Zinc in PDB 2dvu: Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with 2,6-Dihydroxybenzoate

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

Resolution Low / High (Å)	40.22 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.071, 113.611, 119.102, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.6

The binding sites of Zinc atom in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with 2,6-Dihydroxybenzoate (pdb code 2dvu). 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 2,6-Dihydroxybenzoate, PDB code: 2dvu:
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 2,6-Dihydroxybenzoate


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 2,6-Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:22.6 occ:1.00 O1A A:GRE1511 2.0 26.7 1.0 OE1 A:GLU8 2.1 15.6 1.0 NE2 A:HIS10 2.2 14.4 1.0 NE2 A:HIS164 2.2 12.9 1.0 OD1 A:ASP287 2.2 18.5 1.0 CD A:GLU8 3.0 12.6 1.0 C1A A:GRE1511 3.0 30.1 1.0 CD2 A:HIS10 3.1 16.5 1.0 CD2 A:HIS164 3.1 12.9 1.0 CG A:ASP287 3.1 19.4 1.0 CE1 A:HIS10 3.2 16.0 1.0 CE1 A:HIS164 3.2 13.9 1.0 CG A:GLU8 3.2 13.8 1.0 O2A A:GRE1511 3.3 29.2 1.0 OD2 A:ASP287 3.4 19.0 1.0 OE2 A:GLU8 4.2 12.4 1.0 CG A:HIS10 4.2 15.1 1.0 ND1 A:HIS10 4.2 14.9 1.0 O2 A:GRE1511 4.3 32.8 1.0 CG A:HIS164 4.3 13.2 1.0 ND1 A:HIS164 4.3 14.6 1.0 C1 A:GRE1511 4.3 29.3 1.0 NE2 A:HIS218 4.3 15.8 1.0 O A:HOH1581 4.4 16.0 1.0 CB A:ASP287 4.5 14.1 1.0 CE1 A:HIS218 4.6 15.0 1.0 CB A:GLU8 4.7 12.8 1.0 CA A:ASP287 4.7 15.1 1.0 C2 A:GRE1511 4.8 30.4 1.0 CD2 A:PHE290 4.8 14.8 1.0 O A:HOH1702 4.9 24.0 1.0 O A:GLU8 4.9 13.2 1.0

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


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 2,6-Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:21.6 occ:1.00 O2A B:GRE1512 2.0 27.1 1.0 OE1 B:GLU8 2.1 15.9 1.0 NE2 B:HIS10 2.2 13.2 1.0 OD1 B:ASP287 2.2 17.0 1.0 NE2 B:HIS164 2.2 14.0 1.0 C1A B:GRE1512 3.0 29.3 1.0 CD B:GLU8 3.1 14.0 1.0 CD2 B:HIS10 3.1 13.6 1.0 O1A B:GRE1512 3.2 30.6 1.0 CE1 B:HIS10 3.2 14.9 1.0 CD2 B:HIS164 3.2 14.1 1.0 CG B:ASP287 3.2 18.8 1.0 CE1 B:HIS164 3.2 15.6 1.0 CG B:GLU8 3.3 13.3 1.0 OD2 B:ASP287 3.6 20.3 1.0 CG B:HIS10 4.2 13.6 1.0 OE2 B:GLU8 4.2 15.2 1.0 ND1 B:HIS10 4.2 13.6 1.0 C1 B:GRE1512 4.3 28.2 1.0 ND1 B:HIS164 4.3 14.3 1.0 CG B:HIS164 4.3 12.7 1.0 O6 B:GRE1512 4.4 28.6 1.0 O B:HOH1568 4.4 16.8 1.0 NE2 B:HIS218 4.4 15.9 1.0 CB B:ASP287 4.5 13.1 1.0 CE1 B:HIS218 4.7 15.2 1.0 CB B:GLU8 4.7 14.3 1.0 CA B:ASP287 4.7 13.8 1.0 CD2 B:PHE290 4.8 16.3 1.0 C6 B:GRE1512 4.8 27.6 1.0 O B:GLU8 4.9 14.2 1.0 O B:HOH1564 5.0 13.6 1.0

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


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 2,6-Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1503 b:25.7 occ:1.00 OE1 C:GLU8 2.1 15.5 1.0 NE2 C:HIS10 2.2 13.8 1.0 NE2 C:HIS164 2.2 10.4 1.0 OD1 C:ASP287 2.3 19.7 1.0 O1A C:GRE1513 2.3 46.0 1.0 CD C:GLU8 3.0 16.2 1.0 O2A C:GRE1513 3.0 46.6 1.0 CD2 C:HIS10 3.0 15.7 1.0 C1A C:GRE1513 3.1 46.1 1.0 CD2 C:HIS164 3.1 12.4 1.0 CG C:ASP287 3.1 20.8 1.0 CE1 C:HIS10 3.2 16.6 1.0 CE1 C:HIS164 3.2 14.8 1.0 CG C:GLU8 3.2 14.7 1.0 OD2 C:ASP287 3.4 21.7 1.0 OE2 C:GLU8 4.2 15.5 1.0 CG C:HIS10 4.2 13.9 1.0 ND1 C:HIS10 4.3 15.7 1.0 O C:HOH1609 4.3 25.2 1.0 CG C:HIS164 4.3 11.4 1.0 ND1 C:HIS164 4.3 13.4 1.0 NE2 C:HIS218 4.4 16.1 1.0 CB C:ASP287 4.5 16.2 1.0 C1 C:GRE1513 4.5 45.6 1.0 CE1 C:HIS218 4.6 16.7 1.0 CB C:GLU8 4.7 14.6 1.0 CA C:ASP287 4.7 15.1 1.0 CD2 C:PHE290 4.8 17.3 1.0 O2 C:GRE1513 4.8 46.3 1.0 O C:GLU8 4.9 13.0 1.0 O C:HOH1596 5.0 18.8 1.0

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


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 2,6-Dihydroxybenzoate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1504 b:26.4 occ:1.00 OE1 D:GLU8 2.1 18.0 1.0 NE2 D:HIS10 2.3 15.4 1.0 NE2 D:HIS164 2.3 17.1 1.0 OD1 D:ASP287 2.3 18.3 1.0 O1A D:GRE1514 2.6 49.6 1.0 CD D:GLU8 3.1 18.8 1.0 CD2 D:HIS10 3.1 16.8 1.0 CD2 D:HIS164 3.1 15.3 1.0 CG D:ASP287 3.2 20.6 1.0 O2A D:GRE1514 3.3 49.1 1.0 CG D:GLU8 3.3 16.5 1.0 CE1 D:HIS164 3.3 16.0 1.0 CE1 D:HIS10 3.3 17.2 1.0 C1A D:GRE1514 3.4 48.7 1.0 OD2 D:ASP287 3.6 21.6 1.0 OE2 D:GLU8 4.2 16.8 1.0 CG D:HIS10 4.3 15.5 1.0 NE2 D:HIS218 4.3 14.7 1.0 O D:HOH1591 4.3 20.9 1.0 CG D:HIS164 4.3 14.6 1.0 ND1 D:HIS10 4.3 16.5 1.0 ND1 D:HIS164 4.4 14.9 1.0 CB D:ASP287 4.5 15.1 1.0 CE1 D:HIS218 4.5 15.4 1.0 CA D:ASP287 4.7 15.6 1.0 CB D:GLU8 4.8 16.6 1.0 O D:HOH1616 4.8 25.6 1.0 C1 D:GRE1514 4.8 47.1 1.0 CD2 D:PHE290 4.8 17.7 1.0 O D:HOH1542 4.9 15.3 1.0 O D:GLU8 5.0 15.1 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.