Zinc in PDB 5vo3: Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid)

All present enzymatic activity of Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid):
3.5.1.18;

The structure of Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid), PDB code: 5vo3 was solved by B.Nocek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.32 / 1.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.648, 135.536, 149.613, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.5

The binding sites of Zinc atom in the Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid) (pdb code 5vo3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid), PDB code: 5vo3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid)


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 Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:16.6 occ:1.00 OD1 A:ASP100 2.0 22.5 1.0 NE2 A:HIS67 2.0 15.2 1.0 OE2 A:GLU163 2.0 13.0 1.0 O2 A:SIN501 2.4 13.0 0.9 OE1 A:GLU163 2.6 11.7 1.0 CD A:GLU163 2.6 11.4 1.0 CE1 A:HIS67 2.9 16.5 1.0 CG A:ASP100 3.0 21.2 1.0 HE1 A:HIS67 3.1 19.9 1.0 CD2 A:HIS67 3.1 14.2 1.0 H22 A:SIN501 3.1 16.1 0.9 C1 A:SIN501 3.2 12.2 0.9 HD2 A:HIS67 3.3 17.1 1.0 OD2 A:ASP100 3.4 25.1 1.0 HB3 A:MET101 3.4 19.3 1.0 C2 A:SIN501 3.5 13.4 0.9 H21 A:SIN501 3.6 16.1 0.9 HG2 A:MET101 3.7 20.4 1.0 OE1 A:GLU134 3.7 19.3 1.0 ZN A:ZN504 3.9 20.0 1.0 OE1 A:GLU135 4.0 20.0 1.0 HD2 A:PRO164 4.0 16.9 1.0 ND1 A:HIS67 4.1 16.0 1.0 CG A:GLU163 4.1 11.8 1.0 CG A:HIS67 4.2 14.6 1.0 CG A:MET101 4.2 17.0 1.0 CD A:GLU134 4.2 19.2 1.0 HA A:ASP100 4.2 20.2 1.0 CB A:MET101 4.2 16.1 1.0 O1 A:SIN501 4.2 12.3 0.9 SD A:MET101 4.3 16.4 1.0 CB A:ASP100 4.3 18.6 1.0 HN61 A:API502 4.3 36.6 0.9 HN62 A:API502 4.4 36.6 0.9 HA A:GLU163 4.4 15.5 1.0 OE2 A:GLU134 4.4 18.7 1.0 HB3 A:GLU163 4.5 14.5 1.0 CD A:GLU135 4.5 19.7 1.0 HG3 A:GLU163 4.5 14.2 1.0 C A:ASP100 4.6 16.7 1.0 HG2 A:GLU163 4.6 14.2 1.0 CA A:ASP100 4.6 16.8 1.0 HD3 A:PRO164 4.6 16.9 1.0 HB2 A:ASP100 4.7 22.4 1.0 CB A:GLU163 4.8 12.1 1.0 CD A:PRO164 4.8 14.1 1.0 O A:ASP100 4.8 17.7 1.0 N6 A:API502 4.8 30.5 0.9 HD1 A:HIS67 4.8 19.2 1.0 N A:MET101 4.8 16.5 1.0 HG2 A:GLU135 4.9 22.6 1.0 HB2 A:MET101 4.9 19.3 1.0 OE2 A:GLU135 4.9 20.8 1.0 HG3 A:GLU134 4.9 21.1 1.0 HB3 A:ASP100 5.0 22.4 1.0 HB3 A:GLU134 5.0 21.9 1.0 C3 A:SIN501 5.0 14.2 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid)


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 Dape in Complex with the Products (Succinic Acid and Diaminopimelic Acid) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:20.0 occ:1.00 OD2 A:ASP100 1.9 25.1 1.0 OE1 A:GLU135 2.0 20.0 1.0 NE2 A:HIS349 2.1 20.8 1.0 O1 A:SIN501 2.3 12.3 0.9 OE2 A:GLU135 2.5 20.8 1.0 O2 A:SIN501 2.5 13.0 0.9 CD A:GLU135 2.6 19.7 1.0 C1 A:SIN501 2.6 12.2 0.9 CE1 A:HIS349 3.0 21.9 1.0 HN62 A:API502 3.1 36.6 0.9 CG A:ASP100 3.1 21.2 1.0 CD2 A:HIS349 3.1 22.1 1.0 HE1 A:HIS349 3.2 26.3 1.0 HD2 A:HIS349 3.3 26.6 1.0 OD1 A:ASP100 3.6 22.5 1.0 HG13 A:VAL71 3.9 37.1 1.0 ZN A:ZN503 3.9 16.6 1.0 O A:HOH709 3.9 14.2 1.0 C2 A:SIN501 4.0 13.4 0.9 N6 A:API502 4.0 30.5 0.9 CG A:GLU135 4.1 18.9 1.0 HD12 A:ILE348 4.1 22.2 1.0 ND1 A:HIS349 4.2 23.4 1.0 H22 A:SIN501 4.2 16.1 0.9 HG11 A:VAL71 4.2 37.1 1.0 CG A:HIS349 4.2 22.5 1.0 H32 A:SIN501 4.3 17.1 0.9 CB A:ASP100 4.3 18.6 1.0 HB3 A:ASP100 4.3 22.4 1.0 HE1 A:HIS67 4.4 19.9 1.0 HG2 A:GLU135 4.4 22.6 1.0 HG3 A:GLU135 4.4 22.6 1.0 HN61 A:API502 4.5 36.6 0.9 CG1 A:VAL71 4.5 31.0 1.0 OE1 A:GLU134 4.6 19.3 1.0 HB2 A:ASP100 4.6 22.4 1.0 HB A:ILE348 4.6 21.8 1.0 H21 A:SIN501 4.7 16.1 0.9 C3 A:SIN501 4.7 14.2 0.9 HB3 A:GLU135 4.8 22.5 1.0 CE1 A:HIS67 4.9 16.5 1.0 H52 A:API502 4.9 30.7 0.9 HD1 A:HIS349 4.9 28.0 1.0 NE2 A:HIS67 5.0 15.2 1.0 HA A:GLU135 5.0 22.6 1.0 HG12 A:VAL71 5.0 37.1 1.0 O3 A:API502 5.0 14.8 0.9

B.Nocek, C.Reidl, A.Starus, T.Heath, D.Bienvenue, J.Osipiuk, R.Jedrzejczak, A.Joachimiak, D.P.Becker, R.C.Holz. Structural Evidence of A Major Conformational Change Triggered By Substrate Binding in Dape Enzymes: Impact on the Catalytic Mechanism. Biochemistry V. 57 574 2018.
ISSN: ISSN 1520-4995
PubMed: 29272107
DOI: 10.1021/ACS.BIOCHEM.7B01151