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Chlorine in PDB 6ndc: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound, PDB code: 6ndc 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) 92.90 / 3.35
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.140, 131.140, 251.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.6

Other elements in 6ndc:

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

Chromium (Cr) 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 with Chromium Bound (pdb code 6ndc). 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 with Chromium Bound, PDB code: 6ndc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:31.8
occ:1.00
 NH2 C:ARG339 3.3 88.5 1.0
NH2 O:ARG339 3.6 0.8 1.0
CZ O:ARG339 4.4 88.8 1.0
NH1 O:ARG339 4.5 93.8 1.0
CZ C:ARG339 4.6 80.0 1.0

Chlorine binding site 2 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:37.8
occ:1.00
 OD1 F:ASP321 3.3 60.9 1.0
N E:LYS59 3.8 45.4 1.0
CD2 E:TYR60 3.9 47.0 1.0
N E:TYR60 3.9 50.5 1.0
CD2 E:LEU58 4.2 39.4 1.0
CB E:LYS59 4.3 57.7 1.0
CG F:ASP321 4.3 61.0 1.0
CA E:LEU58 4.4 42.0 1.0
CA E:LYS59 4.5 52.4 1.0
CB E:TYR60 4.5 43.5 1.0
OD2 F:ASP321 4.5 55.2 1.0
C E:LEU58 4.6 41.3 1.0
CG E:TYR60 4.7 43.7 1.0
C E:LYS59 4.7 58.2 1.0
CB E:LEU58 4.7 42.9 1.0
CA E:TYR60 4.8 45.0 1.0
CE2 E:TYR60 4.8 50.0 1.0
CB E:SER17 5.0 68.1 1.0
O E:TYR60 5.0 46.1 1.0

Chlorine binding site 3 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:38.9
occ:1.00
 N G:GLY7 3.4 68.6 1.0
CA G:GLY7 3.7 63.2 1.0
NH1 C:ARG260 3.7 40.5 1.0
NH2 C:ARG260 3.7 44.8 1.0
CZ C:ARG260 4.2 42.9 1.0
CE C:LYS261 4.3 51.1 1.0
C G:GLY7 4.4 59.1 1.0
C G:PRO6 4.6 65.3 1.0
O G:TRP8 4.7 55.4 1.0
O G:GLY7 4.7 55.9 1.0
CA G:PRO6 4.9 57.1 1.0

Chlorine binding site 4 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl401

b:38.0
occ:1.00
 OD2 I:ASP321 3.5 58.2 1.0
N H:LYS59 3.7 49.2 1.0
N H:TYR60 3.9 54.8 1.0
CD2 H:LEU58 4.1 54.8 1.0
CD2 H:TYR60 4.1 36.0 1.0
CA H:LEU58 4.2 47.6 1.0
OG H:SER17 4.2 63.4 1.0
CB H:LYS59 4.3 51.5 1.0
CG I:ASP321 4.3 64.0 1.0
OD1 I:ASP321 4.4 58.4 1.0
C H:LEU58 4.4 45.6 1.0
CA H:LYS59 4.4 52.7 1.0
CB H:LEU58 4.5 54.7 1.0
CB H:TYR60 4.5 38.6 1.0
C H:LYS59 4.7 62.9 1.0
CA H:TYR60 4.7 43.2 1.0
CG H:TYR60 4.8 35.6 1.0
O H:TYR60 4.8 39.5 1.0
CG H:LEU58 4.9 58.5 1.0
CE2 H:TYR60 5.0 38.7 1.0

Chlorine binding site 5 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl202

b:57.5
occ:1.00
 NH2 J:ARG73 3.2 93.7 1.0
CD J:ARG75 3.6 71.2 1.0
NH1 J:ARG75 3.7 69.8 1.0
NE J:ARG75 4.2 71.8 1.0
CZ J:ARG75 4.3 75.0 1.0
CG J:ARG75 4.4 73.6 1.0
CZ J:ARG73 4.5 90.6 1.0
CB J:ARG75 4.6 76.9 1.0

Chlorine binding site 6 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:49.0
occ:1.00
 NH2 K:ARG14 3.3 83.7 1.0
NH1 K:ARG14 4.1 73.8 1.0
CZ K:ARG14 4.2 76.7 1.0
ND1 K:HIS4 4.5 0.3 1.0
CE1 K:HIS4 4.8 96.5 1.0

Chlorine binding site 7 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl403

b:38.2
occ:1.00
 NH2 L:ARG260 3.7 38.9 1.0
NH1 L:ARG260 3.9 34.0 1.0
CZ L:ARG260 4.3 35.1 1.0
CE L:LYS261 4.6 44.4 1.0

Chlorine binding site 8 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:48.0
occ:1.00
 NH1 N:ARG91 3.1 57.1 1.0
NE2 M:GLN102 3.3 49.8 1.0
OE1 M:GLN102 3.9 60.6 1.0
CD M:GLN102 4.1 51.9 1.0
CZ N:ARG91 4.1 55.8 1.0
OE1 M:GLU100 4.4 37.4 1.0
NH2 N:ARG91 4.4 53.8 1.0
CE2 N:TYR94 4.5 45.2 1.0
O N:ASN109 4.6 31.8 1.0
OE2 M:GLU100 4.6 29.8 1.0
CD2 N:TYR94 4.8 44.3 1.0
CD M:GLU100 4.9 36.1 1.0

Chlorine binding site 9 out of 9 in 6ndc

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


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 with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl403

b:35.4
occ:1.00
 NH2 R:ARG339 3.9 0.9 1.0
CZ R:ARG339 4.9 87.5 1.0
NE R:ARG339 5.0 81.2 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound To Be Published.
Page generated: Sat Jul 12 17:09:14 2025

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