Atomistry » Zinc » PDB 6dq3-6e86 » 6e13
Atomistry »
  Zinc »
    PDB 6dq3-6e86 »
      6e13 »

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.

Protein crystallography data

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

Other elements in 6e13:

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

Zinc Binding Sites:

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 6e13

Go back to Zinc Binding Sites List in 6e13
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 6e13

Go back to Zinc Binding Sites List in 6e13
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

Reference:

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
Page generated: Wed Dec 16 11:41:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy