Potassium in PDB 8bv3: Bacillus Subtilis Dnaa Domain III Structure

Protein crystallography data

The structure of Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3 was solved by S.Pintar, J.A.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.40 / 2.38
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.578, 81.578, 223.196, 90, 90, 120
R / Rfree (%) 19.1 / 23.9

Other elements in 8bv3:

The structure of Bacillus Subtilis Dnaa Domain III Structure also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Bacillus Subtilis Dnaa Domain III Structure (pdb code 8bv3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 8bv3

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Potassium binding site 1 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K302

b:48.0
occ:1.00
 NH2 A:ARG157 3.2 59.4 1.0
NE A:ARG157 3.3 64.0 1.0
CZ A:ARG157 3.7 58.2 1.0
N A:GLU124 3.7 45.4 1.0
CA A:GLU124 3.8 52.1 1.0
C A:GLN123 3.9 41.5 1.0
CG A:GLU155 4.0 85.3 1.0
CB A:PHE127 4.1 46.6 1.0
O A:GLN123 4.1 39.3 1.0
CD2 A:LEU158 4.2 56.0 1.0
CB A:GLU155 4.2 82.8 1.0
CB A:LEU158 4.4 50.9 1.0
CB A:GLN123 4.4 48.6 1.0
CG A:PHE127 4.4 53.6 1.0
CD A:ARG157 4.4 69.1 1.0
CB A:GLU124 4.5 53.9 1.0
CG A:ARG157 4.6 69.0 1.0
CD1 A:PHE127 4.6 60.7 1.0
CA A:GLN123 4.8 45.9 1.0
CG A:LEU158 4.8 49.4 1.0
CG A:GLU124 4.8 60.6 1.0
C A:GLU124 5.0 47.6 1.0

Potassium binding site 2 out of 9 in 8bv3

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Potassium binding site 2 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K302

b:72.2
occ:1.00
 OE1 B:GLU196 3.6 54.6 1.0
N B:ALA232 3.6 47.6 1.0
CB B:GLU196 3.7 50.6 1.0
CB B:ASN231 4.0 55.0 1.0
CA B:ASN231 4.0 49.6 1.0
CB B:PRO194 4.1 39.2 1.0
CB B:ALA232 4.1 55.5 1.0
CG B:GLU196 4.2 56.8 1.0
C B:ASN231 4.3 48.2 1.0
CD B:GLU196 4.3 58.3 1.0
CG2 B:VAL197 4.3 37.7 1.0
CG B:PRO194 4.3 40.5 1.0
CA B:ALA232 4.5 56.6 1.0
CA B:GLU196 4.8 47.8 1.0
N B:VAL197 4.9 40.7 1.0

Potassium binding site 3 out of 9 in 8bv3

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Potassium binding site 3 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K303

b:64.5
occ:1.00
 OG1 B:THR122 3.3 35.4 1.0
CB B:LYS119 3.6 53.7 1.0
CA B:LYS119 3.7 53.6 1.0
N B:THR122 3.7 39.3 1.0
C B:LYS119 3.8 51.8 1.0
CB B:GLN121 3.8 61.1 1.0
N B:GLN121 4.0 51.5 1.0
CD1 B:ILE87 4.1 51.4 1.0
O B:LYS119 4.1 49.6 1.0
CB B:THR122 4.1 39.6 1.0
N B:GLU120 4.2 53.4 1.0
CA B:GLN121 4.3 53.8 1.0
CG B:LYS119 4.3 55.7 1.0
OE1 B:GLN121 4.4 81.0 1.0
C B:GLN121 4.5 41.9 1.0
CD B:LYS119 4.5 62.1 1.0
CA B:THR122 4.6 42.2 1.0
CG B:GLN121 4.7 71.8 1.0
CG1 B:ILE87 4.8 45.6 1.0
C B:GLU120 4.8 49.8 1.0
CD B:GLN121 5.0 81.1 1.0
CG2 B:THR83 5.0 33.1 1.0

Potassium binding site 4 out of 9 in 8bv3

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Potassium binding site 4 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K302

b:34.2
occ:1.00
 NH2 C:ARG157 3.2 49.2 1.0
NE C:ARG157 3.3 50.4 1.0
CZ C:ARG157 3.7 52.1 1.0
CA C:GLU124 3.9 34.4 1.0
N C:GLU124 3.9 34.1 1.0
C C:GLN123 4.0 31.3 1.0
O C:GLN123 4.0 31.4 1.0
CB C:PHE127 4.0 31.4 1.0
CB C:GLU155 4.1 53.9 1.0
CG C:GLU155 4.2 56.7 1.0
CB C:GLN123 4.3 34.7 1.0
CG C:PHE127 4.3 31.6 1.0
CD C:ARG157 4.5 48.9 1.0
CB C:LEU158 4.5 37.4 1.0
CG C:ARG157 4.5 47.1 1.0
CD2 C:LEU158 4.5 39.4 1.0
CB C:GLU124 4.6 39.0 1.0
CD1 C:PHE127 4.6 30.0 1.0
CG C:GLU124 4.7 45.0 1.0
CA C:GLN123 4.8 33.2 1.0
OE1 C:GLN123 4.8 49.4 1.0
CD2 C:PHE127 4.9 35.7 1.0
CG C:LEU158 5.0 39.0 1.0
NH1 C:ARG157 5.0 47.7 1.0

Potassium binding site 5 out of 9 in 8bv3

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Potassium binding site 5 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K303

b:55.6
occ:1.00
 OG1 C:THR122 3.4 35.4 1.0
CB C:GLN121 3.6 50.7 1.0
N C:THR122 3.7 41.5 1.0
N C:GLN121 3.8 45.3 1.0
C C:LYS119 3.8 45.0 1.0
CA C:LYS119 3.8 46.7 1.0
CB C:LYS119 3.9 50.3 1.0
O C:LYS119 4.0 46.0 1.0
CA C:GLN121 4.1 47.5 1.0
N C:GLU120 4.1 50.0 1.0
CB C:THR122 4.2 36.4 1.0
CD1 C:ILE87 4.2 46.4 1.0
OE1 C:GLN121 4.2 69.8 1.0
CD C:LYS119 4.3 61.7 1.0
C C:GLN121 4.4 46.7 1.0
CA C:THR122 4.6 36.5 1.0
CG C:LYS119 4.7 54.0 1.0
C C:GLU120 4.7 46.0 1.0
CG C:GLN121 4.9 59.2 1.0
CD C:GLN121 5.0 68.8 1.0

Potassium binding site 6 out of 9 in 8bv3

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Potassium binding site 6 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K304

b:67.2
occ:1.00
 O C:ALA38 3.6 37.9 1.0
O C:HOH413 3.7 37.1 1.0
O C:HOH422 3.8 35.5 1.0
C C:LYS39 4.2 41.1 1.0
CA C:LYS39 4.3 39.5 1.0
C C:ALA38 4.3 37.2 1.0
N C:ALA40 4.4 36.7 1.0
CB C:ASN42 4.4 31.5 1.0
NZ B:LYS11 4.4 88.2 1.0
C C:ALA40 4.5 38.7 1.0
O C:LYS39 4.5 40.8 1.0
N C:LYS39 4.6 38.5 1.0
O C:ALA40 4.6 48.2 1.0
N C:ASN42 4.7 37.4 1.0
N C:TYR41 4.8 36.3 1.0
CA C:ALA40 5.0 35.7 1.0
CA C:TYR41 5.0 31.6 1.0
C C:TYR41 5.0 37.0 1.0

Potassium binding site 7 out of 9 in 8bv3

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Potassium binding site 7 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K302

b:45.4
occ:1.00
 NH2 D:ARG157 3.2 62.1 1.0
NE D:ARG157 3.4 58.6 1.0
O D:HOH401 3.5 30.0 1.0
CZ D:ARG157 3.5 67.9 1.0
CA D:GLU124 4.0 43.0 1.0
O D:GLN123 4.1 42.3 1.0
C D:GLN123 4.1 39.5 1.0
N D:GLU124 4.1 42.0 1.0
CB D:PHE127 4.2 38.3 1.0
CB D:GLU155 4.2 68.6 1.0
CG D:GLU155 4.3 78.0 1.0
CG D:ARG157 4.3 49.7 1.0
CB D:GLN123 4.3 46.1 1.0
NH1 D:ARG157 4.3 71.9 1.0
CG D:PHE127 4.4 41.8 1.0
CD D:ARG157 4.4 52.0 1.0
CG D:GLU124 4.5 64.1 1.0
CD2 D:LEU158 4.5 43.3 1.0
CD1 D:PHE127 4.6 46.2 1.0
CB D:LEU158 4.6 47.0 1.0
CB D:GLU124 4.6 49.9 1.0
OE1 D:GLN123 4.7 57.3 1.0
CA D:GLN123 4.9 41.5 1.0

Potassium binding site 8 out of 9 in 8bv3

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Potassium binding site 8 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K303

b:73.3
occ:1.00
 ND2 D:ASN208 3.4 37.9 1.0
OD2 E:ASP156 3.4 83.3 1.0
NH2 E:ARG159 3.8 98.7 1.0
CB D:SER207 3.9 50.0 1.0
C D:SER207 4.2 46.3 1.0
CA D:SER207 4.3 49.3 1.0
CG E:ASP156 4.3 78.1 1.0
O D:SER207 4.4 48.5 1.0
CG D:ASN208 4.5 39.7 1.0
N D:ASN208 4.6 45.5 1.0
CB D:ASN208 4.7 41.6 1.0
CB E:ASP156 4.9 68.5 1.0
CB D:VAL50 4.9 38.5 1.0
OG D:SER207 4.9 43.4 1.0

Potassium binding site 9 out of 9 in 8bv3

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Potassium binding site 9 out of 9 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K302

b:47.5
occ:1.00
 NH2 E:ARG157 3.1 61.5 1.0
NE E:ARG157 3.4 63.9 1.0
CZ E:ARG157 3.7 65.3 1.0
N E:GLU124 3.9 47.3 1.0
CA E:GLU124 3.9 45.2 1.0
CB E:PHE127 4.1 36.5 1.0
C E:GLN123 4.1 46.1 1.0
CB E:GLU155 4.1 64.3 1.0
CB E:GLN123 4.3 48.8 1.0
CG E:GLU155 4.3 67.2 1.0
CG E:PHE127 4.4 39.0 1.0
CD2 E:LEU158 4.4 43.8 1.0
O E:GLN123 4.4 50.9 1.0
CB E:LEU158 4.4 41.3 1.0
CB E:GLU124 4.5 47.4 1.0
CG E:ARG157 4.6 57.8 1.0
CD E:ARG157 4.6 58.6 1.0
CD1 E:PHE127 4.6 38.3 1.0
CG E:GLU124 4.7 53.7 1.0
CA E:GLN123 4.8 48.5 1.0
OE1 E:GLN123 4.8 45.7 1.0

Reference:

S.Pintar, A.Basle, J.A.Hubbard. Bacillus Subtilis Dnaa Domain III_IV Structure To Be Published.
Page generated: Mon Aug 12 22:08:07 2024

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