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Potassium in PDB 4ddq: Structural Plasticity of the Bacillus Subtilis Gyra Homodimer

Enzymatic activity of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer

All present enzymatic activity of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer:
5.99.1.3;

Protein crystallography data

The structure of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer, PDB code: 4ddq was solved by M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.803, 165.106, 180.582, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer (pdb code 4ddq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer, PDB code: 4ddq:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 1 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:0.6
occ:1.00
 O A:GLN327 2.8 0.1 1.0
O A:THR324 2.9 0.1 1.0
O A:LYS322 3.1 0.1 1.0
O A:TYR321 3.1 0.3 1.0
C A:LYS322 3.8 0.9 1.0
C A:GLN327 4.0 0.3 1.0
C A:THR324 4.1 0.8 1.0
C A:TYR321 4.3 0.1 1.0
CA A:LYS322 4.4 0.5 1.0
N A:THR324 4.5 0.6 1.0
N A:GLN323 4.7 0.1 1.0
CB A:GLN327 4.8 0.9 1.0
C A:GLN323 4.8 0.4 1.0
CA A:GLN327 4.8 0.0 1.0
N A:LYS322 4.9 0.7 1.0
N A:THR328 4.9 0.3 1.0
CA A:THR328 4.9 0.8 1.0
N A:GLN327 4.9 0.7 1.0
CA A:THR324 5.0 0.5 1.0

Potassium binding site 2 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 2 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:0.9
occ:1.00
 O B:GLN327 2.9 0.9 1.0
O B:LYS322 3.1 0.6 1.0
O B:THR324 3.2 0.3 1.0
O B:TYR321 3.3 0.6 1.0
C B:LYS322 3.6 0.3 1.0
CA B:LYS322 4.0 0.9 1.0
C B:GLN327 4.1 0.9 1.0
C B:TYR321 4.3 0.4 1.0
C B:THR324 4.4 0.1 1.0
N B:GLN323 4.5 0.4 1.0
NE2 B:GLN327 4.5 0.5 1.0
N B:LYS322 4.6 0.5 1.0
N B:THR324 4.6 0.9 1.0
C B:GLN323 4.8 0.9 1.0
CB B:GLN327 4.9 0.4 1.0
CA B:GLN327 5.0 0.6 1.0

Potassium binding site 3 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 3 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:0.7
occ:1.00
 O C:GLN327 2.7 0.3 1.0
O C:THR324 3.0 0.7 1.0
O C:TYR321 3.0 0.0 1.0
O C:LYS322 3.1 0.7 1.0
C C:GLN327 3.9 0.8 1.0
C C:LYS322 3.9 0.4 1.0
C C:THR324 4.2 0.8 1.0
C C:TYR321 4.2 0.9 1.0
CA C:LYS322 4.3 0.1 1.0
N C:THR324 4.6 0.3 1.0
NE2 C:GLN327 4.7 0.0 1.0
CA C:GLN327 4.7 1.0 1.0
CB C:GLN327 4.7 0.7 1.0
N C:LYS322 4.8 0.2 1.0
N C:GLN327 4.8 1.0 1.0
N C:THR328 4.8 0.1 1.0
N C:GLN323 4.8 0.7 1.0
CA C:THR328 4.9 0.3 1.0
CG C:GLN327 4.9 0.6 1.0
CA C:THR324 5.0 0.5 1.0

Potassium binding site 4 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 4 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K601

b:0.4
occ:1.00
 O D:GLN327 2.6 1.0 1.0
O D:THR324 2.8 0.5 1.0
O D:LYS322 3.0 0.2 1.0
O D:TYR321 3.2 0.3 1.0
C D:LYS322 3.7 0.0 1.0
C D:GLN327 3.8 0.8 1.0
C D:THR324 4.0 0.3 1.0
CA D:LYS322 4.2 0.5 1.0
N D:THR324 4.2 0.0 1.0
C D:TYR321 4.3 0.7 1.0
CB D:GLN327 4.6 0.5 1.0
CA D:GLN327 4.6 0.7 1.0
N D:GLN323 4.6 0.0 1.0
N D:GLN327 4.7 0.5 1.0
CA D:THR324 4.7 0.9 1.0
N D:THR328 4.8 0.6 1.0
N D:LYS322 4.8 0.2 1.0
CA D:THR328 4.8 0.9 1.0
C D:GLN323 4.8 0.8 1.0
N D:ALA325 5.0 0.1 1.0

Potassium binding site 5 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 5 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K601

b:0.8
occ:1.00
 O E:GLN327 2.8 0.4 1.0
O E:LYS322 3.0 0.7 1.0
O E:THR324 3.0 0.7 1.0
O E:TYR321 3.1 0.1 1.0
C E:LYS322 3.6 0.3 1.0
C E:GLN327 4.0 0.3 1.0
CA E:LYS322 4.0 0.2 1.0
C E:TYR321 4.2 1.0 1.0
C E:THR324 4.3 0.7 1.0
N E:GLN323 4.5 0.6 1.0
CB E:GLN327 4.5 1.0 1.0
N E:THR324 4.5 0.5 1.0
N E:LYS322 4.6 0.5 1.0
C E:GLN323 4.7 0.3 1.0
CA E:GLN327 4.7 0.7 1.0
N E:GLN327 4.9 0.8 1.0
CA E:GLN323 5.0 0.4 1.0

Potassium binding site 6 out of 6 in 4ddq

Go back to Potassium Binding Sites List in 4ddq
Potassium binding site 6 out of 6 in the Structural Plasticity of the Bacillus Subtilis Gyra Homodimer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structural Plasticity of the Bacillus Subtilis Gyra Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K601

b:0.2
occ:1.00
 O F:GLN327 2.8 0.2 1.0
O F:THR324 2.9 0.5 1.0
O F:LYS322 2.9 1.0 1.0
O F:TYR321 3.2 0.1 1.0
C F:LYS322 3.7 1.0 1.0
C F:THR324 4.0 0.8 1.0
C F:GLN327 4.0 0.1 1.0
N F:THR324 4.3 0.3 1.0
CA F:LYS322 4.3 0.2 1.0
C F:TYR321 4.4 0.6 1.0
N F:GLN323 4.7 0.3 1.0
CB F:GLN327 4.7 0.5 1.0
C F:GLN323 4.7 0.5 1.0
CA F:THR324 4.7 0.7 1.0
CA F:GLN327 4.8 0.1 1.0
N F:LYS322 4.9 0.6 1.0

Reference:

M.G.Rudolph, D.Klostermeier. Mapping the Spectrum of Conformational States of the Dna- and C-Gates in Bacillus Subtilis Gyrase. J.Mol.Biol. V. 425 2632 2013.
ISSN: ISSN 0022-2836
PubMed: 23602808
DOI: 10.1016/J.JMB.2013.04.010
Page generated: Mon Aug 12 10:31:20 2024

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