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Chlorine in PDB 3vbg: Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443

Protein crystallography data

The structure of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443, PDB code: 3vbg was solved by C.M.Lukacs, C.A.Janson, B.J.Graves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 64.392, 64.392, 167.587, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22

Other elements in 3vbg:

The structure of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 (pdb code 3vbg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443, PDB code: 3vbg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3vbg

Go back to Chlorine Binding Sites List in 3vbg
Chlorine binding site 1 out of 4 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:0.3
occ:1.00
CL A:03M1 0.0 0.3 1.0
C2 A:03M1 1.8 92.0 1.0
C1 A:03M1 2.7 95.0 1.0
C3 A:03M1 2.8 92.4 1.0
C27 A:03M1 3.1 83.1 1.0
C20 B:03M1 3.5 0.8 1.0
C21 B:03M1 3.6 0.2 1.0
C15 B:03M1 3.7 99.6 1.0
C19 B:03M1 3.7 0.7 1.0
CD1 A:ILE61 3.7 79.0 1.0
N14 B:03M1 3.8 96.0 1.0
C13 B:03M1 3.8 98.2 1.0
C11 B:03M1 3.9 96.8 1.0
N12 B:03M1 4.0 0.4 1.0
C22 B:03M1 4.0 0.1 1.0
C4 A:03M1 4.0 94.6 1.0
C9 A:03M1 4.1 0.6 1.0
CG2 A:ILE61 4.1 75.9 1.0
C24 B:03M1 4.1 0.5 1.0
CA A:GLY58 4.1 76.4 1.0
CG1 A:VAL93 4.2 74.5 1.0
O17 B:03M1 4.2 0.6 1.0
CB A:ILE61 4.2 81.5 1.0
C23 B:03M1 4.2 0.9 1.0
C18 B:03M1 4.4 0.9 1.0
O16 B:03M1 4.4 99.3 1.0
C8 A:03M1 4.5 0.6 1.0
CG1 A:ILE61 4.6 81.3 1.0
C10 B:03M1 4.6 92.9 1.0
F26 B:03M1 4.7 1.0 1.0
N A:GLY58 4.8 99.9 1.0

Chlorine binding site 2 out of 4 in 3vbg

Go back to Chlorine Binding Sites List in 3vbg
Chlorine binding site 2 out of 4 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1

b:0.0
occ:1.00
CL B:03M1 0.0 0.0 1.0
C2 B:03M1 1.7 96.5 1.0
C3 B:03M1 2.6 0.5 1.0
C1 B:03M1 2.7 95.3 1.0
C27 B:03M1 2.8 87.6 1.0
CG2 B:ILE61 3.5 76.1 1.0
CD1 B:ILE61 3.7 82.1 1.0
CB B:ILE61 3.9 71.6 1.0
C19 A:03M1 3.9 0.8 1.0
C15 A:03M1 3.9 96.0 1.0
C20 A:03M1 3.9 0.1 1.0
C9 B:03M1 3.9 96.6 1.0
C21 A:03M1 3.9 0.7 1.0
C4 B:03M1 4.0 86.3 1.0
C24 A:03M1 4.0 0.8 1.0
C22 A:03M1 4.0 0.3 1.0
C23 A:03M1 4.1 0.3 1.0
O17 A:03M1 4.1 96.8 1.0
N14 A:03M1 4.1 96.2 1.0
C11 A:03M1 4.2 0.8 1.0
CG1 B:ILE61 4.2 76.7 1.0
CA B:GLY58 4.2 78.9 1.0
C8 B:03M1 4.4 88.5 1.0
C13 A:03M1 4.4 98.0 1.0
O B:GLY58 4.4 81.0 1.0
N12 A:03M1 4.5 0.4 1.0
C18 A:03M1 4.6 0.9 1.0
CG1 B:VAL93 4.6 74.4 1.0
F26 A:03M1 4.7 0.4 1.0
C10 A:03M1 4.7 0.5 1.0
F25 A:03M1 4.8 0.2 1.0
C B:GLY58 4.8 77.4 1.0
N B:GLY58 4.9 87.3 1.0

Chlorine binding site 3 out of 4 in 3vbg

Go back to Chlorine Binding Sites List in 3vbg
Chlorine binding site 3 out of 4 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1

b:0.4
occ:1.00
CL C:03M1 0.0 0.4 1.0
C2 C:03M1 1.8 0.9 1.0
C1 C:03M1 2.7 0.7 1.0
C3 C:03M1 2.7 0.6 1.0
C27 C:03M1 3.1 89.1 1.0
C15 D:03M1 3.8 91.5 1.0
CD1 C:ILE61 3.8 68.5 1.0
O17 D:03M1 3.8 0.7 1.0
CG2 C:ILE61 3.9 73.2 1.0
C4 C:03M1 4.0 0.2 1.0
C9 C:03M1 4.0 0.1 1.0
CA C:GLY58 4.1 86.4 1.0
C11 D:03M1 4.1 94.7 1.0
C24 D:03M1 4.1 0.8 1.0
N14 D:03M1 4.1 95.8 1.0
C19 D:03M1 4.2 0.6 1.0
C23 D:03M1 4.2 0.3 1.0
CB C:ILE61 4.2 72.4 1.0
C20 D:03M1 4.3 0.2 1.0
C22 D:03M1 4.4 0.2 1.0
C21 D:03M1 4.4 0.7 1.0
C8 C:03M1 4.4 0.5 1.0
C10 D:03M1 4.5 0.4 1.0
C13 D:03M1 4.6 98.2 1.0
N12 D:03M1 4.6 98.4 1.0
CG1 C:ILE61 4.7 69.5 1.0
C18 D:03M1 4.7 0.8 1.0
CG1 C:VAL93 4.8 74.9 1.0
F25 D:03M1 4.8 0.2 1.0
N C:GLY58 4.8 91.3 1.0
O C:GLY58 5.0 94.3 1.0

Chlorine binding site 4 out of 4 in 3vbg

Go back to Chlorine Binding Sites List in 3vbg
Chlorine binding site 4 out of 4 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1

b:0.6
occ:1.00
CL D:03M1 0.0 0.6 1.0
C2 D:03M1 1.8 92.2 1.0
C1 D:03M1 2.7 95.7 1.0
C3 D:03M1 2.8 96.5 1.0
C27 D:03M1 3.0 87.6 1.0
CD1 D:ILE61 3.6 76.2 1.0
C15 C:03M1 3.6 0.4 1.0
C20 C:03M1 3.6 89.7 1.0
C21 C:03M1 3.8 99.1 1.0
C19 C:03M1 3.8 0.9 1.0
C11 C:03M1 3.8 0.9 1.0
N14 C:03M1 3.9 0.8 1.0
CG2 D:ILE61 3.9 72.5 1.0
O17 C:03M1 4.0 0.3 1.0
CB D:ILE61 4.0 73.6 1.0
C4 D:03M1 4.0 82.7 1.0
C22 C:03M1 4.0 0.6 1.0
C9 D:03M1 4.1 0.5 1.0
C13 C:03M1 4.1 0.5 1.0
C24 C:03M1 4.1 0.7 1.0
N12 C:03M1 4.1 0.7 1.0
C23 C:03M1 4.2 91.9 1.0
CA D:GLY58 4.3 77.4 1.0
CG1 D:ILE61 4.3 84.0 1.0
CG1 D:VAL93 4.3 88.3 1.0
C10 C:03M1 4.4 0.5 1.0
C18 C:03M1 4.5 0.9 1.0
C8 D:03M1 4.5 93.1 1.0
O D:GLY58 4.6 77.8 1.0
O16 C:03M1 4.7 0.7 1.0
F26 C:03M1 4.8 0.6 1.0
N D:GLY58 4.9 75.5 1.0
CG2 D:VAL75 5.0 74.2 1.0
C D:GLY58 5.0 74.6 1.0

Reference:

B.Graves, T.Thompson, M.Xia, C.Janson, C.Lukacs, D.Deo, P.Di Lello, D.Fry, C.Garvie, K.S.Huang, L.Gao, C.Tovar, A.Lovey, J.Wanner, L.T.Vassilev. Activation of the P53 Pathway By Small-Molecule-Induced MDM2 and Mdmx Dimerization. Proc.Natl.Acad.Sci.Usa V. 109 11788 2012.
ISSN: ISSN 0027-8424
PubMed: 22745160
DOI: 10.1073/PNAS.1203789109
Page generated: Sat Dec 12 10:17:02 2020

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