Zinc in PDB 3o93: High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes

The structure of High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes, PDB code: 3o93 was solved by J.B.French, Y.Cen, A.A.Sauve, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.05 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.178, 121.167, 63.201, 90.00, 114.55, 90.00
R / Rfree (%)	20.9 / 23.6

The binding sites of Zinc atom in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes (pdb code 3o93). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes, PDB code: 3o93:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn192 b:25.6 occ:1.00 OD2 A:ASP53 2.0 24.0 1.0 OE1 A:GLU64 2.0 27.9 1.0 NE2 A:HIS71 2.1 25.1 1.0 NE2 A:HIS55 2.1 26.8 1.0 N1 A:JJJ136 2.2 22.3 1.0 O A:HOH205 2.4 22.2 1.0 CE1 A:HIS71 2.8 25.4 1.0 CE1 A:HIS55 2.9 27.1 1.0 CD A:GLU64 3.0 28.9 1.0 C6 A:JJJ136 3.0 21.7 1.0 CG A:ASP53 3.1 22.3 1.0 C2 A:JJJ136 3.1 21.0 1.0 CD2 A:HIS55 3.2 27.1 1.0 CD2 A:HIS71 3.3 25.5 1.0 OE2 A:GLU64 3.3 29.1 1.0 OD1 A:ASP53 3.7 23.3 1.0 ND1 A:HIS71 4.0 25.0 1.0 ND1 A:HIS55 4.1 27.5 1.0 CB A:ASP53 4.2 21.2 1.0 CG A:HIS55 4.2 27.2 1.0 CG A:HIS71 4.3 25.7 1.0 C5 A:JJJ136 4.4 21.8 1.0 CG A:GLU64 4.4 29.4 1.0 C3 A:JJJ136 4.4 20.5 1.0 CZ A:PHE14 4.5 24.0 1.0 CE1 A:TYR106 4.8 17.0 1.0 C4 A:JJJ136 4.9 20.6 1.0

Zinc binding site 2 out of 4 in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn192 b:20.0 occ:1.00 OD2 B:ASP53 2.0 18.2 1.0 OE1 B:GLU64 2.0 21.4 1.0 NE2 B:HIS71 2.1 19.5 1.0 NE2 B:HIS55 2.1 22.7 1.0 N1 B:JJJ136 2.2 16.2 1.0 O B:HOH260 2.5 16.5 1.0 CD B:GLU64 3.0 21.6 1.0 CE1 B:HIS71 3.0 19.2 1.0 C6 B:JJJ136 3.0 15.6 1.0 CG B:ASP53 3.0 18.0 1.0 CE1 B:HIS55 3.0 22.9 1.0 CD2 B:HIS55 3.1 22.9 1.0 C2 B:JJJ136 3.1 15.5 1.0 CD2 B:HIS71 3.1 19.4 1.0 OE2 B:GLU64 3.2 21.8 1.0 OD1 B:ASP53 3.5 19.2 1.0 ND1 B:HIS71 4.1 19.5 1.0 ND1 B:HIS55 4.2 23.6 1.0 CG B:HIS55 4.2 23.2 1.0 CG B:HIS71 4.2 19.7 1.0 CB B:ASP53 4.2 17.5 1.0 CG B:GLU64 4.3 22.7 1.0 C5 B:JJJ136 4.4 15.8 1.0 C3 B:JJJ136 4.4 15.4 1.0 CZ B:PHE14 4.4 17.9 1.0 CE1 B:TYR106 4.8 11.0 1.0 C4 B:JJJ136 4.9 15.1 1.0

Zinc binding site 3 out of 4 in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn192 b:23.4 occ:1.00 OD2 C:ASP53 2.0 20.8 1.0 OE1 C:GLU64 2.0 25.5 1.0 NE2 C:HIS71 2.1 25.2 1.0 NE2 C:HIS55 2.1 24.1 1.0 N1 C:JJJ136 2.2 19.5 1.0 O C:HOH229 2.4 19.4 1.0 CD C:GLU64 3.0 27.1 1.0 CE1 C:HIS55 3.0 24.6 1.0 CG C:ASP53 3.0 19.2 1.0 C6 C:JJJ136 3.0 18.6 1.0 CE1 C:HIS71 3.0 25.8 1.0 C2 C:JJJ136 3.1 18.0 1.0 CD2 C:HIS71 3.1 25.9 1.0 CD2 C:HIS55 3.1 24.3 1.0 OE2 C:GLU64 3.3 27.0 1.0 OD1 C:ASP53 3.6 20.6 1.0 ND1 C:HIS55 4.1 24.6 1.0 ND1 C:HIS71 4.2 25.8 1.0 CB C:ASP53 4.2 18.1 1.0 CG C:HIS71 4.2 26.1 1.0 CG C:HIS55 4.2 24.3 1.0 CG C:GLU64 4.4 28.6 1.0 C5 C:JJJ136 4.4 18.4 1.0 C3 C:JJJ136 4.4 17.1 1.0 CZ C:PHE14 4.6 24.6 1.0 CE1 C:TYR106 4.9 11.1 1.0 C4 C:JJJ136 4.9 17.2 1.0

Zinc binding site 4 out of 4 in the High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into Catalytic Mechanism and Inhibition By Aldehydes within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn192 b:26.5 occ:1.00 OD2 D:ASP53 2.0 24.6 1.0 OE1 D:GLU64 2.0 28.7 1.0 NE2 D:HIS71 2.1 25.9 1.0 NE2 D:HIS55 2.1 26.4 1.0 N1 D:JJJ136 2.1 23.3 1.0 O D:HOH266 2.5 28.0 1.0 CE1 D:HIS71 2.9 26.0 1.0 CD D:GLU64 2.9 29.5 1.0 C6 D:JJJ136 3.0 22.5 1.0 CE1 D:HIS55 3.0 26.6 1.0 CG D:ASP53 3.0 23.9 1.0 CD2 D:HIS55 3.1 26.4 1.0 C2 D:JJJ136 3.1 22.2 1.0 OE2 D:GLU64 3.2 29.8 1.0 CD2 D:HIS71 3.2 25.8 1.0 OD1 D:ASP53 3.5 25.9 1.0 O D:HOH648 4.0 25.2 1.0 ND1 D:HIS71 4.1 25.7 1.0 ND1 D:HIS55 4.1 26.6 1.0 CG D:HIS55 4.2 26.3 1.0 CB D:ASP53 4.3 22.9 1.0 CG D:HIS71 4.3 26.0 1.0 C5 D:JJJ136 4.3 22.1 1.0 CG D:GLU64 4.3 30.1 1.0 C3 D:JJJ136 4.4 21.2 1.0 CZ D:PHE14 4.7 25.9 1.0 CE1 D:TYR106 4.8 14.4 1.0 C4 D:JJJ136 4.9 21.6 1.0 CD1 D:TYR106 5.0 14.3 1.0

J.B.French, Y.Cen, A.A.Sauve, S.E.Ealick. High-Resolution Crystal Structures of Streptococcus Pneumoniae Nicotinamidase with Trapped Intermediates Provide Insights Into the Catalytic Mechanism and Inhibition By Aldehydes . Biochemistry V. 49 8803 2010.
ISSN: ISSN 0006-2960
PubMed: 20853856
DOI: 10.1021/BI1012436