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Chlorine in PDB 6ndf: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium, PDB code: 6ndf 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) 48.50 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.395, 132.395, 252.991, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 31.7

Other elements in 6ndf:

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

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

Chlorine binding site 1 out of 9 in 6ndf

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


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

b:82.1
occ:1.00
 NH2 C:ARG339 2.9 0.4 1.0
NH2 O:ARG339 3.9 0.3 1.0
CZ C:ARG339 4.2 0.8 1.0
NE C:ARG339 4.8 0.2 1.0
CZ O:ARG339 4.8 0.5 1.0

Chlorine binding site 2 out of 9 in 6ndf

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


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

b:73.5
occ:1.00
 N E:LYS59 3.2 72.0 1.0
N E:TYR60 3.7 80.5 1.0
CA E:LEU58 3.8 74.0 1.0
CB E:LYS59 3.9 94.5 1.0
C E:LEU58 4.0 65.7 1.0
CA E:LYS59 4.0 85.5 1.0
CD2 E:LEU58 4.0 72.2 1.0
OD1 F:ASP321 4.0 77.6 1.0
CB E:LEU58 4.3 82.4 1.0
CD2 E:TYR60 4.3 83.3 1.0
C E:LYS59 4.4 88.0 1.0
CB E:TYR60 4.7 68.5 1.0
CA E:TYR60 4.7 67.5 1.0
O E:TYR60 4.7 71.1 1.0
CG E:LEU58 4.8 75.1 1.0
O E:THR57 5.0 67.2 1.0
CG E:TYR60 5.0 71.5 1.0

Chlorine binding site 3 out of 9 in 6ndf

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


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 Strontium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:75.8
occ:1.00
 N G:GLY7 3.4 89.9 1.0
NH2 C:ARG260 3.5 0.7 1.0
CA G:GLY7 3.6 86.3 1.0
NH1 C:ARG260 3.9 79.2 1.0
CZ C:ARG260 4.2 87.8 1.0
CE C:LYS261 4.2 73.2 1.0
C G:GLY7 4.3 92.8 1.0
O G:TRP8 4.5 46.1 1.0
C G:PRO6 4.6 94.5 1.0
O G:GLY7 4.6 99.0 1.0
NZ C:LYS261 4.9 86.0 1.0
N G:TRP8 5.0 72.0 1.0

Chlorine binding site 4 out of 9 in 6ndf

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


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

b:77.4
occ:1.00
 N H:LYS59 3.1 76.7 1.0
N H:TYR60 3.6 69.8 1.0
CA H:LEU58 3.8 69.7 1.0
OD2 I:ASP321 3.9 71.7 1.0
CB H:LYS59 3.9 88.1 1.0
C H:LEU58 3.9 68.3 1.0
CA H:LYS59 3.9 80.3 1.0
CD2 H:LEU58 4.0 76.5 1.0
CB H:LEU58 4.2 76.7 1.0
CD2 H:TYR60 4.2 78.4 1.0
C H:LYS59 4.3 82.3 1.0
CA H:TYR60 4.6 62.5 1.0
CB H:TYR60 4.6 66.7 1.0
O H:TYR60 4.6 58.0 1.0
OG H:SER17 4.7 76.7 1.0
CG H:LEU58 4.7 73.0 1.0
CG I:ASP321 4.8 79.8 1.0
CG H:TYR60 4.9 68.0 1.0
OD1 I:ASP321 4.9 89.4 1.0
C H:TYR60 5.0 59.6 1.0
CG H:LYS59 5.0 89.0 1.0

Chlorine binding site 5 out of 9 in 6ndf

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


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

b:87.1
occ:1.00
 NH2 J:ARG73 3.6 0.1 1.0
CD J:ARG75 3.8 99.1 1.0
NH1 J:ARG75 3.9 0.2 1.0
NE J:ARG75 4.4 91.8 1.0
CZ J:ARG75 4.5 0.1 1.0
CG J:ARG75 4.6 93.4 1.0
CZ J:ARG73 4.9 0.3 1.0
CB J:ARG75 4.9 90.7 1.0

Chlorine binding site 6 out of 9 in 6ndf

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


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

b:92.2
occ:1.00
 NH2 K:ARG14 3.1 0.1 1.0
NH1 K:ARG14 3.7 1.0 1.0
CZ K:ARG14 3.9 0.8 1.0

Chlorine binding site 7 out of 9 in 6ndf

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


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

b:77.6
occ:1.00
 NH2 L:ARG260 3.7 1.0 1.0
NH1 L:ARG260 3.9 81.1 1.0
CZ L:ARG260 4.3 94.8 1.0
CE L:LYS261 4.4 76.7 1.0
NZ L:LYS261 5.0 91.9 1.0

Chlorine binding site 8 out of 9 in 6ndf

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


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

b:71.4
occ:1.00
 NE2 M:GLN102 3.0 52.1 1.0
NH1 N:ARG91 3.1 67.3 1.0
OE1 M:GLN102 3.8 87.9 1.0
CD M:GLN102 3.8 66.5 1.0
CZ N:ARG91 4.0 74.8 1.0
NH2 N:ARG91 4.2 63.0 1.0
OE1 M:GLU100 4.5 55.0 1.0
CE2 N:TYR94 4.9 58.9 1.0
OE2 M:GLU100 5.0 42.2 1.0

Chlorine binding site 9 out of 9 in 6ndf

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


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

b:75.9
occ:1.00
 NH2 R:ARG339 4.1 0.5 1.0

Reference:

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

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