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Chlorine in PDB 6nda: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium, PDB code: 6nda 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) 92.47 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.530, 130.530, 250.919, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 6nda:

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

Cadmium (Cd) 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 Cadmium (pdb code 6nda). 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 Cadmium, PDB code: 6nda:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:53.4
occ:1.00
 NH2 C:ARG260 3.4 49.5 1.0
N G:GLY7 3.4 74.6 1.0
CA G:GLY7 3.7 77.9 1.0
NH1 C:ARG260 3.9 44.3 1.0
CZ C:ARG260 4.1 48.2 1.0
C G:GLY7 4.2 64.9 1.0
CE C:LYS261 4.3 62.1 1.0
O G:TRP8 4.5 49.7 1.0
O G:GLY7 4.6 64.4 1.0
C G:PRO6 4.6 62.4 1.0
N G:TRP8 4.9 49.1 1.0
CA G:PRO6 4.9 61.5 1.0

Chlorine binding site 2 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:60.5
occ:1.00
 NH2 C:ARG339 3.1 94.4 1.0
NH2 O:ARG339 3.8 0.6 1.0
CZ C:ARG339 4.3 82.5 1.0
CZ O:ARG339 4.8 0.1 1.0
NE C:ARG339 4.8 71.6 1.0

Chlorine binding site 3 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:56.4
occ:1.00
 N E:LYS59 3.2 51.3 1.0
N E:TYR60 3.8 53.0 1.0
CA E:LEU58 3.8 55.2 1.0
CD2 E:LEU58 3.8 66.2 1.0
CB E:LYS59 3.9 56.3 1.0
C E:LEU58 4.0 47.8 1.0
OD1 F:ASP321 4.0 61.6 1.0
CA E:LYS59 4.0 56.4 1.0
CB E:LEU58 4.2 67.9 1.0
CD2 E:TYR60 4.4 43.5 1.0
C E:LYS59 4.4 57.6 1.0
CG E:LEU58 4.7 67.3 1.0
O E:TYR60 4.7 49.3 1.0
CB E:TYR60 4.7 40.2 1.0
CA E:TYR60 4.7 44.0 1.0
CB E:SER17 4.7 66.5 1.0
O E:THR57 4.8 40.0 1.0

Chlorine binding site 4 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl201

b:55.4
occ:1.00
 N H:LYS59 3.2 58.3 1.0
CA H:LEU58 3.7 56.1 1.0
N H:TYR60 3.7 52.2 1.0
CD2 H:LEU58 3.8 63.7 1.0
CB H:LYS59 3.9 57.5 1.0
C H:LEU58 3.9 52.6 1.0
OD2 I:ASP321 3.9 66.1 1.0
CA H:LYS59 4.0 58.0 1.0
CB H:LEU58 4.1 63.9 1.0
CD2 H:TYR60 4.4 42.8 1.0
C H:LYS59 4.4 57.4 1.0
OG H:SER17 4.4 61.7 1.0
CG H:LEU58 4.6 65.2 1.0
CB H:TYR60 4.6 37.4 1.0
CA H:TYR60 4.7 42.6 1.0
O H:TYR60 4.8 44.9 1.0
O H:THR57 4.8 51.7 1.0
N H:LEU58 5.0 55.9 1.0
CG I:ASP321 5.0 59.7 1.0

Chlorine binding site 5 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl202

b:77.7
occ:1.00
 NH2 J:ARG73 3.1 96.3 1.0
CD J:ARG75 3.7 69.5 1.0
NH1 J:ARG75 3.9 99.2 1.0
CZ J:ARG73 4.4 0.7 1.0
NE J:ARG75 4.4 81.1 1.0
CG J:ARG75 4.4 63.6 1.0
CZ J:ARG75 4.5 0.8 1.0
CB J:ARG75 4.7 58.6 1.0

Chlorine binding site 6 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:49.3
occ:1.00
 NH2 K:ARG14 2.9 78.2 1.0
CZ K:ARG14 3.9 61.4 1.0
NH1 K:ARG14 3.9 56.8 1.0
ND1 K:HIS4 4.6 0.2 1.0
CE1 K:HIS4 4.9 0.7 1.0

Chlorine binding site 7 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl403

b:61.2
occ:1.00
 NH2 L:ARG260 3.5 54.8 1.0
NH1 L:ARG260 3.8 40.4 1.0
CZ L:ARG260 4.2 47.4 1.0
CE L:LYS261 4.4 58.1 1.0

Chlorine binding site 8 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:51.0
occ:1.00
 NE2 M:GLN102 2.8 43.5 1.0
NH1 N:ARG91 3.2 51.2 1.0
CD M:GLN102 3.7 47.5 1.0
OE1 M:GLN102 3.7 59.0 1.0
OE1 M:GLU100 3.8 48.5 1.0
OE2 M:GLU100 4.0 33.1 1.0
CZ N:ARG91 4.2 52.0 1.0
CD M:GLU100 4.3 40.5 1.0
NH2 N:ARG91 4.4 54.7 1.0
O N:ASN109 4.6 31.5 1.0
CE2 N:TYR94 4.7 35.0 1.0
O M:GLY99 4.9 66.4 1.0
CD2 N:TYR94 5.0 33.4 1.0

Chlorine binding site 9 out of 9 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl403

b:55.9
occ:1.00
 NH2 R:ARG339 3.8 0.8 1.0
CZ R:ARG339 4.8 0.8 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium To Be Published.
Page generated: Sat Jul 12 17:08:30 2025

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