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Chlorine in PDB 6ndg: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound, PDB code: 6ndg 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) 46.94 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.846, 130.846, 251.167, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.1

Other elements in 6ndg:

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

Yttrium (Y) 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 Yttrium Bound (pdb code 6ndg). 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 Yttrium Bound, PDB code: 6ndg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6ndg

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Chlorine binding site 1 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:77.7
occ:1.00
 NH2 C:ARG260 3.5 69.9 1.0
N G:GLY7 3.5 83.7 1.0
CA G:GLY7 3.7 85.7 1.0
NH1 C:ARG260 3.9 54.1 1.0
CZ C:ARG260 4.1 62.6 1.0
C G:GLY7 4.2 77.1 1.0
CE C:LYS261 4.2 69.5 1.0
O G:TRP8 4.5 65.7 1.0
O G:GLY7 4.5 97.2 1.0
C G:PRO6 4.7 70.7 1.0
N G:TRP8 4.8 59.5 1.0
NZ C:LYS261 4.9 80.7 1.0
CA G:PRO6 5.0 71.8 1.0

Chlorine binding site 2 out of 9 in 6ndg

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Chlorine binding site 2 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:59.8
occ:1.00
 NH2 C:ARG339 3.1 99.6 1.0
NH2 O:ARG339 3.6 95.5 1.0
CZ C:ARG339 4.4 88.5 1.0
CZ O:ARG339 4.5 1.0 1.0
NH1 O:ARG339 4.7 1.0 1.0
NE C:ARG339 5.0 73.8 1.0

Chlorine binding site 3 out of 9 in 6ndg

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Chlorine binding site 3 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:63.5
occ:1.00
 N E:LYS59 3.2 62.8 1.0
CB E:LYS59 3.8 62.5 1.0
N E:TYR60 3.8 56.4 1.0
CD2 E:LEU58 3.8 79.9 1.0
CA E:LEU58 3.8 65.0 1.0
CA E:LYS59 4.0 61.7 1.0
C E:LEU58 4.0 61.1 1.0
OD1 F:ASP321 4.1 83.8 1.0
CB E:LEU58 4.3 80.1 1.0
CD2 E:TYR60 4.4 49.8 1.0
C E:LYS59 4.4 62.8 1.0
CG E:LEU58 4.7 82.5 1.0
CB E:TYR60 4.8 46.4 1.0
CA E:TYR60 4.8 49.4 1.0
O E:TYR60 4.8 57.2 1.0
O E:THR57 4.9 66.6 1.0
CB E:SER17 4.9 88.0 1.0

Chlorine binding site 4 out of 9 in 6ndg

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Chlorine binding site 4 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl201

b:65.1
occ:1.00
 N H:LYS59 3.2 62.3 1.0
CA H:LEU58 3.8 56.8 1.0
N H:TYR60 3.8 54.5 1.0
CB H:LYS59 3.8 63.1 1.0
CD2 H:LEU58 3.9 74.4 1.0
C H:LEU58 3.9 55.1 1.0
CA H:LYS59 4.0 64.0 1.0
OD2 I:ASP321 4.0 76.9 1.0
CB H:LEU58 4.2 69.4 1.0
OG H:SER17 4.3 70.0 1.0
C H:LYS59 4.4 63.0 1.0
CD2 H:TYR60 4.4 48.1 1.0
CG H:LEU58 4.7 74.7 1.0
CB H:TYR60 4.8 43.5 1.0
O H:THR57 4.8 61.4 1.0
CA H:TYR60 4.8 45.6 1.0
O H:TYR60 5.0 44.4 1.0

Chlorine binding site 5 out of 9 in 6ndg

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Chlorine binding site 5 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl202

b:84.6
occ:1.00
 NH2 J:ARG73 3.2 95.5 1.0
CD J:ARG75 4.1 76.6 1.0
NH1 J:ARG75 4.2 0.3 1.0
CZ J:ARG73 4.5 0.4 1.0
CG J:ARG75 4.7 81.3 1.0
NE J:ARG75 4.8 94.1 1.0
CZ J:ARG75 4.8 0.0 1.0
CB J:ARG75 4.9 74.9 1.0

Chlorine binding site 6 out of 9 in 6ndg

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Chlorine binding site 6 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:69.5
occ:1.00
 NH2 K:ARG14 3.0 96.4 1.0
CZ K:ARG14 3.9 76.1 1.0
NH1 K:ARG14 4.0 70.8 1.0
ND1 K:HIS4 4.6 0.4 1.0
CE1 K:HIS4 4.9 0.3 1.0

Chlorine binding site 7 out of 9 in 6ndg

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Chlorine binding site 7 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl403

b:84.5
occ:1.00
 NH2 L:ARG260 3.6 73.2 1.0
NH1 L:ARG260 4.0 56.7 1.0
CZ L:ARG260 4.3 62.9 1.0
CE L:LYS261 4.5 70.9 1.0

Chlorine binding site 8 out of 9 in 6ndg

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Chlorine binding site 8 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:60.0
occ:1.00
 NH1 N:ARG91 2.9 67.7 1.0
NE2 M:GLN102 2.9 43.0 1.0
OE1 M:GLN102 3.7 64.3 1.0
CD M:GLN102 3.8 53.0 1.0
CZ N:ARG91 3.9 73.0 1.0
NH2 N:ARG91 4.2 72.0 1.0
OE1 M:GLU100 4.2 54.5 1.0
OE2 M:GLU100 4.3 42.5 1.0
CE2 N:TYR94 4.5 53.9 1.0
CD M:GLU100 4.7 48.8 1.0
CD2 N:TYR94 4.9 53.5 1.0
O N:ASN109 5.0 43.0 1.0

Chlorine binding site 9 out of 9 in 6ndg

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Chlorine binding site 9 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl403

b:51.9
occ:1.00
 NH2 R:ARG339 3.7 0.0 1.0
CZ R:ARG339 4.8 0.7 1.0

Reference:

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

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