Zinc in PDB 3qn0: Structure of 6-Pyruvoyltetrahydropterin Synthase

All present enzymatic activity of Structure of 6-Pyruvoyltetrahydropterin Synthase:
4.1.2.50;

The structure of Structure of 6-Pyruvoyltetrahydropterin Synthase, PDB code: 3qn0 was solved by K.H.Seo, N.N.Zhuang, K.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.57 / 2.34
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.853, 117.680, 153.828, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.7

The binding sites of Zinc atom in the Structure of 6-Pyruvoyltetrahydropterin Synthase (pdb code 3qn0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of 6-Pyruvoyltetrahydropterin Synthase, PDB code: 3qn0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn121 b:55.1 occ:1.00 NE2 A:HIS30 2.0 50.6 1.0 NE2 A:HIS15 2.1 56.3 1.0 CE1 A:HIS30 2.3 61.4 1.0 NE2 A:HIS32 2.5 60.0 1.0 CE1 A:HIS15 2.9 53.9 1.0 CD2 A:HIS15 3.3 51.2 1.0 CD2 A:HIS30 3.3 53.0 1.0 CD2 A:HIS32 3.4 51.2 1.0 CE1 A:HIS32 3.5 53.6 1.0 ND1 A:HIS30 3.6 51.5 1.0 OE2 A:GLU109 3.7 72.5 1.0 CD A:GLU109 4.1 70.7 1.0 ND1 A:HIS15 4.1 52.2 1.0 CG A:HIS30 4.1 54.4 1.0 OE1 A:GLU109 4.2 70.3 1.0 CG A:HIS15 4.3 53.6 1.0 CE1 D:HIS70 4.5 62.6 1.0 CG A:HIS32 4.5 55.5 1.0 ND1 A:HIS32 4.6 57.4 1.0 SG A:CYS26 4.7 62.5 1.0

Zinc binding site 2 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn121 b:50.1 occ:1.00 NE2 B:HIS30 1.8 35.4 1.0 CE1 B:HIS30 2.1 46.2 1.0 NE2 B:HIS32 2.3 47.2 1.0 NE2 B:HIS15 2.3 43.9 1.0 CE1 B:HIS32 3.1 45.0 1.0 CE1 B:HIS15 3.2 36.3 1.0 CD2 B:HIS30 3.2 41.8 1.0 CD2 B:HIS15 3.3 40.9 1.0 CD2 B:HIS32 3.4 34.1 1.0 ND1 B:HIS30 3.5 35.3 1.0 OE2 B:GLU109 3.7 60.9 1.0 OE1 B:GLU109 3.9 60.9 1.0 CG B:HIS30 4.0 37.1 1.0 CD B:GLU109 4.0 59.0 1.0 ND1 B:HIS15 4.3 40.2 1.0 ND1 B:HIS32 4.3 40.8 1.0 CG B:HIS15 4.4 40.6 1.0 CG B:HIS32 4.4 39.8 1.0 NE2 F:HIS70 4.6 51.1 1.0 SG B:CYS26 4.7 53.9 1.0

Zinc binding site 3 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn121 b:52.4 occ:1.00 NE2 C:HIS30 1.9 33.0 1.0 NE2 C:HIS15 2.1 40.9 1.0 NE2 C:HIS32 2.1 41.2 1.0 CE1 C:HIS30 2.3 39.9 1.0 CE1 C:HIS15 3.1 38.1 1.0 CE1 C:HIS32 3.1 41.5 1.0 CD2 C:HIS32 3.1 35.2 1.0 CD2 C:HIS15 3.1 33.4 1.0 CD2 C:HIS30 3.3 38.4 1.0 ND1 C:HIS30 3.6 33.4 1.0 OE1 C:GLU109 3.7 60.8 1.0 OE2 C:GLU109 3.9 59.9 1.0 CD C:GLU109 4.0 57.4 1.0 CG C:HIS30 4.1 40.3 1.0 ND1 C:HIS32 4.2 40.8 1.0 ND1 C:HIS15 4.2 36.5 1.0 CG C:HIS32 4.2 39.8 1.0 CG C:HIS15 4.3 38.4 1.0 SG C:CYS26 4.5 52.3 1.0 CE1 E:HIS70 4.7 52.8 1.0

Zinc binding site 4 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn121 b:58.2 occ:1.00 NE2 D:HIS30 1.9 44.3 1.0 NE2 D:HIS15 2.1 50.6 1.0 CE1 D:HIS30 2.2 54.5 1.0 NE2 D:HIS32 2.3 51.6 1.0 CE1 D:HIS15 2.9 46.7 1.0 CD2 D:HIS15 3.1 44.6 1.0 CE1 D:HIS32 3.3 50.4 1.0 CD2 D:HIS30 3.3 45.8 1.0 CD2 D:HIS32 3.3 46.1 1.0 OE2 D:GLU109 3.5 66.8 1.0 ND1 D:HIS30 3.5 45.6 1.0 OE1 D:GLU109 3.9 67.0 1.0 CD D:GLU109 4.0 66.2 1.0 CG D:HIS30 4.0 47.7 1.0 ND1 D:HIS15 4.1 48.3 1.0 CG D:HIS15 4.2 48.9 1.0 ND1 D:HIS32 4.4 48.8 1.0 CG D:HIS32 4.4 49.2 1.0 SG D:CYS26 4.8 60.2 1.0 NE2 A:HIS70 4.9 65.1 1.0

Zinc binding site 5 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn121 b:49.8 occ:1.00 NE2 E:HIS30 1.9 32.3 1.0 NE2 E:HIS15 2.1 35.9 1.0 NE2 E:HIS32 2.2 41.7 1.0 CE1 E:HIS30 2.5 39.8 1.0 CE1 E:HIS15 3.0 38.8 1.0 CE1 E:HIS32 3.2 39.4 1.0 CD2 E:HIS32 3.2 31.5 1.0 CD2 E:HIS15 3.2 37.8 1.0 CD2 E:HIS30 3.2 36.2 1.0 OE2 E:GLU109 3.3 60.7 1.0 ND1 E:HIS30 3.7 33.5 1.0 CG E:HIS30 4.1 38.0 1.0 ND1 E:HIS15 4.2 40.4 1.0 CD E:GLU109 4.2 57.2 1.0 CG E:HIS15 4.3 38.2 1.0 ND1 E:HIS32 4.3 41.5 1.0 CG E:HIS32 4.3 38.9 1.0 OE1 E:GLU109 4.5 60.6 1.0 CE1 C:HIS70 4.7 49.6 1.0 SG E:CYS26 4.7 53.1 1.0

Zinc binding site 6 out of 6 in the Structure of 6-Pyruvoyltetrahydropterin Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of 6-Pyruvoyltetrahydropterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn121 b:53.9 occ:1.00 NE2 F:HIS30 1.8 34.6 1.0 NE2 F:HIS32 2.1 40.7 1.0 NE2 F:HIS15 2.3 39.8 1.0 CE1 F:HIS30 2.4 42.6 1.0 O B:HOH122 2.8 50.8 1.0 CD2 F:HIS32 3.0 37.0 1.0 CE1 F:HIS32 3.1 41.4 1.0 CD2 F:HIS30 3.1 39.6 1.0 CE1 F:HIS15 3.1 35.3 1.0 CD2 F:HIS15 3.3 36.2 1.0 OE1 F:GLU109 3.6 56.1 1.0 ND1 F:HIS30 3.7 39.5 1.0 OE2 F:GLU109 3.7 60.2 1.0 CD F:GLU109 3.9 55.2 1.0 CG F:HIS30 4.0 40.1 1.0 CG F:HIS32 4.2 40.2 1.0 ND1 F:HIS32 4.2 41.2 1.0 ND1 F:HIS15 4.3 38.3 1.0 CG F:HIS15 4.4 39.7 1.0 NE2 B:HIS70 4.5 50.3 1.0 SG F:CYS26 4.7 55.1 1.0 CD2 B:HIS70 4.9 48.9 1.0

K.H.Seo, N.Zhuang, Y.S.Park, K.H.Park, K.H.Lee. Structural Basis of A Novel Activity of Bacterial 6-Pyruvoyltetrahydropterin Synthase Homologues Distinct From Mammalian 6-Pyruvoyltetrahydropterin Synthase Activity. Acta Crystallogr.,Sect.D V. 70 1212 2014.
ISSN: ISSN 0907-4449
PubMed: 24816091
DOI: 10.1107/S1399004714002016