Zinc in PDB 6e13: Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis.

The structure of Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis., PDB code: 6e13 was solved by R.L.Evans Iii, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.47 / 2.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.038, 86.038, 107.128, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.6

The structure of Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis. (pdb code 6e13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis., PDB code: 6e13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.6 occ:1.00 OD1 A:ASN272 2.1 38.9 1.0 SG A:CYS19 2.3 40.3 1.0 SG A:CYS24 2.3 42.0 1.0 SG A:CYS21 2.4 40.0 1.0 CG A:ASN272 3.0 36.6 1.0 CB A:CYS24 3.2 42.6 1.0 CB A:CYS19 3.3 37.5 1.0 CB A:CYS21 3.4 30.6 1.0 CB A:ASN272 3.5 28.9 1.0 O A:ASN272 3.9 39.6 1.0 N A:CYS24 4.0 43.4 1.0 N A:CYS21 4.0 50.6 1.0 ND2 A:ASN272 4.1 38.9 1.0 C A:ASN272 4.1 40.1 1.0 CA A:CYS24 4.2 44.4 1.0 CA A:CYS21 4.3 39.0 1.0 CA A:ASN272 4.4 39.0 1.0 CA A:CYS19 4.5 38.4 1.0 C A:CYS19 4.5 38.6 1.0 N A:THR273 4.6 38.2 1.0 CG2 A:THR273 4.6 31.7 1.0 O A:CYS19 4.6 38.5 1.0 C A:CYS21 4.8 38.7 1.0 N A:ASN20 4.9 46.8 1.0 CA A:THR273 4.9 43.5 1.0 CB A:GLN16 4.9 37.3 1.0 O A:CYS21 4.9 46.9 1.0 CB A:ASN23 5.0 44.8 1.0

Zinc binding site 2 out of 2 in the Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pseudomonas Putida Pqqb with A Non-Physiological Zinc at the Active Site Binds the Substrate Mimic, 5-Cysteinyl-3,4- Dihydroxyphenylalanine (5-Cys-Dopa), Non-Specifically But Supports the Proposed Function of the Enzyme in Pyrroloquinoline Quinone Biosynthesis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.1 occ:1.00 NE2 A:HIS93 2.1 34.7 1.0 NE2 A:HIS269 2.1 32.1 1.0 O A:HOH528 2.4 19.7 1.0 CD2 A:HIS93 3.0 30.4 1.0 CD2 A:HIS269 3.1 35.7 1.0 CE1 A:HIS93 3.1 34.7 1.0 CE1 A:HIS269 3.1 34.0 1.0 O20 A:HKS404 3.7 49.1 0.9 N A:ALA11 3.8 35.8 1.0 CB A:ASP92 3.9 40.0 1.0 CG A:HIS93 4.2 36.4 1.0 ND1 A:HIS93 4.2 41.6 1.0 CG A:HIS269 4.2 36.6 1.0 ND1 A:HIS269 4.2 38.8 1.0 O18 A:HKS404 4.3 53.6 0.9 OD2 A:ASP92 4.3 51.4 1.0 CA A:ALA10 4.4 36.0 1.0 C A:ALA10 4.4 36.8 1.0 CG A:ASP92 4.5 48.0 1.0 OE1 A:GLN90 4.8 44.4 1.0 CB A:ALA10 4.9 36.9 1.0 C19 A:HKS404 4.9 53.1 0.9 CA A:ALA11 5.0 36.5 1.0

E.M.Koehn, J.A.Latham, T.Armand, R.L.Evans 3Rd, X.Tu, C.M.Wilmot, A.T.Iavarone, J.P.Klinman. Discovery of Hydroxylase Activity For Pqqb Provides A Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway. J.Am.Chem.Soc. V. 141 4398 2019.
ISSN: ESSN 1520-5126
PubMed: 30811189
DOI: 10.1021/JACS.8B13453