Chlorine in PDB 8r5q: Structure of Apo Tdo with A Bound Inhibitor

Protein crystallography data

The structure of Structure of Apo Tdo with A Bound Inhibitor, PDB code: 8r5q was solved by M.Wicki, A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.75 / 2.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.33, 132.49, 135.57, 90, 90, 90
R / Rfree (%) 25.4 / 26.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Apo Tdo with A Bound Inhibitor (pdb code 8r5q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Apo Tdo with A Bound Inhibitor, PDB code: 8r5q:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8r5q

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Chlorine binding site 1 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:77.6
occ:1.00
 CL1 A:Y5N501 0.0 77.6 1.0
C1 A:Y5N501 1.7 76.0 1.0
C19 A:Y5N501 2.7 75.0 1.0
C2 A:Y5N501 2.7 75.4 1.0
CD2 B:LEU46 3.4 62.7 1.0
CG A:HIS76 3.6 52.4 1.0
CD1 B:LEU46 3.6 62.5 1.0
CG B:LEU46 3.7 62.6 1.0
CB A:HIS76 3.7 51.1 1.0
CD2 B:TYR45 3.7 66.4 1.0
ND1 A:HIS76 3.8 53.7 1.0
CE2 A:PHE72 3.8 57.8 1.0
CE1 B:TYR42 3.8 60.3 1.0
CE2 B:TYR45 3.8 67.1 1.0
CD1 B:TYR42 3.9 60.1 1.0
C5 A:Y5N501 4.0 74.0 1.0
C3 A:Y5N501 4.0 74.9 1.0
CD2 A:HIS76 4.1 53.0 1.0
CD2 A:PHE72 4.1 57.4 1.0
CE1 A:HIS76 4.3 54.0 1.0
O A:PHE72 4.4 58.1 1.0
C4 A:Y5N501 4.5 74.5 1.0
NE2 A:HIS76 4.5 54.2 1.0
CZ A:PHE72 4.6 57.5 1.0
CZ B:TYR42 4.7 61.2 1.0
CG B:TYR42 4.9 60.0 1.0

Chlorine binding site 2 out of 8 in 8r5q

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Chlorine binding site 2 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:68.7
occ:1.00
 CL2 A:Y5N501 0.0 68.7 1.0
CE A:Y5N501 1.7 68.5 1.0
NZ A:Y5N501 2.5 69.1 1.0
CD A:Y5N501 2.7 68.2 1.0
CB A:SER155 3.4 68.7 1.0
N A:SER155 3.7 68.9 1.0
N A:GLN154 3.8 74.3 1.0
C17 A:Y5N501 3.8 69.6 1.0
CA A:PHE153 3.9 78.1 1.0
CG A:Y5N501 4.0 68.7 1.0
CD1 A:PHE153 4.0 79.7 1.0
CA A:SER155 4.2 67.7 1.0
CH2 A:TRP324 4.2 57.8 1.0
CB A:PHE153 4.2 77.9 1.0
C A:PHE153 4.2 76.6 1.0
OH B:TYR42 4.4 62.8 1.0
CB A:Y5N501 4.4 69.6 1.0
CB A:PHE158 4.5 64.3 1.0
OG A:SER155 4.5 71.3 1.0
C A:GLN154 4.6 70.6 1.0
CZ3 A:TRP324 4.6 57.4 1.0
CZ B:TYR42 4.6 61.2 1.0
CG A:PHE153 4.6 78.7 1.0
NE2 A:HIS328 4.6 68.4 1.0
CA A:GLN154 4.7 72.2 1.0
CE1 B:TYR42 4.8 60.3 1.0
CD2 A:HIS328 4.8 67.3 1.0
CG A:PHE158 4.9 65.3 1.0
CE2 A:PHE83 5.0 54.2 1.0

Chlorine binding site 3 out of 8 in 8r5q

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Chlorine binding site 3 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:71.4
occ:1.00
 CL1 B:Y5N501 0.0 71.4 1.0
C1 B:Y5N501 1.7 70.3 1.0
C19 B:Y5N501 2.7 69.7 1.0
C2 B:Y5N501 2.7 69.9 1.0
CD2 A:LEU46 3.4 61.6 1.0
CG B:HIS76 3.5 55.9 1.0
CB B:HIS76 3.6 54.6 1.0
ND1 B:HIS76 3.6 57.2 1.0
CD1 A:LEU46 3.6 62.0 1.0
CE2 B:PHE72 3.7 55.0 1.0
CG A:LEU46 3.7 61.7 1.0
CD2 A:TYR45 3.8 66.0 1.0
CE2 A:TYR45 3.9 66.8 1.0
CE1 A:TYR42 3.9 60.0 1.0
C3 B:Y5N501 4.0 69.6 1.0
C5 B:Y5N501 4.0 69.2 1.0
CD2 B:PHE72 4.0 54.1 1.0
CD1 A:TYR42 4.0 59.5 1.0
CD2 B:HIS76 4.1 56.8 1.0
O B:PHE72 4.2 52.6 1.0
CE1 B:HIS76 4.2 58.0 1.0
C4 B:Y5N501 4.5 69.4 1.0
NE2 B:HIS76 4.5 58.2 1.0
CZ B:PHE72 4.6 54.6 1.0
CZ A:TYR42 4.8 60.6 1.0
CG A:TYR42 4.9 59.1 1.0

Chlorine binding site 4 out of 8 in 8r5q

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Chlorine binding site 4 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:69.7
occ:1.00
 CL2 B:Y5N501 0.0 69.7 1.0
CE B:Y5N501 1.7 68.9 1.0
NZ B:Y5N501 2.6 68.7 1.0
CD B:Y5N501 2.7 68.6 1.0
CB B:SER155 3.3 61.3 1.0
N B:SER155 3.7 62.8 1.0
N B:GLN154 3.8 68.8 1.0
C17 B:Y5N501 3.8 68.5 1.0
CA B:PHE153 4.0 72.5 1.0
CG B:Y5N501 4.0 68.3 1.0
CD1 B:PHE153 4.0 73.6 1.0
CH2 B:TRP324 4.1 52.3 1.0
CA B:SER155 4.1 60.8 1.0
CB B:PHE153 4.2 72.0 1.0
C B:PHE153 4.2 70.6 1.0
CB B:PHE158 4.4 54.4 1.0
CB B:Y5N501 4.4 68.2 1.0
CZ3 B:TRP324 4.5 51.9 1.0
OH A:TYR42 4.5 61.3 1.0
OG B:SER155 4.5 63.7 1.0
C B:GLN154 4.5 65.0 1.0
CG B:PHE153 4.6 72.5 1.0
NE2 B:HIS328 4.7 65.0 1.0
CZ A:TYR42 4.7 60.6 1.0
CA B:GLN154 4.7 67.3 1.0
CE1 A:TYR42 4.8 60.0 1.0
CG B:PHE158 4.8 54.7 1.0
CD2 B:HIS328 4.8 64.0 1.0
CD2 B:PHE158 4.9 55.4 1.0
CE2 B:PHE83 5.0 50.7 1.0

Chlorine binding site 5 out of 8 in 8r5q

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Chlorine binding site 5 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:77.5
occ:1.00
 CL1 C:Y5N501 0.0 77.5 1.0
C1 C:Y5N501 1.7 76.3 1.0
C19 C:Y5N501 2.7 75.7 1.0
C2 C:Y5N501 2.7 76.1 1.0
CD2 D:LEU46 3.4 85.2 1.0
CG C:HIS76 3.5 62.5 1.0
CD1 D:LEU46 3.6 85.3 1.0
CG D:LEU46 3.6 84.5 1.0
CB C:HIS76 3.7 61.8 1.0
ND1 C:HIS76 3.7 63.7 1.0
CD2 D:TYR45 3.7 85.1 1.0
CE2 C:PHE72 3.8 65.4 1.0
CE2 D:TYR45 3.9 86.1 1.0
CD1 D:TYR42 3.9 82.0 1.0
CE1 D:TYR42 3.9 82.6 1.0
C3 C:Y5N501 4.0 75.8 1.0
C5 C:Y5N501 4.0 75.1 1.0
CD2 C:HIS76 4.1 62.8 1.0
CD2 C:PHE72 4.1 64.5 1.0
CE1 C:HIS76 4.2 63.8 1.0
O C:PHE72 4.4 64.1 1.0
NE2 C:HIS76 4.5 63.7 1.0
C4 C:Y5N501 4.5 75.5 1.0
CZ C:PHE72 4.6 65.3 1.0
CG D:TYR42 4.8 81.6 1.0
CZ D:TYR42 4.8 83.5 1.0
O D:TYR42 4.9 81.5 1.0
CG D:TYR45 5.0 84.2 1.0

Chlorine binding site 6 out of 8 in 8r5q

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Chlorine binding site 6 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:72.0
occ:1.00
 CL2 C:Y5N501 0.0 72.0 1.0
CE C:Y5N501 1.7 72.0 1.0
NZ C:Y5N501 2.6 71.9 1.0
CD C:Y5N501 2.7 71.8 1.0
CB C:SER155 3.4 76.7 1.0
N C:SER155 3.6 78.0 1.0
N C:GLN154 3.8 83.9 1.0
C17 C:Y5N501 3.9 72.0 1.0
CG C:Y5N501 4.0 71.8 1.0
CA C:PHE153 4.0 86.8 1.0
CD1 C:PHE153 4.0 87.7 1.0
CH2 C:TRP324 4.1 63.3 1.0
CA C:SER155 4.1 75.7 1.0
CB C:PHE153 4.2 86.6 1.0
C C:PHE153 4.2 85.3 1.0
OH D:TYR42 4.4 84.7 1.0
CB C:Y5N501 4.5 72.1 1.0
CB C:PHE158 4.5 63.9 1.0
C C:GLN154 4.5 80.8 1.0
CZ3 C:TRP324 4.5 63.3 1.0
OG C:SER155 4.5 78.3 1.0
CZ D:TYR42 4.6 83.5 1.0
CG C:PHE153 4.6 87.0 1.0
CE1 D:TYR42 4.6 82.6 1.0
NE2 C:HIS328 4.7 70.1 1.0
CA C:GLN154 4.7 82.9 1.0
CD2 C:HIS328 4.8 68.9 1.0
CG C:PHE158 4.8 64.1 1.0
CE2 C:PHE83 5.0 57.3 1.0

Chlorine binding site 7 out of 8 in 8r5q

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Chlorine binding site 7 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:77.6
occ:1.00
 CL1 D:Y5N501 0.0 77.6 1.0
C1 D:Y5N501 1.7 76.5 1.0
C2 D:Y5N501 2.7 76.2 1.0
C19 D:Y5N501 2.7 75.9 1.0
CD2 C:LEU46 3.3 80.2 1.0
CG D:HIS76 3.6 60.9 1.0
CD1 C:LEU46 3.6 80.5 1.0
CG C:LEU46 3.6 79.9 1.0
ND1 D:HIS76 3.7 62.1 1.0
CB D:HIS76 3.7 61.1 1.0
CD2 C:TYR45 3.7 84.5 1.0
CE2 D:PHE72 3.8 64.3 1.0
CE2 C:TYR45 3.8 85.6 1.0
CE1 C:TYR42 3.9 87.9 1.0
C3 D:Y5N501 4.0 76.0 1.0
C5 D:Y5N501 4.0 75.6 1.0
CD1 C:TYR42 4.1 87.0 1.0
CD2 D:PHE72 4.1 63.7 1.0
CD2 D:HIS76 4.1 61.6 1.0
CE1 D:HIS76 4.2 62.5 1.0
O D:PHE72 4.3 64.4 1.0
C4 D:Y5N501 4.5 75.8 1.0
NE2 D:HIS76 4.5 62.5 1.0
CZ D:PHE72 4.7 64.0 1.0
CZ C:TYR42 4.7 88.9 1.0
CG C:TYR42 4.9 85.8 1.0

Chlorine binding site 8 out of 8 in 8r5q

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Chlorine binding site 8 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:72.4
occ:1.00
 CL2 D:Y5N501 0.0 72.4 1.0
CE D:Y5N501 1.8 73.5 1.0
NZ D:Y5N501 2.6 74.0 1.0
CD D:Y5N501 2.7 74.0 1.0
CB D:SER155 3.3 82.2 1.0
N D:SER155 3.7 81.3 1.0
N D:GLN154 3.8 82.4 1.0
C17 D:Y5N501 3.9 74.2 1.0
CG D:Y5N501 4.0 74.1 1.0
CA D:PHE153 4.0 83.6 1.0
CD1 D:PHE153 4.1 83.3 1.0
CH2 D:TRP324 4.1 62.4 1.0
CA D:SER155 4.1 81.0 1.0
CB D:PHE153 4.2 83.1 1.0
OH C:TYR42 4.3 90.5 1.0
C D:PHE153 4.3 83.1 1.0
CB D:Y5N501 4.5 74.4 1.0
CZ3 D:TRP324 4.5 62.6 1.0
OG D:SER155 4.5 84.0 1.0
CB D:PHE158 4.5 74.9 1.0
C D:GLN154 4.5 82.1 1.0
CZ C:TYR42 4.6 88.9 1.0
CG D:PHE153 4.6 82.8 1.0
CE1 C:TYR42 4.7 87.9 1.0
NE2 D:HIS328 4.7 70.1 1.0
CA D:GLN154 4.7 82.5 1.0
CD2 D:HIS328 4.8 68.9 1.0
CG D:PHE158 4.9 75.8 1.0
CE2 D:PHE83 5.0 64.2 1.0

Reference:

C.Lotz-Jenne, R.Lange, S.Cren, G.Bourquin, L.Goglia, T.Kimmerlin, M.Wicki, M.Mueller, N.Artico, S.Ackerknecht, C.Joesch, A.Mac Sweeney. Discovery and Binding Mode of A Small Molecule Inhibitor of the Apo Form of Human TDO2 Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.09.574827
Page generated: Tue Jul 30 12:08:22 2024

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