Chlorine in PDB 6s40: Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites

Protein crystallography data

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40 was solved by S.Leysen, X.Guillory, M.Wolter, S.Genet, B.Somsen, J.Patel, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.04 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.090, 112.115, 62.604, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.7

Other elements in 6s40:

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites (pdb code 6s40). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6s40

Go back to Chlorine Binding Sites List in 6s40
Chlorine binding site 1 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:0.5
occ:1.00
CD A:LYS87 3.8 21.7 0.5
CB A:LYS87 4.0 15.9 0.5
CB A:LYS87 4.0 15.0 0.5
CA A:TYR84 4.1 11.5 1.0
O A:GLU83 4.2 11.3 1.0
CD1 A:TYR84 4.2 11.5 1.0
C A:GLU83 4.3 11.5 1.0
N A:TYR84 4.3 10.4 1.0
CG A:LYS87 4.3 18.5 0.5
CG A:LYS87 4.4 16.9 0.5
CB A:TYR84 4.5 11.9 1.0
O A:HOH462 4.5 22.1 1.0
CB A:GLU83 4.6 11.8 1.0
CD A:LYS87 4.6 19.8 0.5
CG A:TYR84 4.8 10.9 1.0
CE A:LYS87 4.8 24.2 0.5
NZ A:LYS87 4.8 24.9 0.5
CE A:LYS87 5.0 19.8 0.5

Chlorine binding site 2 out of 6 in 6s40

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Chlorine binding site 2 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:41.8
occ:0.47
CL A:KTW306 0.0 41.8 0.5
C7 A:KTW306 1.7 36.2 0.5
C1 A:KTW306 1.9 27.4 0.5
C2 A:KTW306 2.5 28.6 0.5
C8 A:KTW306 2.7 38.5 0.5
C3 A:KTW306 2.7 35.9 0.5
S A:KTW306 2.8 31.2 0.5
C A:KTW306 3.1 29.9 0.5
C4 A:KTW306 3.3 35.4 0.5
CG A:GLU39 3.5 19.2 1.0
CB A:GLU39 3.6 16.3 1.0
O A:HOH584 3.6 34.4 1.0
C1 A:KTW308 3.6 66.0 1.0
CA A:GLU39 3.8 12.2 1.0
C3 A:KTW306 3.8 30.2 0.5
C A:KTW306 4.0 39.4 0.5
C2 A:KTW306 4.0 36.9 0.5
CD A:GLU39 4.0 24.4 1.0
C A:KTW308 4.0 64.1 1.0
C8 A:KTW306 4.2 31.9 0.5
C2 A:KTW308 4.3 69.4 1.0
OE2 A:GLU39 4.3 25.0 1.0
C5 A:KTW306 4.4 29.7 0.5
C7 A:KTW306 4.5 31.4 0.5
C1 A:KTW306 4.5 38.4 0.5
N A:GLU39 4.6 11.5 1.0
OE1 A:GLU39 4.6 24.1 1.0
C5 A:KTW306 4.6 33.4 0.5
C4 A:KTW306 4.7 30.4 0.5
O A:HOH437 4.8 20.8 1.0
S A:KTW308 4.9 77.9 1.0
C8 A:KTW308 4.9 73.1 1.0
C A:GLU39 5.0 11.6 1.0

Chlorine binding site 3 out of 6 in 6s40

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Chlorine binding site 3 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:34.0
occ:0.53
CL A:KTW306 0.0 34.0 0.5
C7 A:KTW306 1.7 31.4 0.5
C1 A:KTW306 1.8 38.4 0.5
C2 A:KTW306 2.5 36.9 0.5
C8 A:KTW306 2.7 31.9 0.5
C3 A:KTW306 2.7 30.2 0.5
C A:KTW306 2.9 39.4 0.5
S A:KTW306 3.0 35.6 0.5
C4 A:KTW306 3.2 30.4 0.5
OD1 A:ASN42 3.5 17.1 1.0
CL A:KTW308 3.6 88.2 1.0
C3 A:KTW306 3.9 35.9 0.5
C8 A:KTW308 4.0 73.1 1.0
CG A:ASN42 4.0 14.6 1.0
C A:KTW306 4.0 29.9 0.5
C2 A:KTW306 4.0 28.6 0.5
C7 A:KTW308 4.0 73.8 1.0
C8 A:KTW306 4.1 38.5 0.5
O A:HOH563 4.5 29.1 1.0
C7 A:KTW306 4.5 36.2 0.5
O P:HOH414 4.5 42.0 1.0
C1 A:KTW306 4.5 27.4 0.5
C5 A:KTW306 4.6 33.4 0.5
C5 A:KTW306 4.6 29.7 0.5
O A:HOH512 4.6 31.1 1.0
CB A:ASN42 4.6 13.7 1.0
ND2 A:ASN42 4.7 15.6 1.0
O A:HOH414 4.7 28.1 1.0
C4 A:KTW306 4.8 35.4 0.5
C A:KTW308 4.9 64.1 1.0

Chlorine binding site 4 out of 6 in 6s40

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Chlorine binding site 4 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:84.0
occ:1.00
CL A:KTW307 0.0 84.0 1.0
C7 A:KTW307 1.7 60.7 1.0
O A:HOH567 2.6 39.7 1.0
C8 A:KTW307 2.7 66.6 1.0
C3 A:KTW307 2.7 54.4 1.0
OD1 A:ASP97 2.7 31.1 1.0
C4 A:KTW307 3.3 49.5 1.0
O A:ASP97 3.4 13.6 1.0
CB A:LEU100 3.5 11.2 1.0
O A:HOH542 3.6 41.4 1.0
CG A:ASP97 3.8 25.4 1.0
CA A:ASP97 3.8 14.4 1.0
N A:GLY101 4.0 12.1 1.0
C A:KTW307 4.0 71.4 1.0
C2 A:KTW307 4.0 56.9 1.0
C A:ASP97 4.1 13.1 1.0
C A:LEU100 4.2 11.2 1.0
CB A:ASP97 4.3 19.4 1.0
CD1 A:LEU100 4.3 11.4 1.0
CA A:LEU100 4.4 10.7 1.0
C1 A:KTW307 4.5 67.1 1.0
CG A:LEU100 4.5 11.7 1.0
CA A:GLY101 4.6 12.7 1.0
C5 A:KTW307 4.6 51.5 1.0
OD2 A:ASP97 4.7 39.0 1.0
O A:LEU100 4.9 10.6 1.0

Chlorine binding site 5 out of 6 in 6s40

Go back to Chlorine Binding Sites List in 6s40
Chlorine binding site 5 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:88.2
occ:1.00
CL A:KTW308 0.0 88.2 1.0
C7 A:KTW308 1.7 73.8 1.0
C8 A:KTW308 2.7 73.1 1.0
C3 A:KTW308 2.7 69.8 1.0
C4 A:KTW308 3.2 65.4 1.0
CL A:KTW306 3.6 34.0 0.5
O A:HOH512 3.6 31.1 1.0
S A:KTW306 3.6 35.6 0.5
C4 A:KTW306 3.9 30.4 0.5
C2 A:KTW308 4.0 69.4 1.0
C A:KTW308 4.0 64.1 1.0
C2 A:KTW306 4.0 36.9 0.5
C7 A:KTW306 4.1 31.4 0.5
C3 A:KTW306 4.1 30.2 0.5
C1 A:KTW306 4.3 38.4 0.5
C1 A:KTW308 4.5 66.0 1.0
C5 A:KTW306 4.5 33.4 0.5
C5 A:KTW308 4.6 65.8 1.0
C5 A:KTW306 4.7 29.7 0.5
C3 A:KTW306 4.8 35.9 0.5
O P:HOH414 5.0 42.0 1.0

Chlorine binding site 6 out of 6 in 6s40

Go back to Chlorine Binding Sites List in 6s40
Chlorine binding site 6 out of 6 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:74.1
occ:1.00
CL A:KTW309 0.0 74.1 1.0
C7 A:KTW309 1.7 58.0 1.0
C3 A:KTW309 2.7 57.1 1.0
C8 A:KTW309 2.7 54.5 1.0
C4 A:KTW309 3.2 59.9 1.0
NE A:ARG224 3.7 48.8 1.0
CG A:ARG224 3.9 33.3 1.0
CE1 A:PHE198 3.9 16.2 1.0
C2 A:KTW309 4.0 59.1 1.0
C A:KTW309 4.0 53.4 1.0
CD1 A:PHE198 4.1 15.3 1.0
CZ A:PHE198 4.2 16.6 1.0
CD1 A:LEU227 4.2 19.9 1.0
CG A:PHE198 4.3 15.3 1.0
CD A:ARG224 4.4 40.6 1.0
CE2 A:PHE198 4.4 15.3 1.0
CB A:ARG224 4.5 23.8 1.0
C1 A:KTW309 4.5 56.5 1.0
CD2 A:PHE198 4.5 15.5 1.0
C5 A:KTW309 4.5 70.8 1.0
CA A:ARG224 4.6 20.6 1.0

Reference:

X.Guillory, M.Wolter, S.Leysen, J.F.Neves, A.Kuusk, S.Genet, B.Somsen, J.Morrow, E.Rivers, L.Van Beek, J.Patel, R.Goodnow, H.Schoenherr, N.Fuller, Q.Cao, R.G.Doveston, L.Brunsveld, M.R.Arkin, M.P.Castaldi, H.Boyd, I.Landrieu, H.Chen, C.Ottmann. Fragment-Based Differential Targeting of Ppi Stabilizer Interfaces. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32501690
DOI: 10.1021/ACS.JMEDCHEM.9B01942
Page generated: Sat Dec 12 13:38:23 2020

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