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Chlorine in PDB 6rk1: Crystal Structure of TSP1 Domain From CCN3

Protein crystallography data

The structure of Crystal Structure of TSP1 Domain From CCN3, PDB code: 6rk1 was solved by E.-R.Xu, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.13 / 1.63
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.860, 52.860, 102.390, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.4

Other elements in 6rk1:

The structure of Crystal Structure of TSP1 Domain From CCN3 also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of TSP1 Domain From CCN3 (pdb code 6rk1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of TSP1 Domain From CCN3, PDB code: 6rk1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6rk1

Go back to Chlorine Binding Sites List in 6rk1
Chlorine binding site 1 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:33.0
occ:1.00
 O A:HOH412 3.3 20.6 1.0
N A:TRP207 3.3 16.8 1.0
CD1 A:TRP207 3.7 21.9 1.0
CA A:GLU206 3.7 18.8 1.0
O A:HOH407 3.7 35.4 1.0
CB A:GLU206 3.9 24.7 1.0
C A:GLU206 4.0 17.1 1.0
CB A:TRP207 4.2 17.2 1.0
CG A:GLU206 4.3 37.3 1.0
CG A:TRP207 4.3 19.1 1.0
CA A:TRP207 4.3 16.6 1.0
NE1 A:TRP207 4.8 22.1 1.0
O A:HOH457 4.8 60.7 1.0
O A:HOH460 4.8 62.6 1.0
N A:GLU206 4.9 17.8 1.0
O A:TRP207 4.9 20.2 1.0
O A:THR205 5.0 15.9 1.0

Chlorine binding site 2 out of 6 in 6rk1

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Chlorine binding site 2 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:17.5
occ:1.00
 NH1 A:ARG236 3.1 17.5 1.0
N B:LEU237 3.2 16.9 1.0
O A:HOH424 3.2 17.6 1.0
NE2 A:GLN234 3.3 17.3 1.0
NH2 A:ARG236 3.4 18.1 1.0
CZ A:ARG236 3.7 16.0 1.0
CG B:LEU237 3.7 19.1 1.0
CA B:ARG236 3.8 16.8 1.0
CG A:GLN234 3.8 15.4 1.0
CB B:LEU237 3.9 17.3 1.0
C B:ARG236 4.0 17.2 1.0
CD B:ARG236 4.0 17.0 1.0
CD A:GLN234 4.1 17.5 1.0
CB A:GLN234 4.2 15.8 1.0
CA B:LEU237 4.2 17.8 1.0
CD1 B:LEU237 4.2 18.8 1.0
O B:THR235 4.5 17.3 1.0
CB B:ARG236 4.5 17.7 1.0
CA A:GLN234 4.6 15.0 1.0
N B:ARG236 4.9 16.4 1.0
CG B:ARG236 4.9 16.0 1.0
CD2 B:LEU237 5.0 20.6 1.0
NA A:NA302 5.0 17.9 1.0

Chlorine binding site 3 out of 6 in 6rk1

Go back to Chlorine Binding Sites List in 6rk1
Chlorine binding site 3 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:28.2
occ:1.00
 O B:HOH434 3.0 27.1 1.0
N B:CYS243 3.0 24.1 1.0
O A:HOH447 3.1 18.4 1.0
CG A:GLN228 3.5 33.0 0.5
CA B:PRO242 3.5 21.9 1.0
CG A:GLN228 3.6 33.6 0.5
CA B:GLY215 3.7 21.2 1.0
C B:PRO242 3.8 21.9 1.0
NE2 A:GLN228 3.9 39.2 0.5
CB A:LEU227 3.9 16.8 1.0
CB B:PRO242 4.0 24.6 1.0
CD A:GLN228 4.0 39.3 0.5
CB B:CYS243 4.0 28.4 1.0
CA B:CYS243 4.0 25.9 1.0
N B:GLY215 4.1 21.8 1.0
SG B:CYS243 4.3 31.5 1.0
O B:CYS243 4.3 33.8 1.0
N A:GLN228 4.4 17.2 1.0
CD A:GLN228 4.5 40.8 0.5
CD1 A:LEU227 4.5 20.9 1.0
SD B:MET239 4.5 22.5 1.0
O A:HOH403 4.6 36.7 1.0
C B:CYS243 4.6 31.9 1.0
CB A:GLN228 4.7 26.0 0.5
CB A:GLN228 4.7 25.5 0.5
C A:LEU227 4.8 17.6 1.0
OE1 A:GLN228 4.8 45.7 0.5
CG A:LEU227 4.8 19.5 1.0
CA A:LEU227 4.8 16.3 1.0
N B:PRO242 4.8 20.7 1.0
O B:ARG241 4.9 22.6 1.0
OE1 A:GLN228 4.9 44.7 0.5
C B:GLY215 5.0 21.1 1.0
O A:HOH434 5.0 23.8 1.0

Chlorine binding site 4 out of 6 in 6rk1

Go back to Chlorine Binding Sites List in 6rk1
Chlorine binding site 4 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:27.3
occ:1.00
 N A:GLU202 3.2 15.7 1.0
O A:HOH417 3.2 18.4 1.0
CA A:ILE201 3.8 20.5 1.0
CB A:GLU202 3.9 17.1 1.0
CG2 A:ILE201 3.9 20.1 1.0
C A:ILE201 4.0 18.4 1.0
CA A:GLU202 4.2 16.0 1.0
CD1 A:ILE201 4.2 22.8 1.0
CB A:ILE201 4.4 19.7 1.0
O A:CYS200 4.5 24.2 1.0
NA A:NA303 4.8 22.5 1.0
O A:HOH401 4.8 18.7 1.0
O A:GLU202 4.8 16.6 1.0
CG1 A:ILE201 5.0 21.9 1.0
N A:ILE201 5.0 20.5 1.0

Chlorine binding site 5 out of 6 in 6rk1

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Chlorine binding site 5 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:18.5
occ:1.00
 NH1 B:ARG236 3.1 18.3 1.0
N A:LEU237 3.2 16.5 1.0
O B:HOH427 3.3 17.0 1.0
NH2 B:ARG236 3.3 18.5 1.0
NE2 B:GLN234 3.3 18.5 1.0
CZ B:ARG236 3.7 17.0 1.0
CG A:LEU237 3.7 20.1 1.0
CA A:ARG236 3.8 15.2 1.0
CG B:GLN234 3.9 17.9 1.0
CB A:LEU237 3.9 18.7 1.0
C A:ARG236 4.0 16.8 1.0
CD A:ARG236 4.1 17.8 1.0
CD B:GLN234 4.1 19.2 1.0
CD1 A:LEU237 4.1 17.7 1.0
CA A:LEU237 4.2 17.4 1.0
CB B:GLN234 4.3 17.2 1.0
O A:THR235 4.4 16.4 1.0
CB A:ARG236 4.5 18.4 1.0
CA B:GLN234 4.8 17.4 1.0
N A:ARG236 4.9 16.3 1.0
CG A:ARG236 4.9 18.5 1.0
CD2 A:LEU237 5.0 21.9 1.0
NE B:ARG236 5.0 18.5 1.0
NA A:NA302 5.0 17.9 1.0

Chlorine binding site 6 out of 6 in 6rk1

Go back to Chlorine Binding Sites List in 6rk1
Chlorine binding site 6 out of 6 in the Crystal Structure of TSP1 Domain From CCN3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of TSP1 Domain From CCN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:42.1
occ:1.00
 N B:TRP207 3.3 30.3 1.0
O B:HOH410 3.3 29.8 1.0
O B:HOH422 3.5 43.3 1.0
CD1 B:TRP207 3.6 28.5 1.0
CA B:GLU206 3.7 32.4 1.0
CB B:GLU206 3.9 37.9 1.0
C B:GLU206 4.0 31.4 1.0
CB B:TRP207 4.1 27.9 1.0
CG B:GLU206 4.2 46.8 1.0
CG B:TRP207 4.2 26.8 1.0
CA B:TRP207 4.3 30.1 1.0
NE1 B:TRP207 4.7 27.6 1.0
N B:GLU206 4.9 30.6 1.0
O B:THR205 4.9 29.7 1.0
O B:TRP207 5.0 33.6 1.0

Reference:

E.-R.Xu, M.Hyvonen. Thrombospondin Module 1 Domain (TSP1) of the Matricellular Protein CCN3 Shows An Atypical Disulfide Pattern and Incomplete Cwr Layers To Be Published.
Page generated: Sat Jul 12 19:23:40 2025

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