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Chlorine in PDB 8r5r: Structure of Apo Tdo with A Bound Inhibitor

Protein crystallography data

The structure of Structure of Apo Tdo with A Bound Inhibitor, PDB code: 8r5r 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) 50.83 / 3.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.738, 132.906, 137.495, 90, 90, 90
R / Rfree (%) 22.7 / 25.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Apo Tdo with A Bound Inhibitor (pdb code 8r5r). 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: 8r5r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8r5r

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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:79.0
occ:1.00
 CL1 A:Y5N501 0.0 79.0 1.0
C1 A:Y5N501 1.7 77.8 1.0
C2 A:Y5N501 2.7 77.4 1.0
C19 A:Y5N501 2.7 76.9 1.0
CD2 B:LEU46 3.4 66.7 1.0
CD2 B:TYR45 3.5 66.5 1.0
CE2 B:TYR45 3.7 67.4 1.0
ND1 A:HIS76 3.8 57.1 1.0
CE2 A:PHE72 3.8 66.7 1.0
CG B:LEU46 3.8 66.3 1.0
CG A:HIS76 3.8 55.7 1.0
CB A:HIS76 3.8 55.7 1.0
CD1 B:LEU46 3.9 66.6 1.0
CE1 B:TYR42 3.9 71.8 1.0
C3 A:Y5N501 4.0 77.1 1.0
C5 A:Y5N501 4.0 76.3 1.0
CD1 B:TYR42 4.0 71.1 1.0
CD2 A:PHE72 4.0 65.9 1.0
O A:PHE72 4.4 62.9 1.0
CE1 A:HIS76 4.4 57.5 1.0
C4 A:Y5N501 4.5 76.9 1.0
CD2 A:HIS76 4.5 56.5 1.0
CZ A:PHE72 4.6 66.6 1.0
CG B:TYR45 4.8 65.9 1.0
CZ B:TYR42 4.8 72.7 1.0
NE2 A:HIS76 4.8 57.4 1.0
CG B:TYR42 4.9 70.5 1.0

Chlorine binding site 2 out of 8 in 8r5r

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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:71.7
occ:1.00
 CL2 A:Y5N501 0.0 71.7 1.0
CE A:Y5N501 1.7 72.0 1.0
NZ A:Y5N501 2.6 72.1 1.0
CD A:Y5N501 2.7 72.2 1.0
CB A:SER155 3.3 71.7 1.0
N A:SER155 3.6 72.7 1.0
C17 A:Y5N501 3.9 72.5 1.0
CA A:PHE153 3.9 79.1 1.0
CG A:Y5N501 3.9 72.6 1.0
C A:PHE153 4.0 78.2 1.0
N A:GLN154 4.1 76.6 1.0
CD1 A:PHE153 4.1 80.3 1.0
CA A:SER155 4.1 71.7 1.0
CB A:PHE153 4.1 79.0 1.0
CH2 A:TRP324 4.1 64.6 1.0
OH B:TYR42 4.4 74.4 1.0
CB A:Y5N501 4.4 72.9 1.0
OG A:SER155 4.5 72.3 1.0
CZ B:TYR42 4.5 72.7 1.0
O A:PHE153 4.6 78.7 1.0
CG A:PHE153 4.6 79.6 1.0
C A:GLN154 4.6 74.3 1.0
CZ3 A:TRP324 4.6 64.6 1.0
CE1 B:TYR42 4.6 71.8 1.0
NE2 A:HIS328 4.7 69.5 1.0
CB A:PHE158 4.7 68.9 1.0
CD2 A:HIS328 4.7 68.7 1.0
CA A:GLN154 4.9 75.5 1.0
CD2 A:PHE158 4.9 69.4 1.0

Chlorine binding site 3 out of 8 in 8r5r

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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:82.0
occ:1.00
 CL1 B:Y5N501 0.0 82.0 1.0
C1 B:Y5N501 1.7 81.2 1.0
C19 B:Y5N501 2.7 80.5 1.0
C2 B:Y5N501 2.7 80.9 1.0
CD2 A:LEU46 3.4 71.0 1.0
CD2 A:TYR45 3.6 73.1 1.0
CG B:HIS76 3.7 54.6 1.0
CE2 A:TYR45 3.7 73.9 1.0
ND1 B:HIS76 3.7 55.3 1.0
CB B:HIS76 3.7 54.8 1.0
CG A:LEU46 3.8 70.5 1.0
CE2 B:PHE72 3.8 64.2 1.0
CD1 A:LEU46 3.9 71.3 1.0
CE1 A:TYR42 3.9 76.1 1.0
CD1 A:TYR42 4.0 75.4 1.0
C3 B:Y5N501 4.0 80.6 1.0
C5 B:Y5N501 4.0 79.8 1.0
CD2 B:PHE72 4.1 63.5 1.0
O B:PHE72 4.4 61.6 1.0
CE1 B:HIS76 4.4 55.5 1.0
CD2 B:HIS76 4.4 55.1 1.0
C4 B:Y5N501 4.5 80.3 1.0
CZ B:PHE72 4.6 63.9 1.0
NE2 B:HIS76 4.8 55.6 1.0
CG A:TYR42 4.8 74.9 1.0
CZ A:TYR42 4.8 76.6 1.0
CG A:TYR45 4.9 72.2 1.0

Chlorine binding site 4 out of 8 in 8r5r

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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:75.8
occ:1.00
 CL2 B:Y5N501 0.0 75.8 1.0
CE B:Y5N501 1.7 75.7 1.0
NZ B:Y5N501 2.6 75.7 1.0
CD B:Y5N501 2.7 75.9 1.0
CB B:SER155 3.3 69.9 1.0
N B:SER155 3.6 69.8 1.0
C17 B:Y5N501 3.8 75.9 1.0
CA B:PHE153 3.9 77.1 1.0
CG B:Y5N501 3.9 76.3 1.0
C B:PHE153 4.0 75.6 1.0
CD1 B:PHE153 4.1 78.7 1.0
N B:GLN154 4.1 74.0 1.0
CH2 B:TRP324 4.1 63.5 1.0
CA B:SER155 4.1 68.7 1.0
CB B:PHE153 4.1 77.0 1.0
CB B:Y5N501 4.4 76.4 1.0
OH A:TYR42 4.4 77.6 1.0
OG B:SER155 4.5 72.1 1.0
O B:PHE153 4.5 75.7 1.0
CZ3 B:TRP324 4.5 63.4 1.0
NE2 B:HIS328 4.6 69.3 1.0
CG B:PHE153 4.6 77.7 1.0
C B:GLN154 4.6 71.4 1.0
CZ A:TYR42 4.6 76.6 1.0
CD2 B:HIS328 4.6 68.3 1.0
CB B:PHE158 4.7 61.8 1.0
CE1 A:TYR42 4.7 76.1 1.0
CA B:GLN154 4.9 73.1 1.0
CD2 B:PHE158 4.9 62.8 1.0

Chlorine binding site 5 out of 8 in 8r5r

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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:90.3
occ:1.00
 CL1 C:Y5N501 0.0 90.3 1.0
C1 C:Y5N501 1.7 89.8 1.0
C19 C:Y5N501 2.7 89.5 1.0
C2 C:Y5N501 2.7 89.4 1.0
CD2 D:LEU46 3.3 94.2 1.0
CD2 D:TYR45 3.6 94.1 1.0
CG D:LEU46 3.7 93.4 1.0
CG C:HIS76 3.8 68.3 1.0
CE2 D:TYR45 3.8 94.7 1.0
CE2 C:PHE72 3.8 70.3 1.0
CB C:HIS76 3.8 67.1 1.0
ND1 C:HIS76 3.8 69.7 1.0
CD1 D:LEU46 3.9 93.9 1.0
C3 C:Y5N501 4.0 89.2 1.0
C5 C:Y5N501 4.0 89.2 1.0
CE1 D:TYR42 4.0 93.6 1.0
CD1 D:TYR42 4.1 92.9 1.0
CD2 C:PHE72 4.1 69.6 1.0
O C:PHE72 4.4 67.9 1.0
CD2 C:HIS76 4.4 69.2 1.0
CE1 C:HIS76 4.4 70.0 1.0
C4 C:Y5N501 4.5 89.3 1.0
CZ C:PHE72 4.6 70.2 1.0
CG D:TYR45 4.8 93.3 1.0
NE2 C:HIS76 4.8 70.0 1.0
CZ D:TYR42 4.8 94.5 1.0
CG D:TYR42 4.9 92.4 1.0
O D:TYR42 5.0 92.9 1.0

Chlorine binding site 6 out of 8 in 8r5r

Go back to Chlorine Binding Sites List in 8r5r
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:87.5
occ:1.00
 CL2 C:Y5N501 0.0 87.5 1.0
CE C:Y5N501 1.7 87.8 1.0
NZ C:Y5N501 2.6 88.0 1.0
CD C:Y5N501 2.7 88.1 1.0
CB C:SER155 3.3 78.0 1.0
N C:SER155 3.6 78.6 1.0
C17 C:Y5N501 3.9 88.2 1.0
CA C:PHE153 3.9 86.5 1.0
CG C:Y5N501 4.0 88.2 1.0
C C:PHE153 4.0 85.0 1.0
CD1 C:PHE153 4.0 87.9 1.0
N C:GLN154 4.1 83.3 1.0
CA C:SER155 4.1 77.3 1.0
CH2 C:TRP324 4.1 71.0 1.0
CB C:PHE153 4.1 86.4 1.0
OH D:TYR42 4.4 95.9 1.0
CB C:Y5N501 4.5 88.3 1.0
OG C:SER155 4.5 79.7 1.0
O C:PHE153 4.6 85.5 1.0
CG C:PHE153 4.6 87.0 1.0
CZ D:TYR42 4.6 94.5 1.0
CZ3 C:TRP324 4.6 70.8 1.0
C C:GLN154 4.6 80.6 1.0
CE1 D:TYR42 4.6 93.6 1.0
CB C:PHE158 4.7 71.8 1.0
NE2 C:HIS328 4.7 79.1 1.0
CD2 C:HIS328 4.7 78.0 1.0
CD2 C:PHE158 4.8 72.8 1.0
CA C:GLN154 4.9 82.2 1.0
CG C:PHE158 5.0 71.9 1.0

Chlorine binding site 7 out of 8 in 8r5r

Go back to Chlorine Binding Sites List in 8r5r
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:86.7
occ:1.00
 CL1 D:Y5N501 0.0 86.7 1.0
C1 D:Y5N501 1.7 86.7 1.0
C19 D:Y5N501 2.7 86.8 1.0
C2 D:Y5N501 2.7 86.8 1.0
CD2 C:LEU46 3.3 88.9 1.0
CD2 C:TYR45 3.7 90.0 1.0
ND1 D:HIS76 3.7 65.9 1.0
CG D:HIS76 3.8 64.4 1.0
CG C:LEU46 3.8 88.1 1.0
CE2 C:TYR45 3.8 90.8 1.0
CB D:HIS76 3.8 63.7 1.0
CE2 D:PHE72 3.8 69.0 1.0
CD1 C:LEU46 3.9 88.5 1.0
C3 D:Y5N501 4.0 87.0 1.0
C5 D:Y5N501 4.0 87.1 1.0
CE1 C:TYR42 4.1 92.2 1.0
CD2 D:PHE72 4.1 68.3 1.0
CD1 C:TYR42 4.2 91.6 1.0
O D:PHE72 4.3 66.0 1.0
CE1 D:HIS76 4.4 66.4 1.0
CD2 D:HIS76 4.5 65.3 1.0
C4 D:Y5N501 4.5 87.1 1.0
CZ D:PHE72 4.6 68.6 1.0
NE2 D:HIS76 4.8 66.3 1.0
CZ C:TYR42 4.9 93.0 1.0
CG C:TYR45 5.0 89.1 1.0
CG C:TYR42 5.0 90.8 1.0

Chlorine binding site 8 out of 8 in 8r5r

Go back to Chlorine Binding Sites List in 8r5r
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:88.2
occ:1.00
 CL2 D:Y5N501 0.0 88.2 1.0
CE D:Y5N501 1.7 88.2 1.0
NZ D:Y5N501 2.6 88.3 1.0
CD D:Y5N501 2.7 88.1 1.0
CB D:SER155 3.3 79.9 1.0
N D:SER155 3.6 78.7 1.0
C17 D:Y5N501 3.8 88.2 1.0
CG D:Y5N501 3.9 88.1 1.0
CA D:PHE153 4.0 81.7 1.0
C D:PHE153 4.0 81.3 1.0
N D:GLN154 4.0 80.4 1.0
CA D:SER155 4.1 78.5 1.0
CD1 D:PHE153 4.1 81.3 1.0
CH2 D:TRP324 4.1 71.5 1.0
CB D:PHE153 4.2 81.2 1.0
OH C:TYR42 4.2 94.5 1.0
OG D:SER155 4.4 81.8 1.0
CB D:Y5N501 4.4 88.0 1.0
CZ C:TYR42 4.5 93.0 1.0
C D:GLN154 4.5 79.4 1.0
O D:PHE153 4.6 81.8 1.0
CE1 C:TYR42 4.6 92.2 1.0
CG D:PHE153 4.6 81.0 1.0
NE2 D:HIS328 4.6 73.5 1.0
CZ3 D:TRP324 4.6 71.6 1.0
CB D:PHE158 4.7 73.1 1.0
CD2 D:HIS328 4.7 72.5 1.0
CA D:GLN154 4.8 80.0 1.0
CD2 D:PHE158 4.9 73.4 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 12:08:59 2024

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