Potassium in PDB 6eng: Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin

Enzymatic activity of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin

All present enzymatic activity of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin, PDB code: 6eng was solved by A.Vanden Broeck, A.G.Mcewen, V.Lamour, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.67 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.830, 128.070, 159.760, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.7

Other elements in 6eng:

The structure of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin (pdb code 6eng). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin, PDB code: 6eng:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6eng

Go back to Potassium Binding Sites List in 6eng
Potassium binding site 1 out of 3 in the Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:83.2
occ:1.00
 O A:HOH543 2.8 55.1 1.0
O A:LYS103 3.0 66.8 1.0
O A:ASP105 3.0 59.3 1.0
O A:GLY102 3.0 63.0 1.0
C A:LYS103 3.6 65.8 1.0
CA A:LYS103 3.7 59.6 1.0
C A:GLY102 4.0 60.8 1.0
C A:ASP105 4.0 59.3 1.0
N A:LYS103 4.3 58.0 1.0
O A:HOH584 4.5 55.3 1.0
N A:ASP105 4.6 56.6 1.0
CD A:LYS103 4.7 73.6 1.0
O A:HOH626 4.7 53.0 0.5
N A:PHE104 4.7 62.1 1.0
O A:HOH648 4.8 69.2 1.0
N A:ASP106 4.9 57.6 1.0
CA A:ASP105 4.9 55.4 1.0
CB A:LYS103 4.9 62.6 1.0
CA A:ASP106 4.9 59.8 1.0
C A:PHE104 5.0 64.5 1.0

Potassium binding site 2 out of 3 in 6eng

Go back to Potassium Binding Sites List in 6eng
Potassium binding site 2 out of 3 in the Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:54.8
occ:1.00
 O A:HOH599 2.4 46.3 1.0
O A:HOH621 2.8 51.3 1.0
O A:ASN271 2.8 42.8 1.0
O A:HOH589 2.9 49.2 1.0
CG1 A:ILE273 3.7 50.0 1.0
CD1 A:ILE273 3.9 49.4 1.0
C A:ASN271 3.9 45.0 1.0
OD2 A:ASP45 4.0 62.9 1.0
O A:HOH606 4.4 54.1 1.0
CB A:ASN272 4.4 43.7 1.0
OD1 A:ASP49 4.5 55.0 1.0
CG A:ASP45 4.5 58.4 1.0
CB A:ASN271 4.5 42.8 1.0
CG2 A:VAL111 4.6 54.7 1.0
CB A:VAL111 4.6 55.6 1.0
N A:ILE273 4.7 45.4 1.0
ND2 A:ASN272 4.7 42.0 1.0
N A:VAL111 4.8 51.9 1.0
N A:ASN272 4.9 44.7 1.0
CA A:ASN271 4.9 42.4 1.0
OD2 A:ASP49 4.9 64.0 1.0
OD1 A:ASP45 4.9 59.4 1.0
CA A:ASN272 5.0 43.8 1.0

Potassium binding site 3 out of 3 in 6eng

Go back to Potassium Binding Sites List in 6eng
Potassium binding site 3 out of 3 in the Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the 43K Atpase Domain of Escherichia Coli Gyrase B in Complex with An Aminocoumarin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:86.2
occ:1.00
 O A:HOH682 2.6 64.0 1.0
O A:HOH640 2.6 47.2 1.0
O A:TYR242 2.9 48.5 1.0
O A:HOH689 3.1 67.0 1.0
CE1 A:TYR242 3.5 50.1 1.0
CZ A:TYR242 3.5 58.3 1.0
CD1 A:TYR242 3.6 47.8 1.0
CE2 A:TYR242 3.7 50.3 1.0
CG A:TYR242 3.8 45.6 1.0
CD2 A:TYR242 3.8 47.7 1.0
C A:TYR242 3.9 48.2 1.0
OH A:TYR242 4.2 62.5 1.0
N A:TYR242 4.2 45.2 1.0
CA A:TYR242 4.4 43.8 1.0
CB A:TYR242 4.7 43.5 1.0
N A:PHE243 4.9 44.8 1.0

Reference:

A.Vanden Broeck, A.G.Mcewen, Y.Chebaro, N.Potier, V.Lamour. Structural Basis For Dna Gyrase Interaction with Coumermycin A1. J.Med.Chem. V. 62 4225 2019.
ISSN: ISSN 0022-2623
PubMed: 30920824
DOI: 10.1021/ACS.JMEDCHEM.8B01928
Page generated: Mon Dec 14 00:35:53 2020

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