Zinc in PDB 2dvt: Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase From Rhizobium

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

Resolution Low / High (Å)	40.29 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.371, 113.807, 119.163, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20

The binding sites of Zinc atom in the Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase From Rhizobium (pdb code 2dvt). 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 From Rhizobium, PDB code: 2dvt:
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 From Rhizobium


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 From Rhizobium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:24.5 occ:1.00 OE1 A:GLU8 2.0 15.9 1.0 NE2 A:HIS164 2.1 12.6 1.0 O A:HOH1529 2.1 19.1 1.0 NE2 A:HIS10 2.2 13.8 1.0 OD1 A:ASP287 2.3 18.9 1.0 CD A:GLU8 3.0 16.4 1.0 CD2 A:HIS10 3.1 15.8 1.0 CD2 A:HIS164 3.1 14.9 1.0 CE1 A:HIS164 3.1 15.2 1.0 CE1 A:HIS10 3.2 15.4 1.0 CG A:ASP287 3.2 19.9 1.0 CG A:GLU8 3.4 17.1 1.0 OD2 A:ASP287 3.5 21.0 1.0 O A:HOH1602 4.1 14.3 1.0 OE2 A:GLU8 4.2 14.1 1.0 CG A:HIS10 4.2 13.5 1.0 ND1 A:HIS164 4.2 14.6 1.0 ND1 A:HIS10 4.2 13.9 1.0 CG A:HIS164 4.2 13.4 1.0 NE2 A:HIS218 4.4 16.1 1.0 CB A:ASP287 4.6 16.3 1.0 CE1 A:HIS218 4.6 17.2 1.0 O B:HOH1631 4.7 25.1 1.0 CB A:GLU8 4.8 14.7 1.0 CA A:ASP287 4.8 14.8 1.0 CD2 A:PHE290 4.8 15.5 1.0 O A:HOH1524 4.9 14.6 1.0

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


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 From Rhizobium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:23.8 occ:1.00 OE1 B:GLU8 2.1 15.4 1.0 NE2 B:HIS164 2.2 13.9 1.0 O B:HOH1541 2.2 20.0 1.0 NE2 B:HIS10 2.2 13.0 1.0 OD1 B:ASP287 2.2 17.1 1.0 CD2 B:HIS10 3.1 14.1 1.0 CD B:GLU8 3.1 15.4 1.0 CD2 B:HIS164 3.1 13.4 1.0 CE1 B:HIS164 3.2 15.9 1.0 CG B:ASP287 3.2 20.3 1.0 CE1 B:HIS10 3.2 14.4 1.0 CG B:GLU8 3.4 15.4 1.0 OD2 B:ASP287 3.5 22.5 1.0 O B:HOH1599 4.1 15.1 1.0 OE2 B:GLU8 4.2 15.1 1.0 CG B:HIS10 4.2 13.5 1.0 ND1 B:HIS10 4.3 14.1 1.0 ND1 B:HIS164 4.3 15.1 1.0 CG B:HIS164 4.3 13.8 1.0 NE2 B:HIS218 4.4 13.5 1.0 CB B:ASP287 4.5 14.8 1.0 O A:HOH1686 4.6 27.4 1.0 CE1 B:HIS218 4.7 14.4 1.0 O B:HOH1824 4.7 43.3 1.0 CA B:ASP287 4.7 13.4 1.0 CB B:GLU8 4.8 13.6 1.0 CD2 B:PHE290 4.8 15.4 1.0 O B:HOH1544 5.0 14.9 1.0

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


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 From Rhizobium within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1503 b:26.6 occ:1.00 OE1 C:GLU8 2.1 17.2 1.0 NE2 C:HIS164 2.1 14.8 1.0 NE2 C:HIS10 2.2 15.9 1.0 O C:HOH1555 2.3 23.3 1.0 OD1 C:ASP287 2.3 20.9 1.0 CD C:GLU8 3.1 18.6 1.0 CD2 C:HIS164 3.1 13.0 1.0 CD2 C:HIS10 3.1 18.2 1.0 CE1 C:HIS164 3.2 16.1 1.0 CE1 C:HIS10 3.2 18.3 1.0 CG C:ASP287 3.2 22.4 1.0 CG C:GLU8 3.4 16.6 1.0 OD2 C:ASP287 3.5 23.4 1.0 O C:HOH1542 4.1 17.1 1.0 OE2 C:GLU8 4.2 16.2 1.0 CG C:HIS164 4.2 14.7 1.0 ND1 C:HIS164 4.2 16.2 1.0 CG C:HIS10 4.3 16.5 1.0 ND1 C:HIS10 4.3 16.5 1.0 NE2 C:HIS218 4.4 17.4 1.0 CB C:ASP287 4.5 18.1 1.0 CE1 C:HIS218 4.6 17.4 1.0 O C:HOH1637 4.7 27.4 1.0 CA C:ASP287 4.8 16.2 1.0 CB C:GLU8 4.8 16.4 1.0 CD2 C:PHE290 4.8 14.6 1.0 O C:HOH1582 4.9 19.5 1.0

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


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 From Rhizobium within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1504 b:26.6 occ:1.00 OE1 D:GLU8 2.1 17.5 1.0 NE2 D:HIS164 2.2 15.9 1.0 NE2 D:HIS10 2.2 14.7 1.0 OD1 D:ASP287 2.3 21.0 1.0 O D:HOH1550 2.3 21.2 1.0 CD D:GLU8 3.1 18.2 1.0 CD2 D:HIS164 3.1 14.6 1.0 CD2 D:HIS10 3.1 17.6 1.0 CE1 D:HIS10 3.1 17.1 1.0 CE1 D:HIS164 3.2 16.0 1.0 CG D:ASP287 3.3 23.1 1.0 CG D:GLU8 3.4 16.7 1.0 OD2 D:ASP287 3.6 24.4 1.0 O D:HOH1589 4.1 18.1 1.0 OE2 D:GLU8 4.2 16.0 1.0 ND1 D:HIS10 4.2 16.4 1.0 CG D:HIS10 4.3 15.7 1.0 CG D:HIS164 4.3 16.6 1.0 ND1 D:HIS164 4.3 15.2 1.0 NE2 D:HIS218 4.4 15.7 1.0 CE1 D:HIS218 4.5 16.6 1.0 CB D:ASP287 4.6 18.6 1.0 O D:HOH1632 4.6 30.2 1.0 CA D:ASP287 4.8 16.2 1.0 CB D:GLU8 4.8 16.3 1.0 CD2 D:PHE290 4.8 14.5 1.0 O D:HOH1549 4.9 17.1 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.