Chlorine in PDB 8qyf: Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib

Protein crystallography data

The structure of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib, PDB code: 8qyf was solved by B.A.Franca, H.Rohde, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.01 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.963, 123.158, 126.244, 90, 91.23, 90
R / Rfree (%) 21.1 / 22.1

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib (pdb code 8qyf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 28 binding sites of Chlorine where determined in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib, PDB code: 8qyf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 28 in 8qyf

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Chlorine binding site 1 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:91.3
occ:0.92
 CL3 A:6V8301 0.0 91.3 0.9
C3 A:6V8301 1.7 79.0 0.9
C4 A:6V8301 2.6 43.1 0.9
C2 A:6V8301 2.7 50.5 0.9
C7 A:6V8301 3.1 31.7 0.9
N9 A:6V8301 3.3 47.1 0.9
O A:LEU126 3.6 43.5 1.0
C5 A:6V8301 3.9 36.9 0.9
O8 A:6V8301 3.9 44.0 0.9
CA A:GLY127 4.0 33.0 1.0
C1 A:6V8301 4.0 51.9 0.9
C10 A:6V8301 4.4 40.1 0.9
C6 A:6V8301 4.4 73.5 0.9
C A:LEU126 4.6 40.3 1.0
N A:GLY127 4.8 45.6 1.0
C A:GLY127 5.0 43.7 1.0
N A:GLY128 5.0 37.9 1.0

Chlorine binding site 2 out of 28 in 8qyf

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Chlorine binding site 2 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:79.8
occ:0.92
 CL6 A:6V8301 0.0 79.8 0.9
C6 A:6V8301 1.7 73.5 0.9
C1 A:6V8301 2.6 51.9 0.9
C5 A:6V8301 2.7 36.9 0.9
OG1 A:THR146 3.3 39.2 1.0
CE1 A:HIS142 3.6 49.1 1.0
CA A:ILE143 3.6 38.0 1.0
CG1 A:ILE143 3.6 35.6 1.0
CB A:THR146 3.6 36.7 1.0
ND1 A:HIS142 3.7 50.7 1.0
CB A:ILE143 3.8 35.7 1.0
CG2 A:THR146 3.9 31.0 1.0
C2 A:6V8301 3.9 50.5 0.9
C4 A:6V8301 4.0 43.1 0.9
NE2 A:HIS142 4.2 38.5 1.0
N A:ILE143 4.2 32.2 1.0
O A:HIS142 4.2 31.0 1.0
CG A:HIS142 4.3 46.8 1.0
C A:HIS142 4.4 52.0 1.0
C3 A:6V8301 4.4 79.0 0.9
CD1 A:ILE143 4.5 36.8 1.0
CD2 A:HIS142 4.6 43.3 1.0
C A:ILE143 4.7 44.3 1.0
O A:ILE143 4.8 35.8 1.0

Chlorine binding site 3 out of 28 in 8qyf

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Chlorine binding site 3 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:127.1
occ:0.81
 CL3 B:6V8301 0.0 127.1 0.8
C3 B:6V8301 1.7 45.7 0.8
C4 B:6V8301 2.6 42.6 0.8
C2 B:6V8301 2.7 75.0 0.8
C7 B:6V8301 3.2 32.2 0.8
N9 B:6V8301 3.4 40.2 0.8
O B:LEU126 3.7 43.5 1.0
C5 B:6V8301 3.9 26.6 0.8
CA B:GLY127 3.9 33.0 1.0
O8 B:6V8301 4.0 56.4 0.8
C1 B:6V8301 4.0 31.9 0.8
C6 B:6V8301 4.4 67.6 0.8
C10 B:6V8301 4.5 32.4 0.8
C B:LEU126 4.6 40.3 1.0
N B:GLY127 4.8 45.6 1.0
N B:GLY128 4.9 37.9 1.0
C B:GLY127 4.9 43.7 1.0

Chlorine binding site 4 out of 28 in 8qyf

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Chlorine binding site 4 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:114.1
occ:0.81
 CL6 B:6V8301 0.0 114.1 0.8
C6 B:6V8301 1.7 67.6 0.8
C1 B:6V8301 2.6 31.9 0.8
C5 B:6V8301 2.7 26.6 0.8
OG1 B:THR146 3.3 39.2 1.0
CA B:ILE143 3.4 38.0 1.0
CG1 B:ILE143 3.5 35.6 1.0
CE1 B:HIS142 3.6 49.1 1.0
CB B:THR146 3.6 36.7 1.0
CB B:ILE143 3.7 35.7 1.0
ND1 B:HIS142 3.7 50.7 1.0
C2 B:6V8301 3.9 75.0 0.8
CG2 B:THR146 3.9 31.0 1.0
C4 B:6V8301 4.0 42.6 0.8
N B:ILE143 4.0 32.2 1.0
O B:HIS142 4.1 31.0 1.0
NE2 B:HIS142 4.2 38.5 1.0
CG B:HIS142 4.3 46.8 1.0
C B:HIS142 4.3 52.0 1.0
C3 B:6V8301 4.4 45.7 0.8
CD1 B:ILE143 4.4 36.8 1.0
C B:ILE143 4.6 44.3 1.0
CD2 B:HIS142 4.6 43.3 1.0
O B:ILE143 4.6 35.8 1.0

Chlorine binding site 5 out of 28 in 8qyf

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Chlorine binding site 5 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:85.9
occ:1.00
 CL3 C:6V8301 0.0 85.9 1.0
C3 C:6V8301 1.7 56.2 1.0
C4 C:6V8301 2.7 69.1 1.0
C2 C:6V8301 2.7 86.5 1.0
C7 C:6V8301 3.2 51.0 1.0
N9 C:6V8301 3.3 39.2 1.0
O C:LEU126 3.6 43.5 1.0
CA C:GLY127 3.9 33.0 1.0
C5 C:6V8301 3.9 50.1 1.0
O8 C:6V8301 3.9 37.9 1.0
C1 C:6V8301 4.0 28.5 1.0
C10 C:6V8301 4.4 48.9 1.0
C6 C:6V8301 4.4 94.4 1.0
C C:LEU126 4.6 40.3 1.0
N C:GLY127 4.8 45.6 1.0
C C:GLY127 4.9 43.7 1.0
N C:GLY128 4.9 37.9 1.0

Chlorine binding site 6 out of 28 in 8qyf

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Chlorine binding site 6 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:74.2
occ:1.00
 CL6 C:6V8301 0.0 74.2 1.0
C6 C:6V8301 1.7 94.4 1.0
C1 C:6V8301 2.6 28.5 1.0
C5 C:6V8301 2.7 50.1 1.0
CE1 C:HIS142 3.4 49.1 1.0
OG1 C:THR146 3.5 39.2 1.0
ND1 C:HIS142 3.5 50.7 1.0
CA C:ILE143 3.7 38.0 1.0
CG1 C:ILE143 3.8 35.6 1.0
O D:HOH448 3.8 49.2 1.0
CB C:THR146 3.8 36.7 1.0
C2 C:6V8301 3.9 86.5 1.0
CB C:ILE143 3.9 35.7 1.0
C4 C:6V8301 4.0 69.1 1.0
NE2 C:HIS142 4.1 38.5 1.0
CG2 C:THR146 4.1 31.0 1.0
CG C:HIS142 4.2 46.8 1.0
N C:ILE143 4.3 32.2 1.0
O C:HIS142 4.3 31.0 1.0
C3 C:6V8301 4.4 56.2 1.0
C C:HIS142 4.5 52.0 1.0
CD2 C:HIS142 4.5 43.3 1.0
CD1 C:ILE143 4.6 36.8 1.0
C C:ILE143 4.9 44.3 1.0
O C:ILE143 5.0 35.8 1.0

Chlorine binding site 7 out of 28 in 8qyf

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Chlorine binding site 7 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:113.4
occ:1.00
 CL3 D:6V8301 0.0 113.4 1.0
C3 D:6V8301 1.7 61.2 1.0
C4 D:6V8301 2.5 58.2 1.0
C2 D:6V8301 2.9 70.6 1.0
C7 D:6V8301 3.5 49.3 1.0
CG2 D:THR146 3.6 31.0 1.0
O D:HOH408 3.7 44.8 1.0
O8 D:6V8301 3.8 50.4 1.0
C5 D:6V8301 3.9 72.8 1.0
OG1 D:THR146 3.9 39.2 1.0
CB D:VAL71 4.0 45.9 1.0
CB D:THR146 4.0 36.7 1.0
CG2 D:VAL71 4.1 38.0 1.0
C1 D:6V8301 4.1 42.6 1.0
CG1 D:ILE143 4.4 35.6 1.0
N9 D:6V8301 4.4 52.6 1.0
C6 D:6V8301 4.5 100.5 1.0
CG1 D:VAL71 4.5 31.4 1.0
CE1 D:HIS142 4.6 49.1 1.0
CA D:ILE143 5.0 38.0 1.0

Chlorine binding site 8 out of 28 in 8qyf

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Chlorine binding site 8 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:99.0
occ:1.00
 CL6 D:6V8301 0.0 99.0 1.0
C6 D:6V8301 1.7 100.5 1.0
C5 D:6V8301 2.7 72.8 1.0
C1 D:6V8301 2.7 42.6 1.0
N D:GLY128 3.2 37.9 1.0
O D:GLY128 3.3 67.3 1.0
CA D:GLY127 3.6 33.0 1.0
C4 D:6V8301 3.9 58.2 1.0
C D:GLY127 3.9 43.7 1.0
C2 D:6V8301 4.0 70.6 1.0
O D:HOH423 4.1 49.7 1.0
C D:GLY128 4.2 45.8 1.0
CA D:GLY128 4.2 41.5 1.0
C3 D:6V8301 4.5 61.2 1.0
O D:HOH415 4.7 38.6 1.0
N D:GLY127 5.0 45.6 1.0
O D:LEU126 5.0 43.5 1.0

Chlorine binding site 9 out of 28 in 8qyf

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Chlorine binding site 9 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:73.5
occ:0.81
 CL3 E:6V8301 0.0 73.5 0.8
C3 E:6V8301 1.7 48.7 0.8
C4 E:6V8301 2.7 40.4 0.8
C2 E:6V8301 2.7 37.6 0.8
C7 E:6V8301 3.1 39.8 0.8
N9 E:6V8301 3.3 31.5 0.8
O E:LEU126 3.4 43.5 1.0
CA E:GLY127 3.7 33.0 1.0
O8 E:6V8301 3.9 40.0 0.8
C5 E:6V8301 3.9 26.6 0.8
C1 E:6V8301 4.0 59.4 0.8
C10 E:6V8301 4.3 31.1 0.8
C E:LEU126 4.3 40.3 1.0
C6 E:6V8301 4.4 37.9 0.8
N E:GLY127 4.6 45.6 1.0
C E:GLY127 4.8 43.7 1.0
N E:GLY128 4.9 37.9 1.0

Chlorine binding site 10 out of 28 in 8qyf

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Chlorine binding site 10 out of 28 in the Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Clpp From Staphylococcus Epidermidis in Complex with Ixazomib within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:65.0
occ:0.81
 CL6 E:6V8301 0.0 65.0 0.8
C6 E:6V8301 1.7 37.9 0.8
C1 E:6V8301 2.6 59.4 0.8
C5 E:6V8301 2.7 26.6 0.8
OG1 E:THR146 3.0 39.2 1.0
CB E:THR146 3.4 36.7 1.0
CE1 E:HIS142 3.4 49.1 1.0
CG2 E:THR146 3.6 31.0 1.0
ND1 E:HIS142 3.7 50.7 1.0
CA E:ILE143 3.8 38.0 1.0
CG1 E:ILE143 3.9 35.6 1.0
C2 E:6V8301 3.9 37.6 0.8
NE2 E:HIS142 4.0 38.5 1.0
C4 E:6V8301 4.0 40.4 0.8
CB E:ILE143 4.1 35.7 1.0
O E:HIS142 4.2 31.0 1.0
CG E:HIS142 4.3 46.8 1.0
N E:ILE143 4.4 32.2 1.0
C3 E:6V8301 4.4 48.7 0.8
CD2 E:HIS142 4.5 43.3 1.0
C E:HIS142 4.5 52.0 1.0
C E:ILE143 4.8 44.3 1.0
O E:ILE143 4.9 35.8 1.0
CD1 E:ILE143 4.9 36.8 1.0
CA E:THR146 4.9 35.2 1.0

Reference:

B.Alves Franca, S.Falke, H.Rohde, C.Betzel. Molecular Insights Into the Dynamic Modulation of Bacterial Clpp Function and Oligomerization By Peptidomimetic Boronate Compounds Sci Rep 2024.
ISSN: ESSN 2045-2322
DOI: 10.1038/S41598-024-51787-0
Page generated: Tue Jul 30 12:06:44 2024

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