Zinc in PDB 1wpp: Structure of Streptococcus Gordonii Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase, PDB code: 1wpp was solved by I.P.Fabrichniy, L.Lehtio, A.Salminen, A.A.Baykov, R.Lahti, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.69 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.080, 148.960, 43.720, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21.6

The structure of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase (pdb code 1wpp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase, PDB code: 1wpp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:19.7 occ:1.00 OD1 A:ASP77 2.0 14.7 1.0 OD1 A:ASP13 2.0 16.1 1.0 O A:HOH807 2.1 17.3 1.0 NE2 A:HIS9 2.1 14.5 1.0 OD2 A:ASP13 2.5 14.2 1.0 O A:HOH852 2.6 24.3 1.0 CG A:ASP13 2.7 16.6 1.0 CG A:ASP77 3.0 15.7 1.0 CE1 A:HIS9 3.1 17.4 1.0 CD2 A:HIS9 3.1 16.3 1.0 OD2 A:ASP77 3.3 14.5 1.0 ZN A:ZN602 3.5 16.2 1.0 O A:HOH835 4.1 14.9 1.0 CB A:ASP13 4.2 15.4 1.0 ND1 A:HIS9 4.2 15.4 1.0 CG A:HIS9 4.3 15.8 1.0 CB A:ALA16 4.3 12.4 1.0 N A:ALA16 4.3 12.4 1.0 CB A:ASP77 4.3 14.9 1.0 OD1 A:ASP151 4.4 15.2 1.0 O A:ASP77 4.4 16.6 1.0 O A:HOH1011 4.4 29.2 1.0 CB A:ASP15 4.5 13.0 1.0 O A:HOH827 4.5 17.7 1.0 CE1 A:HIS100 4.6 16.7 1.0 OD2 A:ASP151 4.7 15.8 1.0 CA A:ALA16 4.7 14.1 1.0 OD2 A:ASP15 4.8 15.2 1.0 O A:HOH938 4.8 46.4 1.0 O A:HOH813 4.8 13.7 1.0 N A:ASP13 4.9 16.3 1.0 NE2 A:HIS100 4.9 16.0 1.0 O A:HOH860 4.9 30.4 1.0

Zinc binding site 2 out of 4 in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.2 occ:1.00 O A:HOH807 1.9 17.3 1.0 OD2 A:ASP151 2.0 15.8 1.0 OD2 A:ASP77 2.0 14.5 1.0 OD2 A:ASP15 2.0 15.2 1.0 NE2 A:HIS99 2.1 15.8 1.0 CG A:ASP77 2.9 15.7 1.0 CG A:ASP15 2.9 15.4 1.0 CE1 A:HIS99 3.0 15.8 1.0 CG A:ASP151 3.1 17.1 1.0 OD1 A:ASP77 3.1 14.7 1.0 CD2 A:HIS99 3.2 12.4 1.0 CB A:ASP15 3.3 13.0 1.0 OD1 A:ASP151 3.4 15.2 1.0 ZN A:ZN601 3.5 19.7 1.0 O A:HOH835 3.7 14.9 1.0 CE1 A:HIS100 3.9 16.7 1.0 N A:ALA121 4.0 15.1 1.0 OD1 A:ASP15 4.1 15.7 1.0 ND1 A:HIS99 4.2 16.9 1.0 CB A:ASP77 4.2 14.9 1.0 CA A:SER120 4.2 15.0 1.0 CG A:HIS99 4.3 14.9 1.0 CB A:ASP151 4.4 14.8 1.0 NE2 A:HIS100 4.4 16.0 1.0 CB A:SER120 4.6 15.4 1.0 C A:SER120 4.6 15.6 1.0 O A:HOH852 4.7 24.3 1.0 OD1 A:ASP13 4.7 16.1 1.0 CA A:ASP15 4.7 13.0 1.0 CB A:ALA121 4.8 13.8 1.0 OD2 A:ASP13 4.8 14.2 1.0 CA A:ASP77 4.9 14.9 1.0 C A:ASP15 5.0 13.2 1.0 ND1 A:HIS100 5.0 12.1 1.0

Zinc binding site 3 out of 4 in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:19.4 occ:1.00 OD1 B:ASP77 2.0 13.9 1.0 OD1 B:ASP13 2.0 15.7 1.0 NE2 B:HIS9 2.1 13.2 1.0 O B:HOH902 2.2 9.1 1.0 OD2 B:ASP13 2.4 16.1 1.0 O B:HOH1007 2.6 22.2 1.0 CG B:ASP13 2.6 14.4 1.0 CE1 B:HIS9 3.0 15.1 1.0 CG B:ASP77 3.1 12.4 1.0 CD2 B:HIS9 3.1 11.2 1.0 OD2 B:ASP77 3.4 12.3 1.0 ZN B:ZN604 3.6 14.4 1.0 O B:HOH928 3.9 20.9 1.0 N B:ALA16 4.1 12.0 1.0 CB B:ASP13 4.1 14.4 1.0 ND1 B:HIS9 4.2 15.1 1.0 CG B:HIS9 4.2 13.8 1.0 CB B:ALA16 4.2 11.7 1.0 CB B:ASP77 4.4 12.0 1.0 OD2 B:ASP151 4.4 10.1 1.0 O B:ASP77 4.4 12.2 1.0 CB B:ASP15 4.4 12.0 1.0 CA B:ALA16 4.6 12.1 1.0 O B:HOH916 4.6 20.8 1.0 CE1 B:HIS100 4.7 14.5 1.0 OD1 B:ASP15 4.7 12.7 1.0 N B:ASP13 4.7 12.8 1.0 O B:HOH941 4.7 13.9 1.0 OD1 B:ASP151 4.8 11.6 1.0 C B:ASP15 4.9 12.0 1.0 CA B:ASP13 5.0 12.7 1.0

Zinc binding site 4 out of 4 in the Structure of Streptococcus Gordonii Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Streptococcus Gordonii Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:14.4 occ:1.00 O B:HOH902 1.9 9.1 1.0 OD1 B:ASP15 2.0 12.7 1.0 OD1 B:ASP151 2.0 11.6 1.0 OD2 B:ASP77 2.0 12.3 1.0 NE2 B:HIS99 2.1 12.3 1.0 CG B:ASP15 3.0 13.4 1.0 CG B:ASP77 3.0 12.4 1.0 CE1 B:HIS99 3.0 12.0 1.0 CD2 B:HIS99 3.1 12.9 1.0 CG B:ASP151 3.1 13.3 1.0 CB B:ASP15 3.3 12.0 1.0 OD1 B:ASP77 3.3 13.9 1.0 OD2 B:ASP151 3.4 10.1 1.0 ZN B:ZN603 3.6 19.4 1.0 O B:HOH928 3.6 20.9 1.0 CE1 B:HIS100 4.0 14.5 1.0 N B:ALA121 4.1 10.8 1.0 ND1 B:HIS99 4.1 13.9 1.0 OD2 B:ASP15 4.2 13.1 1.0 CG B:HIS99 4.2 13.3 1.0 CA B:SER120 4.3 11.9 1.0 CB B:ASP77 4.4 12.0 1.0 NE2 B:HIS100 4.4 15.8 1.0 CB B:ASP151 4.4 12.2 1.0 O B:HOH1007 4.6 22.2 1.0 C B:SER120 4.7 11.4 1.0 CA B:ASP15 4.7 12.0 1.0 CB B:SER120 4.7 11.9 1.0 CB B:ALA121 4.7 12.7 1.0 OD1 B:ASP13 4.8 15.7 1.0 OD2 B:ASP13 4.8 16.1 1.0 CA B:ASP77 5.0 12.3 1.0 C B:ASP15 5.0 12.0 1.0 O B:ASP77 5.0 12.2 1.0 O B:GLY119 5.0 13.9 1.0

I.P.Fabrichniy, L.Lehtio, A.Salminen, A.B.Zyryanov, A.A.Baykov, R.Lahti, A.Goldman. Structural Studies of Metal Ions in Family II Pyrophosphatases: the Requirement For A Janus Ion Biochemistry V. 43 14403 2004.
ISSN: ISSN 0006-2960
PubMed: 15533045
DOI: 10.1021/BI0484973