Zinc in PDB 1p5x: Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus

All present enzymatic activity of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus:
3.1.4.3;

The structure of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus, PDB code: 1p5x was solved by N.M.Antikainen, A.F.Monzingo, C.L.Franklin, J.D.Robertus, S.F.Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.140, 90.140, 74.060, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.6

The binding sites of Zinc atom in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus (pdb code 1p5x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus, PDB code: 1p5x:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn246 b:13.3 occ:1.00 O A:HOH249 1.9 10.4 1.0 OD2 A:ASP122 2.0 11.8 1.0 ND1 A:HIS69 2.0 8.0 1.0 NE2 A:HIS118 2.1 11.7 1.0 OD1 A:ASN55 2.6 15.6 1.0 O A:HOH452 2.7 36.9 1.0 CE1 A:HIS69 2.9 8.4 1.0 CG A:ASP122 3.0 9.0 1.0 CD2 A:HIS118 3.0 12.3 1.0 CE1 A:HIS118 3.1 10.2 1.0 CG A:HIS69 3.2 8.4 1.0 OD1 A:ASP122 3.3 7.9 1.0 ZN A:ZN248 3.3 13.8 1.0 CG A:ASN55 3.6 12.8 1.0 CB A:HIS69 3.6 7.7 1.0 ND2 A:ASN55 3.8 11.9 1.0 NE2 A:HIS14 4.0 7.7 1.0 NE2 A:HIS69 4.0 9.9 1.0 O A:HOH250 4.1 25.0 1.0 CG A:HIS118 4.2 11.1 1.0 ND1 A:HIS118 4.2 11.3 1.0 CD2 A:HIS69 4.2 8.1 1.0 CB A:ASP122 4.4 8.0 1.0 CE1 A:HIS14 4.5 7.9 1.0 CE1 A:HIS128 4.7 12.0 1.0 CA A:HIS69 4.8 8.5 1.0 O A:TRP1 4.9 10.1 1.0 CD2 A:HIS14 4.9 7.5 1.0 CD2 A:PHE66 4.9 16.6 1.0 CB A:ASN55 5.0 12.0 1.0

Zinc binding site 2 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn247 b:18.4 occ:1.00 NE2 A:HIS128 2.0 12.4 1.0 OE2 A:GLU146 2.1 15.4 1.0 NE2 A:HIS142 2.1 14.2 1.0 O A:HOH250 2.3 25.0 1.0 CD A:GLU146 2.7 15.8 1.0 OE1 A:GLU146 2.8 19.2 1.0 CE1 A:HIS128 2.9 12.0 1.0 CD2 A:HIS128 3.0 10.9 1.0 CD2 A:HIS142 3.1 13.8 1.0 CE1 A:HIS142 3.2 13.1 1.0 N A:TRP1 4.0 12.8 1.0 ND1 A:HIS128 4.0 12.1 1.0 CG A:GLU146 4.1 13.5 1.0 CG A:HIS128 4.1 9.7 1.0 CG A:HIS142 4.2 14.4 1.0 ND1 A:HIS142 4.2 13.7 1.0 OE1 A:GLN125 4.3 16.2 1.0 O A:HOH452 4.3 36.9 1.0 ZN A:ZN248 4.7 13.8 1.0 O A:HOH249 4.7 10.4 1.0 CA A:TRP1 4.8 11.2 1.0 CD A:GLN125 5.0 13.7 1.0

Zinc binding site 3 out of 3 in the Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the D55N Mutant of Phospholipase C From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn248 b:13.8 occ:1.00 NE2 A:HIS14 2.0 7.7 1.0 O A:HOH249 2.0 10.4 1.0 N A:TRP1 2.0 12.8 1.0 OD1 A:ASP122 2.1 7.9 1.0 O A:TRP1 2.2 10.1 1.0 C A:TRP1 2.9 11.3 1.0 CE1 A:HIS14 2.9 7.9 1.0 CA A:TRP1 2.9 11.2 1.0 CD2 A:HIS14 3.0 7.5 1.0 CG A:ASP122 3.1 9.0 1.0 O A:HOH250 3.1 25.0 1.0 ZN A:ZN246 3.3 13.3 1.0 OD2 A:ASP122 3.5 11.8 1.0 CB A:TRP1 3.7 11.4 1.0 NE2 A:HIS118 3.9 11.7 1.0 ND1 A:HIS14 4.0 9.8 1.0 CG A:HIS14 4.1 9.3 1.0 O A:HOH452 4.2 36.9 1.0 ND2 A:ASN55 4.2 11.9 1.0 N A:SER2 4.2 12.2 1.0 CE1 A:HIS118 4.2 10.2 1.0 CG A:TRP1 4.3 11.7 1.0 CD1 A:TRP1 4.3 12.8 1.0 CB A:ASP122 4.5 8.0 1.0 CE1 A:HIS128 4.5 12.0 1.0 OE2 A:GLU146 4.6 15.4 1.0 NE2 A:HIS128 4.6 12.4 1.0 ZN A:ZN247 4.7 18.4 1.0 CA A:ASP122 4.7 10.9 1.0 CD2 A:HIS118 4.8 12.3 1.0 OD1 A:ASN55 4.9 15.6 1.0 CA A:SER2 5.0 15.1 1.0 O A:SER2 5.0 15.6 1.0

N.M.Antikainen, A.F.Monzingo, C.L.Franklin, J.D.Robertus, S.F.Martin. Using X-Ray Crystallography of the ASP55ASN Mutant of the Phosphatidylcholine-Preferring Phospholipase C From Bacillus Cereus to Support the Mechanistic Role of ASP55 As the General Base. Arch.Biochem.Biophys. V. 417 81 2003.
ISSN: ISSN 0003-9861
PubMed: 12921783
DOI: 10.1016/S0003-9861(03)00343-6