Zinc in PDB 5uej: 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58

All present enzymatic activity of 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58:
3.5.1.18;

The structure of 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58, PDB code: 5uej was solved by B.Nocek, A.Joachimiak, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.767, 88.644, 133.402, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 15.3

The binding sites of Zinc atom in the 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 (pdb code 5uej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58, PDB code: 5uej:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the 1.30 A Crystal Structure of Dape Enzyme 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 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.1 occ:1.00 O A:HOH857 2.0 16.7 1.0 OE1 A:GLU164 2.0 11.8 1.0 OD1 A:ASP101 2.0 12.6 1.0 NE2 A:HIS68 2.0 12.1 1.0 OE2 A:GLU164 2.6 14.7 1.0 CD A:GLU164 2.7 11.6 1.0 CE1 A:HIS68 2.9 12.2 1.0 CG A:ASP101 3.0 15.1 1.0 CD2 A:HIS68 3.1 12.2 1.0 ZN A:ZN402 3.3 15.9 0.8 OD2 A:ASP101 3.4 18.8 1.0 OE2 A:GLU136 3.8 16.7 1.0 O A:HOH877 3.8 35.3 1.0 ND1 A:HIS68 4.1 12.6 1.0 CG A:GLU164 4.1 11.5 1.0 CG A:HIS68 4.2 11.2 1.0 CG A:MET102 4.3 10.1 0.5 CB A:ASP101 4.3 12.7 1.0 SD A:MET102 4.3 8.3 0.5 CD A:GLU136 4.3 16.2 1.0 CB A:MET102 4.5 10.9 0.5 CB A:MET102 4.5 11.5 0.5 CG A:MET102 4.6 13.5 0.5 OE1 A:GLU136 4.6 18.0 1.0 CA A:ASP101 4.7 12.2 1.0 C A:ASP101 4.7 12.4 1.0 CD A:PRO165 4.7 11.7 1.0 CB A:GLU164 4.8 10.2 1.0 O A:ASP101 4.9 12.5 1.0

Zinc binding site 2 out of 5 in the 1.30 A Crystal Structure of Dape Enzyme 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 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.9 occ:0.80 NE2 A:HIS350 2.0 18.9 1.0 O A:HOH857 2.0 16.7 1.0 OD2 A:ASP101 2.0 18.8 1.0 OE2 A:GLU136 2.1 16.7 1.0 OE1 A:GLU136 2.4 18.0 1.0 CD A:GLU136 2.6 16.2 1.0 CE1 A:HIS350 3.0 24.9 1.0 CG A:ASP101 3.0 15.1 1.0 CD2 A:HIS350 3.1 18.8 1.0 ZN A:ZN401 3.3 13.1 1.0 OD1 A:ASP101 3.4 12.6 1.0 O A:HOH877 4.0 35.3 1.0 CG A:GLU136 4.1 16.7 1.0 O A:HOH715 4.1 16.1 1.0 ND1 A:HIS350 4.2 26.4 1.0 CG A:HIS350 4.2 20.3 1.0 CB A:ASP101 4.3 12.7 1.0 NE2 A:HIS68 4.4 12.1 1.0 CE1 A:HIS68 4.5 12.2 1.0 CD1 A:ILE349 4.7 36.0 1.0 CG1 A:VAL72 4.7 17.2 1.0 O A:HOH729 4.7 28.4 1.0 OE1 A:GLU164 4.8 11.8 1.0

Zinc binding site 3 out of 5 in the 1.30 A Crystal Structure of Dape Enzyme 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 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:16.8 occ:0.80 OE2 B:GLU136 2.0 17.5 1.0 OD2 B:ASP101 2.0 19.4 1.0 O B:HOH863 2.0 17.1 1.0 NE2 B:HIS350 2.0 18.4 1.0 OE1 B:GLU136 2.5 22.6 1.0 CD B:GLU136 2.6 18.9 1.0 CG B:ASP101 3.0 16.2 1.0 CD2 B:HIS350 3.0 23.5 1.0 CE1 B:HIS350 3.1 21.4 1.0 ZN B:ZN402 3.3 13.1 0.9 OD1 B:ASP101 3.3 13.5 1.0 O B:HOH902 3.9 40.6 1.0 O B:HOH716 4.0 18.5 1.0 O B:HOH861 4.0 31.2 1.0 CG B:GLU136 4.1 18.0 1.0 ND1 B:HIS350 4.1 29.1 1.0 CG B:HIS350 4.2 24.8 1.0 CB B:ASP101 4.2 15.1 1.0 NE2 B:HIS68 4.4 12.4 1.0 CE1 B:HIS68 4.5 13.3 1.0 CG1 B:VAL72 4.6 20.4 1.0 O B:HOH639 4.7 32.1 1.0 CD1 B:ILE349 4.7 36.3 1.0 OE1 B:GLU164 4.8 13.5 1.0

Zinc binding site 4 out of 5 in the 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:13.1 occ:0.95 OE1 B:GLU164 1.9 13.5 1.0 OD1 B:ASP101 1.9 13.5 1.0 O B:HOH863 1.9 17.1 1.0 NE2 B:HIS68 2.0 12.4 1.0 OE2 B:GLU164 2.6 15.6 1.0 CD B:GLU164 2.7 13.0 1.0 CG B:ASP101 2.9 16.2 1.0 CE1 B:HIS68 3.0 13.3 1.0 CD2 B:HIS68 3.1 12.0 1.0 ZN B:ZN401 3.3 16.8 0.8 OD2 B:ASP101 3.3 19.4 1.0 O B:HOH902 3.7 40.6 1.0 OE2 B:GLU136 3.7 17.5 1.0 CG B:GLU164 4.1 13.2 1.0 ND1 B:HIS68 4.1 13.1 1.0 O B:HOH861 4.1 31.2 1.0 CG B:HIS68 4.2 12.0 1.0 CB B:ASP101 4.3 15.1 1.0 SD B:MET102 4.4 9.5 0.5 CG B:MET102 4.4 10.5 0.5 CD B:GLU136 4.4 18.9 1.0 CB B:MET102 4.5 12.5 0.5 CB B:MET102 4.5 11.6 0.5 CG B:MET102 4.5 15.1 0.5 O B:HOH847 4.5 31.9 1.0 CA B:ASP101 4.7 12.9 1.0 CD B:PRO165 4.7 13.3 1.0 OE1 B:GLU136 4.7 22.6 1.0 C B:ASP101 4.7 12.9 1.0 CB B:GLU164 4.8 12.7 1.0 O B:ASP101 4.9 14.1 1.0 O B:HOH900 5.0 35.6 1.0

Zinc binding site 5 out of 5 in the 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:31.7 occ:0.50 NE2 B:HIS120 2.2 27.9 1.0 CE1 B:HIS120 2.4 25.2 1.0 O B:HOH882 2.4 61.5 1.0 O B:HOH965 2.4 31.7 1.0 CD2 B:HIS120 3.5 19.9 1.0 ND1 B:HIS120 3.7 23.3 1.0 O B:HOH749 3.8 30.4 1.0 CG B:HIS120 4.2 16.7 1.0 O B:HOH618 4.5 25.7 1.0 CB B:LYS119 5.0 15.1 1.0

B.Nocek, T.Heath, D.Becker, A.Joachimiak, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.30 A Crystal Structure of Dape Enzyme From Neisseria Meningitidis MC58 To Be Published.