Zinc in PDB 2dvx: Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde

The structure of Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde, PDB code: 2dvx was solved by M.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.020, 113.548, 119.322, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.8

The binding sites of Zinc atom in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde (pdb code 2dvx). 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 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde, PDB code: 2dvx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde


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 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:23.7 occ:1.00 O8 A:23A1511 1.9 24.5 1.0 OE1 A:GLU8 2.0 17.4 1.0 NE2 A:HIS164 2.1 14.7 1.0 NE2 A:HIS10 2.2 15.0 1.0 OD1 A:ASP287 2.3 20.2 1.0 C7 A:23A1511 2.8 31.9 1.0 CD A:GLU8 3.0 17.3 1.0 CD2 A:HIS164 3.1 15.4 1.0 CD2 A:HIS10 3.1 17.7 1.0 CE1 A:HIS10 3.1 16.8 1.0 CE1 A:HIS164 3.2 15.3 1.0 CG A:ASP287 3.2 21.7 1.0 CG A:GLU8 3.4 18.6 1.0 OD2 A:ASP287 3.4 23.6 1.0 O A:HOH1545 4.0 16.7 1.0 C1 A:23A1511 4.1 34.5 1.0 OE2 A:GLU8 4.2 16.0 1.0 CG A:HIS10 4.2 15.8 1.0 ND1 A:HIS10 4.2 17.3 1.0 CG A:HIS164 4.2 14.8 1.0 ND1 A:HIS164 4.3 15.4 1.0 NE2 A:HIS218 4.3 15.3 1.0 CB A:ASP287 4.5 17.6 1.0 C6 A:23A1511 4.6 35.0 1.0 CE1 A:HIS218 4.6 16.4 1.0 O B:HOH1632 4.7 25.1 1.0 CA A:ASP287 4.8 16.8 1.0 CB A:GLU8 4.8 16.0 1.0 O A:HOH1526 4.9 16.3 1.0 CD2 A:PHE290 4.9 17.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde


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 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:22.5 occ:1.00 O8 B:23A1512 1.9 26.1 1.0 OE1 B:GLU8 2.1 16.4 1.0 NE2 B:HIS10 2.2 16.0 1.0 NE2 B:HIS164 2.2 15.7 1.0 OD1 B:ASP287 2.2 19.4 1.0 C7 B:23A1512 2.7 31.0 1.0 CD B:GLU8 3.1 18.1 1.0 CD2 B:HIS10 3.1 16.3 1.0 CD2 B:HIS164 3.1 16.5 1.0 CE1 B:HIS10 3.1 16.0 1.0 CG B:ASP287 3.2 21.9 1.0 CE1 B:HIS164 3.2 17.9 1.0 CG B:GLU8 3.3 17.7 1.0 OD2 B:ASP287 3.5 23.6 1.0 C1 B:23A1512 4.0 34.3 1.0 O B:HOH1537 4.1 15.8 1.0 OE2 B:GLU8 4.2 18.6 1.0 ND1 B:HIS10 4.2 16.6 1.0 CG B:HIS10 4.2 15.8 1.0 ND1 B:HIS164 4.3 16.4 1.0 CG B:HIS164 4.3 15.3 1.0 NE2 B:HIS218 4.4 16.4 1.0 CB B:ASP287 4.5 16.5 1.0 O B:HOH1688 4.6 30.3 1.0 C6 B:23A1512 4.6 34.2 1.0 CE1 B:HIS218 4.7 16.8 1.0 CA B:ASP287 4.7 15.3 1.0 CB B:GLU8 4.8 16.3 1.0 CD2 B:PHE290 4.9 18.7 1.0 O B:HOH1568 5.0 15.7 1.0 O B:GLU8 5.0 17.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde


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 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1503 b:25.0 occ:1.00 OE1 C:GLU8 2.1 18.2 1.0 OD1 C:ASP287 2.2 22.0 1.0 NE2 C:HIS10 2.2 16.1 1.0 O8 C:23A1513 2.2 30.9 1.0 NE2 C:HIS164 2.2 16.1 1.0 C7 C:23A1513 3.0 36.7 1.0 CD2 C:HIS10 3.1 19.5 1.0 CD2 C:HIS164 3.1 14.0 1.0 CD C:GLU8 3.1 20.6 1.0 CG C:ASP287 3.1 23.9 1.0 CE1 C:HIS10 3.2 19.2 1.0 CE1 C:HIS164 3.2 18.8 1.0 CG C:GLU8 3.4 18.7 1.0 OD2 C:ASP287 3.4 24.1 1.0 O C:HOH1543 4.0 18.7 1.0 CG C:HIS10 4.2 18.5 1.0 OE2 C:GLU8 4.2 18.0 1.0 ND1 C:HIS10 4.3 18.6 1.0 CG C:HIS164 4.3 16.1 1.0 ND1 C:HIS164 4.3 17.7 1.0 NE2 C:HIS218 4.4 18.6 1.0 C1 C:23A1513 4.4 37.8 1.0 CB C:ASP287 4.5 19.3 1.0 CE1 C:HIS218 4.6 19.3 1.0 CA C:ASP287 4.7 17.8 1.0 O C:HOH1686 4.7 33.2 1.0 CD2 C:PHE290 4.8 18.6 1.0 CB C:GLU8 4.8 18.6 1.0 O C:HOH1566 4.9 19.9 1.0 C6 C:23A1513 4.9 38.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde


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 2,6-Dihydroxybenzoate Decarboxylase Complexed with Inhibitor 2,3-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1504 b:26.1 occ:1.00 OE1 D:GLU8 2.1 17.9 1.0 O8 D:23A1514 2.2 24.3 1.0 NE2 D:HIS10 2.2 16.4 1.0 NE2 D:HIS164 2.2 18.6 1.0 OD1 D:ASP287 2.2 22.7 1.0 C7 D:23A1514 3.0 31.8 1.0 CD2 D:HIS10 3.1 19.6 1.0 CD D:GLU8 3.1 20.2 1.0 CD2 D:HIS164 3.1 17.8 1.0 CE1 D:HIS10 3.1 18.2 1.0 CG D:ASP287 3.2 22.4 1.0 CE1 D:HIS164 3.2 19.0 1.0 CG D:GLU8 3.4 18.7 1.0 OD2 D:ASP287 3.5 25.2 1.0 O D:HOH1571 4.0 21.2 1.0 ND1 D:HIS10 4.2 18.4 1.0 CG D:HIS10 4.2 17.8 1.0 OE2 D:GLU8 4.2 18.2 1.0 CG D:HIS164 4.3 18.0 1.0 ND1 D:HIS164 4.3 18.1 1.0 C1 D:23A1514 4.4 32.9 1.0 NE2 D:HIS218 4.4 17.2 1.0 CB D:ASP287 4.5 19.3 1.0 O C:HOH1634 4.6 33.1 1.0 CE1 D:HIS218 4.6 19.2 1.0 CA D:ASP287 4.7 17.1 1.0 CB D:GLU8 4.8 18.8 1.0 CD2 D:PHE290 4.8 17.8 1.0 O D:HOH1554 4.8 20.4 1.0 C6 D:23A1514 4.9 34.0 1.0

M.Goto, H.Hayashi, I.Miyahara, K.Hirotsu, M.Yoshida, T.Oikawa. Crystal Structures of Nonoxidative Zn-Dependent 2,6-Dihydroxybenzoate (Gamma-Resorcylate) Decarboxylase From Rhizobium Sp. Strain Mtp-10005 To Be Published.