancy, A.Joachimiak. Crystal Structure of Metallophosphoesterase From Sphaerobacter Thermophilus To Be Published.