Zinc in PDB 4o23: Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58

All present enzymatic activity of Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58:
3.5.1.18;

The structure of Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58, PDB code: 4o23 was solved by B.Nocek, R.Holz, W.F.Anderson, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.25 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.324, 111.389, 132.535, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58 (pdb code 4o23). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58, PDB code: 4o23:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58


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 Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:19.5 occ:0.46 OD1 A:ASP101 2.0 28.4 1.0 O A:HOH609 2.1 28.9 1.0 OE1 A:GLU164 2.1 33.9 1.0 NE2 A:HIS68 2.1 24.8 1.0 OE2 A:GLU164 2.3 33.2 1.0 CD A:GLU164 2.5 32.4 1.0 CG A:ASP101 2.9 28.6 1.0 CE1 A:HIS68 3.1 24.9 1.0 CD2 A:HIS68 3.1 24.1 1.0 OD2 A:ASP101 3.2 30.7 1.0 OE1 A:GLU135 3.7 43.8 1.0 OE2 A:GLU136 3.8 49.7 1.0 CG A:GLU164 4.0 29.8 1.0 CG A:MET102 4.2 18.5 1.0 ND1 A:HIS68 4.2 24.8 1.0 CG A:HIS68 4.3 23.8 1.0 SD A:MET102 4.3 25.8 1.0 CD A:GLU135 4.3 42.8 1.0 CB A:ASP101 4.3 26.3 1.0 CB A:MET102 4.3 18.5 1.0 CD A:GLU136 4.6 50.9 1.0 CD A:PRO165 4.6 28.5 1.0 CA A:ASP101 4.7 23.6 1.0 C A:ASP101 4.7 21.8 1.0 CB A:GLU164 4.7 28.2 1.0 OE2 A:GLU135 4.8 43.6 1.0 CA A:GLU164 4.9 26.0 1.0 O A:ASP101 5.0 21.9 1.0 N A:MET102 5.0 20.3 1.0 CG A:GLU135 5.0 40.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58


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 Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:41.9 occ:0.59 OD1 B:ASP101 2.0 49.7 1.0 NE2 B:HIS68 2.1 43.2 1.0 O B:HOH547 2.1 35.8 1.0 OE2 B:GLU164 2.1 55.2 1.0 OE1 B:GLU164 2.2 54.8 1.0 CD B:GLU164 2.5 55.4 1.0 CG B:ASP101 2.9 50.8 1.0 CD2 B:HIS68 3.0 42.7 1.0 CE1 B:HIS68 3.1 43.9 1.0 OD2 B:ASP101 3.2 49.0 1.0 OE1 B:GLU135 3.5 58.9 1.0 OE2 B:GLU136 3.7 60.5 1.0 ZN B:ZN402 3.8 34.5 0.2 CD B:GLU135 3.8 59.3 1.0 CG B:GLU164 4.0 56.5 1.0 OE2 B:GLU135 4.1 59.8 1.0 CG B:HIS68 4.2 43.3 1.0 ND1 B:HIS68 4.2 44.2 1.0 SD B:MET102 4.3 48.3 1.0 CG B:MET102 4.3 49.8 1.0 CB B:ASP101 4.3 54.3 1.0 CB B:MET102 4.5 46.0 1.0 CD B:GLU136 4.5 59.0 1.0 CG B:GLU135 4.7 59.3 1.0 CD B:PRO165 4.7 47.9 1.0 CB B:GLU164 4.7 46.8 1.0 C B:ASP101 4.8 55.7 1.0 CA B:ASP101 4.8 56.1 1.0 CA B:GLU164 4.9 47.7 1.0 OE1 B:GLU136 4.9 58.4 1.0 O B:ASP101 5.0 54.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58


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 Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:34.5 occ:0.18 O B:HOH547 2.1 35.8 1.0 NE2 B:HIS350 2.1 61.5 1.0 OD2 B:ASP101 2.1 49.0 1.0 OE2 B:GLU136 2.5 60.5 1.0 OE1 B:GLU136 2.6 58.4 1.0 CE1 B:HIS350 2.7 59.8 1.0 CD B:GLU136 2.9 59.0 1.0 CD2 B:HIS350 3.3 62.5 1.0 CG B:ASP101 3.3 50.8 1.0 ZN B:ZN401 3.8 41.9 0.6 OD1 B:ASP101 3.9 49.7 1.0 ND1 B:HIS350 3.9 60.3 1.0 OE1 B:GLU135 4.2 58.9 1.0 CG B:HIS350 4.2 62.1 1.0 O B:HOH578 4.4 48.3 1.0 CG B:GLU136 4.4 58.1 1.0 CB B:ASP101 4.5 54.3 1.0 OE2 B:GLU164 4.8 55.2 1.0 CG1 B:VAL72 4.8 48.4 1.0 CD1 B:ILE349 4.8 67.3 1.0 NE2 B:HIS68 4.9 43.2 1.0 OE2 B:GLU135 5.0 59.8 1.0

B.Nocek, R.Holz, W.F.Anderson, A.Joachimiak. Crystal Structure of Mono-Zinc Form of Succinyl Diaminopimelate Desuccinylase From Neisseria Meningitidis MC58 To Be Published.