Atomistry » Chlorine » PDB 5l7i-5lf1 » 5l7i
Atomistry »
  Chlorine »
    PDB 5l7i-5lf1 »
      5l7i »

Chlorine in PDB 5l7i: Structure of Human Smoothened in Complex with Vismodegib

Protein crystallography data

The structure of Structure of Human Smoothened in Complex with Vismodegib, PDB code: 5l7i was solved by E.X.B.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.F.Rambo, M.S.P.Sansom, S.Newstead, R.Rohatgi, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.32 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.820, 71.290, 107.020, 91.53, 98.20, 105.92
R / Rfree (%) 24.5 / 25.7

Other elements in 5l7i:

The structure of Structure of Human Smoothened in Complex with Vismodegib also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Human Smoothened in Complex with Vismodegib (pdb code 5l7i). 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 Human Smoothened in Complex with Vismodegib, PDB code: 5l7i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5l7i

Go back to Chlorine Binding Sites List in 5l7i
Chlorine binding site 1 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1202

b:0.8
occ:1.00
CL1 A:VIS1202 0.0 0.8 1.0
C11 A:VIS1202 1.7 0.8 1.0
C10 A:VIS1202 2.7 0.8 1.0
C12 A:VIS1202 2.7 1.0 1.0
C14 A:VIS1202 3.1 0.7 1.0
C15 A:VIS1202 3.4 0.7 1.0
CD1 A:LEU522 3.5 96.7 1.0
N1 A:VIS1202 3.9 0.1 1.0
C9 A:VIS1202 4.0 0.3 1.0
C13 A:VIS1202 4.0 0.2 1.0
CB A:SER387 4.1 83.2 1.0
CG A:LEU522 4.1 96.2 1.0
CH2 A:TRP281 4.1 77.0 1.0
CB A:GLU518 4.1 0.1 1.0
CA A:SER387 4.2 81.1 1.0
SD A:MET230 4.3 98.0 1.0
CD2 A:LEU522 4.3 96.7 1.0
CE A:MET230 4.4 95.7 1.0
CZ3 A:TRP281 4.4 76.4 1.0
C16 A:VIS1202 4.4 0.1 1.0
O A:GLU518 4.5 0.4 1.0
C8 A:VIS1202 4.5 0.1 1.0
CD1 A:ILE234 4.6 91.0 1.0
CG A:MET230 4.8 93.5 1.0
C18 A:VIS1202 4.8 0.2 1.0
N A:SER387 4.8 82.0 1.0
OE1 A:GLU518 4.9 0.4 1.0
C A:GLU518 4.9 0.1 1.0
CG A:GLU518 4.9 0.5 1.0

Chlorine binding site 2 out of 4 in 5l7i

Go back to Chlorine Binding Sites List in 5l7i
Chlorine binding site 2 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1202

b:0.3
occ:1.00
CL A:VIS1202 0.0 0.3 1.0
C5 A:VIS1202 1.7 0.5 1.0
C6 A:VIS1202 2.7 0.1 1.0
C4 A:VIS1202 2.7 0.0 1.0
O2 A:VIS1202 3.0 0.4 1.0
NH1 A:ARG400 3.0 0.4 1.0
C7 A:VIS1202 3.1 0.7 1.0
NE2 A:GLN477 3.2 0.6 1.0
CD A:GLN477 3.8 0.1 1.0
CG A:GLN477 4.0 0.7 1.0
C1 A:VIS1202 4.0 0.5 1.0
C3 A:VIS1202 4.0 1.0 1.0
CZ A:ARG400 4.3 0.4 1.0
CB A:ASP473 4.3 0.8 1.0
N A:VIS1202 4.3 0.9 1.0
C2 A:VIS1202 4.5 0.8 1.0
CG A:ASP473 4.5 0.5 1.0
OE1 A:GLN477 4.7 0.6 1.0
CD1 A:TYR394 4.8 91.1 1.0
O A:TYR394 4.8 94.2 1.0
OD1 A:ASP473 4.8 0.1 1.0
NH2 A:ARG400 4.9 0.6 1.0
OD2 A:ASP473 5.0 0.7 1.0
CG A:PRO513 5.0 0.4 1.0

Chlorine binding site 3 out of 4 in 5l7i

Go back to Chlorine Binding Sites List in 5l7i
Chlorine binding site 3 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1202

b:0.6
occ:1.00
CL1 B:VIS1202 0.0 0.6 1.0
C11 B:VIS1202 1.7 0.8 1.0
C10 B:VIS1202 2.7 1.0 1.0
C12 B:VIS1202 2.7 0.1 1.0
C14 B:VIS1202 3.1 0.2 1.0
C15 B:VIS1202 3.5 0.3 1.0
CD1 B:LEU522 3.6 0.2 1.0
N1 B:VIS1202 3.9 0.4 1.0
CB B:SER387 3.9 85.9 1.0
CH2 B:TRP281 4.0 87.7 1.0
C9 B:VIS1202 4.0 0.8 1.0
C13 B:VIS1202 4.0 0.6 1.0
CA B:SER387 4.1 84.6 1.0
CG B:LEU522 4.1 0.5 1.0
CZ3 B:TRP281 4.3 88.1 1.0
CD2 B:LEU522 4.3 0.8 1.0
CB B:GLU518 4.3 0.2 1.0
SD B:MET230 4.4 0.4 1.0
C16 B:VIS1202 4.5 0.8 1.0
C8 B:VIS1202 4.5 0.1 1.0
CE B:MET230 4.5 0.6 1.0
CD1 B:ILE234 4.6 0.6 1.0
O B:GLU518 4.6 0.3 1.0
C18 B:VIS1202 4.8 0.9 1.0
N B:SER387 4.8 86.4 1.0
CG B:MET230 4.9 0.6 1.0
OE2 B:GLU518 5.0 0.6 1.0

Chlorine binding site 4 out of 4 in 5l7i

Go back to Chlorine Binding Sites List in 5l7i
Chlorine binding site 4 out of 4 in the Structure of Human Smoothened in Complex with Vismodegib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Human Smoothened in Complex with Vismodegib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1202

b:0.3
occ:1.00
CL B:VIS1202 0.0 0.3 1.0
C5 B:VIS1202 1.7 0.1 1.0
C6 B:VIS1202 2.7 0.2 1.0
C4 B:VIS1202 2.7 0.6 1.0
O2 B:VIS1202 3.0 0.4 1.0
NE2 B:GLN477 3.0 0.1 1.0
NH1 B:ARG400 3.0 0.5 1.0
C7 B:VIS1202 3.1 0.8 1.0
OD2 B:ASP473 3.4 0.3 1.0
CD B:GLN477 3.7 0.6 1.0
CB B:ASP473 3.8 0.1 1.0
CG B:ASP473 3.8 0.4 1.0
OE1 B:GLN477 3.9 0.9 1.0
C1 B:VIS1202 4.0 0.2 1.0
C3 B:VIS1202 4.0 0.1 1.0
CZ B:ARG400 4.3 0.1 1.0
N B:VIS1202 4.3 0.8 1.0
C2 B:VIS1202 4.5 0.3 1.0
CZ3 B:TRP480 4.6 0.1 1.0
CG B:PRO513 4.7 0.9 1.0
CE3 B:TRP480 4.7 0.1 1.0
CA B:ASP473 4.7 1.0 1.0
O B:ASP473 4.7 0.0 1.0
OD1 B:ASP473 4.7 0.2 1.0
CB B:PRO513 4.8 0.8 1.0
CG B:GLN477 4.9 0.9 1.0
C B:ASP473 4.9 0.3 1.0
NH2 B:ARG400 4.9 0.0 1.0

Reference:

E.F.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.P.Rambo, M.S.Sansom, S.Newstead, R.Rohatgi, C.Siebold. Structural Basis of Smoothened Regulation By Its Extracellular Domains. Nature V. 535 517 2016.
ISSN: ESSN 1476-4687
PubMed: 27437577
DOI: 10.1038/NATURE18934
Page generated: Sat Jul 12 04:27:52 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy