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Chlorine in PDB 6ndb: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt, PDB code: 6ndb was solved by J.Stetefeld, M.D.Mcdougall, P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 3.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.836, 131.836, 251.702, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 29.2

Other elements in 6ndb:

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt also contains other interesting chemical elements:

Cobalt (Co) 6 atoms
Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt (pdb code 6ndb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt, PDB code: 6ndb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6ndb

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Chlorine binding site 1 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:66.7
occ:1.00
 NH2 C:ARG339 2.9 0.4 1.0
NH2 O:ARG339 3.7 99.0 1.0
CZ C:ARG339 4.2 92.2 1.0
CZ O:ARG339 4.6 0.0 1.0
NH1 O:ARG339 4.7 0.3 1.0
NE C:ARG339 4.8 81.7 1.0

Chlorine binding site 2 out of 9 in 6ndb

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Chlorine binding site 2 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:62.2
occ:1.00
 N E:LYS59 3.2 61.7 1.0
N E:TYR60 3.7 62.0 1.0
CD2 E:LEU58 3.8 67.3 1.0
CA E:LEU58 3.8 62.5 1.0
CB E:LYS59 4.0 67.5 1.0
C E:LEU58 4.0 58.0 1.0
CA E:LYS59 4.0 64.6 1.0
OD1 F:ASP321 4.1 73.8 1.0
CD2 E:TYR60 4.2 55.4 1.0
CB E:LEU58 4.3 72.5 1.0
C E:LYS59 4.4 67.8 1.0
CB E:TYR60 4.7 51.3 1.0
CA E:TYR60 4.7 54.4 1.0
CG E:LEU58 4.7 70.0 1.0
O E:TYR60 4.7 61.4 1.0
CB E:SER17 4.8 72.4 1.0
O E:THR57 4.9 65.5 1.0
CG E:TYR60 4.9 46.6 1.0

Chlorine binding site 3 out of 9 in 6ndb

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Chlorine binding site 3 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:74.8
occ:1.00
 N G:GLY7 3.4 85.7 1.0
NH2 C:ARG260 3.5 68.6 1.0
CA G:GLY7 3.6 84.7 1.0
NH1 C:ARG260 3.8 57.0 1.0
CZ C:ARG260 4.1 63.1 1.0
C G:GLY7 4.2 85.4 1.0
CE C:LYS261 4.4 71.0 1.0
O G:TRP8 4.5 49.1 1.0
C G:PRO6 4.5 77.7 1.0
O G:GLY7 4.6 90.6 1.0
N G:TRP8 4.8 73.5 1.0
CA G:PRO6 4.9 77.3 1.0

Chlorine binding site 4 out of 9 in 6ndb

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Chlorine binding site 4 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl201

b:69.6
occ:1.00
 N H:LYS59 3.1 66.5 1.0
CA H:LEU58 3.8 59.0 1.0
N H:TYR60 3.8 65.9 1.0
CB H:LYS59 3.8 75.3 1.0
CD2 H:LEU58 3.9 69.7 1.0
C H:LEU58 3.9 57.1 1.0
CA H:LYS59 4.0 70.4 1.0
OD2 I:ASP321 4.0 70.5 1.0
CB H:LEU58 4.2 66.4 1.0
CD2 H:TYR60 4.3 59.3 1.0
C H:LYS59 4.4 69.8 1.0
CB H:TYR60 4.7 53.1 1.0
CG H:LEU58 4.7 69.1 1.0
OG H:SER17 4.7 63.3 1.0
CA H:TYR60 4.8 54.1 1.0
O H:THR57 4.8 58.8 1.0
O H:TYR60 4.9 49.7 1.0
CG I:ASP321 5.0 78.6 1.0
CG H:TYR60 5.0 51.9 1.0

Chlorine binding site 5 out of 9 in 6ndb

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Chlorine binding site 5 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl202

b:80.0
occ:1.00
 NH2 J:ARG73 3.4 0.7 1.0
CD J:ARG75 4.4 76.5 1.0
NH1 J:ARG75 4.4 0.3 1.0
CZ J:ARG73 4.7 0.4 1.0
CG J:ARG75 5.0 72.8 1.0

Chlorine binding site 6 out of 9 in 6ndb

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Chlorine binding site 6 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:70.3
occ:1.00
 NH2 K:ARG14 3.1 96.9 1.0
NH1 K:ARG14 3.7 71.3 1.0
CZ K:ARG14 3.9 74.3 1.0
ND1 K:HIS4 4.7 0.7 1.0

Chlorine binding site 7 out of 9 in 6ndb

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Chlorine binding site 7 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl403

b:70.5
occ:1.00
 NH2 L:ARG260 3.6 70.7 1.0
NH1 L:ARG260 3.9 56.8 1.0
CZ L:ARG260 4.2 65.7 1.0
CE L:LYS261 4.6 77.0 1.0
OE1 L:GLN298 4.9 98.7 1.0

Chlorine binding site 8 out of 9 in 6ndb

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Chlorine binding site 8 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:59.0
occ:1.00
 NH1 N:ARG91 3.0 70.1 1.0
NE2 M:GLN102 3.1 41.7 1.0
OE1 M:GLN102 3.6 65.6 1.0
CD M:GLN102 3.8 53.0 1.0
CZ N:ARG91 4.0 70.7 1.0
NH2 N:ARG91 4.2 64.3 1.0
OE1 M:GLU100 4.3 41.0 1.0
OE2 M:GLU100 4.5 35.8 1.0
CE2 N:TYR94 4.7 51.3 1.0
CD M:GLU100 4.8 41.8 1.0

Chlorine binding site 9 out of 9 in 6ndb

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Chlorine binding site 9 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl403

b:69.0
occ:1.00
 NH2 R:ARG339 3.7 0.5 1.0
CZ R:ARG339 4.8 0.9 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt To Be Published.
Page generated: Sat Jul 12 17:09:06 2025

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