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Chlorine in PDB 6nd8: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium, PDB code: 6nd8 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) 45.64 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.134, 131.134, 251.522, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 30.6

Other elements in 6nd8:

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

Barium (Ba) 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 Barium (pdb code 6nd8). 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 Barium, PDB code: 6nd8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6nd8

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


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

b:72.4
occ:1.00
 N G:GLY7 3.3 87.6 1.0
NH2 C:ARG260 3.3 69.4 1.0
CA G:GLY7 3.5 79.7 1.0
C G:GLY7 3.9 75.2 1.0
NH1 C:ARG260 4.0 61.3 1.0
CE C:LYS261 4.1 63.6 1.0
CZ C:ARG260 4.1 66.1 1.0
O G:TRP8 4.2 58.9 1.0
O G:GLY7 4.3 73.8 1.0
N G:TRP8 4.5 62.8 1.0
C G:PRO6 4.5 77.4 1.0
NZ C:LYS261 4.8 70.8 1.0
CD C:LYS261 4.8 58.3 1.0
CA G:PRO6 4.9 77.1 1.0
CG C:LYS261 5.0 52.9 1.0

Chlorine binding site 2 out of 9 in 6nd8

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


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

b:57.5
occ:1.00
 NH2 C:ARG339 2.9 0.0 1.0
NH2 O:ARG339 3.6 0.1 1.0
CZ C:ARG339 4.2 95.4 1.0
CZ O:ARG339 4.5 0.2 1.0
NH1 O:ARG339 4.6 0.4 1.0
NE C:ARG339 4.9 79.6 1.0

Chlorine binding site 3 out of 9 in 6nd8

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


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

b:50.1
occ:1.00
 N E:LYS59 3.5 49.1 1.0
OD1 F:ASP321 3.6 80.5 1.0
N E:TYR60 3.6 44.0 1.0
CD2 E:TYR60 3.9 38.9 1.0
CB E:LYS59 4.0 57.7 1.0
CD2 E:LEU58 4.0 44.6 1.0
CA E:LYS59 4.2 53.8 1.0
CA E:LEU58 4.2 51.0 1.0
CB E:TYR60 4.3 32.7 1.0
C E:LEU58 4.3 48.6 1.0
C E:LYS59 4.4 51.3 1.0
CA E:TYR60 4.5 37.2 1.0
CB E:LEU58 4.5 53.5 1.0
CG F:ASP321 4.6 83.0 1.0
CG E:TYR60 4.6 33.9 1.0
O E:TYR60 4.7 38.6 1.0
OD2 F:ASP321 4.7 67.0 1.0
CE2 E:TYR60 4.9 39.0 1.0
CG E:LEU58 4.9 49.0 1.0
CB E:SER17 4.9 59.9 1.0
C E:TYR60 4.9 34.7 1.0

Chlorine binding site 4 out of 9 in 6nd8

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


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

b:59.4
occ:1.00
 N H:LYS59 3.4 50.1 1.0
OD2 I:ASP321 3.6 71.1 1.0
N H:TYR60 3.6 46.1 1.0
CD2 H:TYR60 3.9 40.8 1.0
CB H:LYS59 4.0 53.0 1.0
CD2 H:LEU58 4.1 43.7 1.0
CA H:LYS59 4.1 53.5 1.0
CA H:LEU58 4.2 49.8 1.0
C H:LEU58 4.3 48.1 1.0
CB H:TYR60 4.3 36.0 1.0
OG H:SER17 4.3 48.2 1.0
C H:LYS59 4.4 53.6 1.0
CG I:ASP321 4.5 72.6 1.0
CB H:LEU58 4.5 52.7 1.0
CA H:TYR60 4.5 38.5 1.0
CG H:TYR60 4.6 38.9 1.0
OD1 I:ASP321 4.6 58.0 1.0
CE2 H:TYR60 4.9 43.8 1.0
O H:TYR60 4.9 34.8 1.0
CG H:LEU58 4.9 48.7 1.0

Chlorine binding site 5 out of 9 in 6nd8

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


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

b:85.8
occ:1.00
 NH2 J:ARG73 3.0 90.0 1.0
CD J:ARG75 3.8 74.3 1.0
NH1 J:ARG75 3.9 84.8 1.0
CZ J:ARG73 4.3 0.6 1.0
NE J:ARG75 4.4 75.5 1.0
CG J:ARG75 4.4 77.5 1.0
CZ J:ARG75 4.4 93.8 1.0
CB J:ARG75 4.6 68.6 1.0
NE J:ARG73 4.9 0.6 1.0

Chlorine binding site 6 out of 9 in 6nd8

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


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

b:52.5
occ:1.00
 NH2 K:ARG14 3.0 79.1 1.0
CZ K:ARG14 3.9 67.1 1.0
NH1 K:ARG14 3.9 67.7 1.0
ND1 K:HIS4 4.6 0.5 1.0
CE1 K:HIS4 4.9 0.1 1.0

Chlorine binding site 7 out of 9 in 6nd8

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


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

b:67.6
occ:1.00
 NH2 L:ARG260 3.5 65.4 1.0
NH1 L:ARG260 3.9 61.9 1.0
CZ L:ARG260 4.2 63.8 1.0
CE L:LYS261 4.2 62.9 1.0
NZ L:LYS261 4.9 73.8 1.0

Chlorine binding site 8 out of 9 in 6nd8

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


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

b:55.0
occ:1.00
 NE2 M:GLN102 3.0 42.6 1.0
NH1 N:ARG91 3.0 72.3 1.0
OE1 M:GLN102 3.6 45.2 1.0
CD M:GLN102 3.7 44.7 1.0
CZ N:ARG91 4.0 65.0 1.0
OE1 M:GLU100 4.2 41.5 1.0
NH2 N:ARG91 4.2 62.1 1.0
OE2 M:GLU100 4.6 40.5 1.0
CE2 N:TYR94 4.7 45.2 1.0
CD M:GLU100 4.8 44.0 1.0
O M:GLY99 4.9 77.3 1.0
O N:ASN109 5.0 34.0 1.0
CD2 N:TYR94 5.0 43.8 1.0

Chlorine binding site 9 out of 9 in 6nd8

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


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

b:53.9
occ:1.00
 NH2 R:ARG339 3.7 0.5 1.0
CZ R:ARG339 4.7 0.4 1.0
NE R:ARG339 5.0 0.1 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium To Be Published.
Page generated: Sat Jul 12 17:07:40 2025

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