Zinc in PDB 6m53: Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum

The structure of Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum, PDB code: 6m53 was solved by M.K.Song, J.H.Feng, W.D.Liu, Q.Q.Wu, D.M.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.77 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.625, 132.246, 140.593, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 19.9

The binding sites of Zinc atom in the Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum (pdb code 6m53). 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, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum, PDB code: 6m53:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum


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, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:30.0 occ:1.00 O A:HOH741 1.9 28.3 1.0 OE2 A:GLU9 2.2 18.8 1.0 O A:HOH795 2.3 26.4 1.0 OD1 A:ASP292 2.3 19.9 1.0 NE2 A:HIS168 2.3 19.7 1.0 O A:HOH736 2.4 23.8 1.0 OD2 A:ASP292 2.8 30.2 1.0 CG A:ASP292 2.8 19.0 1.0 CE1 A:HIS168 3.1 20.0 1.0 CD A:GLU9 3.4 17.0 1.0 CD2 A:HIS168 3.4 20.2 1.0 CG A:GLU9 3.8 18.0 1.0 O A:HOH767 4.0 22.1 1.0 O A:HOH798 4.1 20.3 1.0 NE2 A:HIS223 4.1 18.2 1.0 CB A:ASP292 4.3 16.2 1.0 ND1 A:HIS168 4.3 17.2 1.0 CE1 A:HIS223 4.3 16.8 1.0 OE1 A:GLU9 4.4 17.4 1.0 CG A:HIS168 4.4 15.0 1.0 O A:HOH586 4.5 20.9 1.0 O A:HOH807 4.6 24.0 1.0 CD2 A:PHE295 4.6 18.0 1.0 O A:GLU9 4.8 16.4 1.0 CA A:ASP292 4.8 14.3 1.0 CE2 A:PHE295 4.9 17.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum


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, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:30.0 occ:1.00 OE2 B:GLU9 2.1 20.5 1.0 O B:HOH759 2.2 23.2 1.0 OD1 B:ASP292 2.2 23.3 1.0 O B:HOH777 2.3 25.8 1.0 O B:HOH585 2.3 27.9 1.0 NE2 B:HIS168 2.5 20.6 1.0 CG B:ASP292 2.7 22.1 1.0 OD2 B:ASP292 2.8 36.1 1.0 CD B:GLU9 3.2 20.7 1.0 CE1 B:HIS168 3.4 18.9 1.0 CD2 B:HIS168 3.4 19.4 1.0 CG B:GLU9 3.6 15.5 1.0 CB B:ASP292 3.9 16.3 1.0 O B:HOH778 4.0 23.3 1.0 O B:HOH665 4.2 21.3 1.0 O B:HOH691 4.3 22.7 1.0 NE2 B:HIS223 4.3 19.4 1.0 OE1 B:GLU9 4.3 16.4 1.0 O B:GLU9 4.3 16.8 1.0 CD2 B:PHE295 4.4 22.3 1.0 CA B:ASP292 4.4 15.2 1.0 ND1 B:HIS168 4.5 17.1 1.0 CG B:HIS168 4.6 18.8 1.0 CE2 B:PHE295 4.6 23.6 1.0 CE1 B:HIS223 4.6 19.6 1.0 CB B:GLU9 4.7 14.8 1.0 O B:HOH855 4.8 34.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum


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, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:30.0 occ:1.00 O C:HOH603 2.0 27.4 1.0 OD1 C:ASP292 2.3 29.1 1.0 NE2 C:HIS168 2.3 21.8 1.0 OE2 C:GLU9 2.4 24.2 1.0 O C:HOH766 2.4 30.9 1.0 O C:HOH678 2.5 27.6 1.0 OD2 C:ASP292 2.7 38.6 1.0 CG C:ASP292 2.8 25.2 1.0 CE1 C:HIS168 3.2 21.6 1.0 CD2 C:HIS168 3.3 21.3 1.0 CD C:GLU9 3.4 23.7 1.0 CG C:GLU9 3.6 21.0 1.0 O C:HOH840 3.9 32.3 1.0 O C:HOH691 4.0 25.6 1.0 O C:HOH590 4.1 24.9 1.0 CB C:ASP292 4.2 19.1 1.0 CD2 C:PHE295 4.3 24.5 1.0 ND1 C:HIS168 4.4 19.4 1.0 CE2 C:PHE295 4.4 25.2 1.0 O C:GLU9 4.4 22.0 1.0 CG C:HIS168 4.4 19.2 1.0 NE2 C:HIS223 4.5 19.3 1.0 OE1 C:GLU9 4.5 19.3 1.0 CA C:ASP292 4.6 18.4 1.0 CE1 C:HIS223 4.8 20.0 1.0 CB C:GLU9 4.8 20.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of 2, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum


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, 3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:30.0 occ:1.00 O D:HOH584 2.1 33.4 1.0 NE2 D:HIS168 2.3 30.6 1.0 OD1 D:ASP292 2.3 32.1 1.0 OE2 D:GLU9 2.4 26.9 1.0 O D:HOH717 2.5 39.1 1.0 CG D:ASP292 2.8 35.3 1.0 OD2 D:ASP292 2.8 42.3 1.0 CE1 D:HIS168 3.2 25.8 1.0 CD2 D:HIS168 3.3 28.3 1.0 CD D:GLU9 3.4 27.0 1.0 CG D:GLU9 3.6 25.1 1.0 O D:HOH697 3.8 32.3 1.0 O D:HOH526 4.0 32.0 1.0 CB D:ASP292 4.1 28.3 1.0 O D:GLU9 4.3 27.3 1.0 ND1 D:HIS168 4.3 24.8 1.0 O D:HOH715 4.4 43.5 1.0 CG D:HIS168 4.4 23.9 1.0 NE2 D:HIS223 4.5 25.7 1.0 OE1 D:GLU9 4.5 25.0 1.0 CD2 D:PHE295 4.5 36.3 1.0 O D:HOH656 4.5 31.2 1.0 CA D:ASP292 4.6 27.6 1.0 CE2 D:PHE295 4.7 40.3 1.0 CB D:GLU9 4.8 24.2 1.0 CE1 D:HIS223 4.8 25.6 1.0 O D:HOH604 4.9 30.4 1.0

M.Song, X.Zhang, W.Liu, J.Feng, Y.Cui, P.Yao, M.Wang, R.T.Guo, Q.Wu, D.Zhu. 2,3-Dihydroxybenzoic Acid Decarboxylase From Fusarium Oxysporum: Crystal Structures and Substrate Recognition Mechanism. Chembiochem V. 21 2950 2020.
ISSN: ESSN 1439-7633
PubMed: 32421914
DOI: 10.1002/CBIC.202000244