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Chlorine in PDB 6ndh: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc, PDB code: 6ndh 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) 47.00 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.399, 131.399, 251.358, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.5

Other elements in 6ndh:

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

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

Chlorine binding site 1 out of 9 in 6ndh

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


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:79.1
occ:1.00
 N G:GLY7 3.4 90.8 1.0
NH2 C:ARG260 3.5 65.2 1.0
CA G:GLY7 3.6 83.7 1.0
NH1 C:ARG260 3.9 67.9 1.0
CZ C:ARG260 4.2 67.1 1.0
CE C:LYS261 4.2 55.1 1.0
C G:GLY7 4.2 78.3 1.0
O G:TRP8 4.4 55.8 1.0
C G:PRO6 4.6 80.3 1.0
O G:GLY7 4.6 84.5 1.0
N G:TRP8 4.7 62.2 1.0
NZ C:LYS261 4.8 61.5 1.0
CA G:PRO6 5.0 77.0 1.0
CD C:LYS261 5.0 47.7 1.0

Chlorine binding site 2 out of 9 in 6ndh

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


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

b:64.6
occ:1.00
 NH2 C:ARG339 2.8 0.1 1.0
NH2 O:ARG339 3.6 98.3 1.0
CZ C:ARG339 4.1 92.3 1.0
CZ O:ARG339 4.5 0.1 1.0
NH1 O:ARG339 4.6 0.9 1.0
NE C:ARG339 4.8 80.9 1.0

Chlorine binding site 3 out of 9 in 6ndh

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


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

b:53.7
occ:1.00
 N E:LYS59 3.3 52.9 1.0
N E:TYR60 3.6 53.8 1.0
CD2 E:LEU58 3.9 56.0 1.0
OD1 F:ASP321 3.9 72.2 1.0
CA E:LEU58 3.9 54.7 1.0
CB E:LYS59 4.0 63.0 1.0
CA E:LYS59 4.1 62.6 1.0
C E:LEU58 4.1 50.6 1.0
CD2 E:TYR60 4.2 49.5 1.0
CB E:LEU58 4.3 61.9 1.0
C E:LYS59 4.4 64.5 1.0
CB E:TYR60 4.5 46.0 1.0
CA E:TYR60 4.6 48.8 1.0
O E:TYR60 4.7 44.5 1.0
CG E:LEU58 4.8 59.0 1.0
CB E:SER17 4.8 62.1 1.0
CG E:TYR60 4.8 45.4 1.0
C E:TYR60 5.0 40.9 1.0
CG F:ASP321 5.0 79.8 1.0

Chlorine binding site 4 out of 9 in 6ndh

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


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

b:58.5
occ:1.00
 N H:LYS59 3.3 56.1 1.0
N H:TYR60 3.6 52.8 1.0
OD2 I:ASP321 3.7 73.3 1.0
CD2 H:LEU58 3.9 53.7 1.0
CB H:LYS59 3.9 62.9 1.0
CA H:LEU58 3.9 51.3 1.0
CA H:LYS59 4.0 61.9 1.0
CD2 H:TYR60 4.1 45.1 1.0
C H:LEU58 4.1 49.3 1.0
C H:LYS59 4.3 62.9 1.0
CB H:LEU58 4.3 57.8 1.0
CB H:TYR60 4.4 44.7 1.0
CA H:TYR60 4.5 46.6 1.0
OG H:SER17 4.6 57.2 1.0
CG H:TYR60 4.7 44.9 1.0
CG H:LEU58 4.8 55.7 1.0
O H:TYR60 4.8 40.6 1.0
CG I:ASP321 4.8 77.2 1.0
C H:TYR60 4.9 37.4 1.0
CG H:LYS59 5.0 63.8 1.0

Chlorine binding site 5 out of 9 in 6ndh

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


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

b:86.3
occ:1.00
 NH2 J:ARG73 3.4 95.0 1.0
CD J:ARG75 3.8 80.0 1.0
NH1 J:ARG75 4.1 0.7 1.0
NE J:ARG75 4.4 82.6 1.0
CG J:ARG75 4.5 75.6 1.0
CZ J:ARG75 4.5 0.6 1.0
CZ J:ARG73 4.7 0.4 1.0
CB J:ARG75 4.8 67.6 1.0

Chlorine binding site 6 out of 9 in 6ndh

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


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

b:60.1
occ:1.00
 NH2 K:ARG14 3.0 82.5 1.0
CZ K:ARG14 3.9 68.5 1.0
NH1 K:ARG14 3.9 64.2 1.0
ND1 K:HIS4 4.6 0.5 1.0
CE1 K:HIS4 4.9 0.9 1.0

Chlorine binding site 7 out of 9 in 6ndh

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


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

b:78.8
occ:1.00
 NH2 L:ARG260 3.6 63.4 1.0
NH1 L:ARG260 4.0 60.6 1.0
CZ L:ARG260 4.3 63.5 1.0
CE L:LYS261 4.5 63.8 1.0

Chlorine binding site 8 out of 9 in 6ndh

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


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

b:63.6
occ:1.00
 NH1 N:ARG91 3.0 62.2 1.0
NE2 M:GLN102 3.1 40.1 1.0
OE1 M:GLN102 3.7 50.5 1.0
CD M:GLN102 3.8 48.7 1.0
CZ N:ARG91 3.9 61.0 1.0
NH2 N:ARG91 4.1 61.3 1.0
OE2 M:GLU100 4.6 43.9 1.0
OE1 M:GLU100 4.6 42.6 1.0
CE2 N:TYR94 4.7 49.1 1.0

Chlorine binding site 9 out of 9 in 6ndh

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


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

b:64.1
occ:1.00
 NH2 R:ARG339 3.7 0.9 1.0
CZ R:ARG339 4.7 0.2 1.0
NE R:ARG339 5.0 0.8 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Zinc Bound To Be Published.
Page generated: Sat Jul 12 17:12:02 2025

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