Zinc in PDB 4op4: Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form:
3.5.1.18;

The structure of Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form, PDB code: 4op4 was solved by B.Nocek, M.Makowska-Grzyska, R.Jedrzejczak, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.71 / 1.65
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	49.898, 49.898, 231.762, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 16.6

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form (pdb code 4op4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form, PDB code: 4op4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form


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 the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.5 occ:0.98 OD2 A:ASP101 2.0 12.9 1.0 OE2 A:GLU136 2.0 23.8 1.0 O1 A:EDO311 2.0 25.3 1.0 O2 A:EDO311 2.0 11.6 1.0 NE2 A:HIS239 2.1 17.9 1.0 OE1 A:GLU136 2.1 29.1 1.0 CD A:GLU136 2.4 23.5 1.0 CE1 A:HIS239 2.9 19.7 1.0 C1 A:EDO311 3.0 23.5 1.0 C2 A:EDO311 3.0 17.4 1.0 CG A:ASP101 3.0 11.4 1.0 CD2 A:HIS239 3.2 11.9 1.0 OD1 A:ASP101 3.4 12.0 1.0 ZN A:ZN303 3.4 14.8 0.8 CG A:GLU136 3.9 19.9 1.0 O A:HOH422 4.0 10.0 1.0 OE1 A:GLU135 4.0 25.3 1.0 ND1 A:HIS239 4.1 19.0 1.0 CG A:HIS239 4.2 14.2 1.0 CB A:ASP101 4.4 8.0 1.0 O A:HOH454 4.5 21.1 1.0 NE2 A:HIS68 4.6 7.5 1.0 O A:HOH532 4.6 30.6 1.0 CE1 A:HIS68 4.7 8.1 1.0 CB A:GLU136 4.8 19.3 1.0 CD1 A:ILE238 4.9 9.0 1.0 OE2 A:GLU164 4.9 11.4 1.0 CD A:GLU135 5.0 24.8 1.0 CG1 A:VAL72 5.0 14.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form


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 the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.8 occ:0.85 NE2 A:HIS68 2.0 7.5 1.0 OD1 A:ASP101 2.0 12.0 1.0 O2 A:EDO311 2.0 11.6 1.0 OE2 A:GLU164 2.1 11.4 1.0 OE1 A:GLU164 2.6 17.8 1.0 CD A:GLU164 2.6 15.4 1.0 C2 A:EDO311 2.7 17.4 1.0 CE1 A:HIS68 2.9 8.1 1.0 CG A:ASP101 3.0 11.4 1.0 CD2 A:HIS68 3.0 8.4 1.0 OD2 A:ASP101 3.3 12.9 1.0 ZN A:ZN302 3.4 15.5 1.0 OE1 A:GLU135 3.4 25.3 1.0 OE2 A:GLU136 3.6 23.8 1.0 CD A:GLU135 4.0 24.8 1.0 C1 A:EDO311 4.0 23.5 1.0 ND1 A:HIS68 4.1 11.9 1.0 CG A:GLU164 4.1 8.6 1.0 CG A:HIS68 4.1 9.2 1.0 O1 A:EDO311 4.1 25.3 1.0 CD A:GLU136 4.2 23.5 1.0 OE2 A:GLU135 4.3 26.8 1.0 CB A:ASP101 4.3 8.0 1.0 CG A:MET102 4.4 9.3 1.0 CB A:MET102 4.5 7.2 1.0 OE1 A:GLU136 4.5 29.1 1.0 SD A:MET102 4.5 10.7 1.0 CD A:PRO165 4.6 11.5 1.0 C A:ASP101 4.6 8.9 1.0 CA A:ASP101 4.7 8.1 1.0 CB A:GLU164 4.8 6.4 1.0 O A:ASP101 4.9 10.8 1.0 N A:MET102 4.9 5.6 1.0 CG A:GLU135 4.9 17.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form


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 the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.2 occ:0.54 OD2 B:ASP101 2.0 21.0 1.0 OE2 B:GLU136 2.0 17.2 1.0 NE2 B:HIS239 2.1 14.2 1.0 O B:HOH635 2.2 28.4 1.0 OE1 B:GLU136 2.3 19.4 1.0 O B:HOH634 2.3 23.4 1.0 CD B:GLU136 2.5 10.8 1.0 CE1 B:HIS239 3.0 10.6 1.0 CG B:ASP101 3.1 15.2 1.0 CD2 B:HIS239 3.1 18.4 1.0 ZN B:ZN303 3.4 13.2 0.7 OD1 B:ASP101 3.5 11.0 1.0 CG B:GLU136 4.0 11.8 1.0 O B:HOH631 4.1 28.2 1.0 ND1 B:HIS239 4.1 12.9 1.0 CG B:HIS239 4.2 15.2 1.0 O B:HOH416 4.3 10.6 1.0 O B:HOH506 4.3 22.4 1.0 CB B:ASP101 4.4 12.7 1.0 CD1 B:ILE238 4.6 17.2 1.0 NE2 B:HIS68 4.7 14.5 1.0 OE2 B:GLU164 4.7 21.6 1.0 O B:HOH461 4.7 41.4 1.0 CE1 B:HIS68 4.8 8.3 1.0 CG1 B:VAL72 4.9 12.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Dape Protein From V.Cholerea in the Zn Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.2 occ:0.67 OD1 B:ASP101 2.0 11.0 1.0 OE2 B:GLU164 2.1 21.6 1.0 NE2 B:HIS68 2.2 14.5 1.0 O B:HOH634 2.2 23.4 1.0 OE1 B:GLU164 2.4 16.0 1.0 CD B:GLU164 2.6 17.8 1.0 CG B:ASP101 2.9 15.2 1.0 CE1 B:HIS68 3.1 8.3 1.0 CD2 B:HIS68 3.2 14.8 1.0 OD2 B:ASP101 3.2 21.0 1.0 ZN B:ZN302 3.4 12.2 0.5 OE2 B:GLU136 3.7 17.2 1.0 O B:HOH635 3.8 28.4 1.0 CG B:GLU164 4.1 13.2 1.0 ND1 B:HIS68 4.2 6.2 1.0 CD B:GLU136 4.3 10.8 1.0 CG B:HIS68 4.3 8.1 1.0 CB B:ASP101 4.3 12.7 1.0 SD B:MET102 4.4 9.7 1.0 CG B:MET102 4.4 5.3 1.0 OE1 B:GLU135 4.5 47.5 1.0 CB B:MET102 4.5 4.4 1.0 OE1 B:GLU136 4.6 19.4 1.0 C B:ASP101 4.6 10.2 1.0 CA B:ASP101 4.7 6.5 1.0 CB B:GLU164 4.7 11.2 1.0 CD B:PRO165 4.7 10.4 1.0 O B:HOH631 4.8 28.2 1.0 O B:ASP101 4.9 10.1 1.0 N B:MET102 4.9 9.5 1.0

B.Nocek, A.Starus, M.Makowska-Grzyska, B.Gutierrez, S.Sanchez, R.Jedrzejczak, J.C.Mack, K.W.Olsen, A.Joachimiak, R.C.Holz. The Dimerization Domain in Dape Enzymes Is Required For Catalysis. Plos One V. 9 93593 2014.
ISSN: ESSN 1932-6203
PubMed: 24806882
DOI: 10.1371/JOURNAL.PONE.0093593