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Chlorine in PDB 6nde: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium, PDB code: 6nde 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) 48.57 / 3.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.351, 132.351, 254.244, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 36.9

Other elements in 6nde:

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

Praseodymium (Pr) 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 Prasedymium (pdb code 6nde). 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 Prasedymium, PDB code: 6nde:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6nde

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


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

b:100.0
occ:1.00
 NH2 C:ARG339 2.6 1.0 1.0
CZ C:ARG339 3.7 0.6 1.0
NE C:ARG339 4.0 0.3 1.0
NH2 O:ARG339 4.3 0.7 1.0
NH1 C:ARG339 4.7 0.7 1.0

Chlorine binding site 2 out of 9 in 6nde

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


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

b:80.6
occ:1.00
 N E:LYS59 3.3 98.0 1.0
CB E:LYS59 3.8 0.8 1.0
CA E:LEU58 4.0 0.2 1.0
N E:TYR60 4.0 0.1 1.0
CA E:LYS59 4.0 0.4 1.0
C E:LEU58 4.1 99.6 1.0
CD2 E:LEU58 4.2 0.0 1.0
OD1 F:ASP321 4.3 0.7 1.0
CD2 E:TYR60 4.5 0.4 1.0
C E:LYS59 4.6 0.1 1.0
CB E:LEU58 4.6 0.6 1.0
O E:THR57 4.8 0.6 1.0
CG E:LYS59 4.9 0.0 1.0

Chlorine binding site 3 out of 9 in 6nde

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


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

b:98.7
occ:1.00
 N G:GLY7 3.5 0.6 1.0
NH2 C:ARG260 3.7 0.6 1.0
CA G:GLY7 3.7 0.3 1.0
NH1 C:ARG260 3.9 0.9 1.0
CZ C:ARG260 4.2 0.5 1.0
C G:GLY7 4.3 0.0 1.0
CE C:LYS261 4.5 0.5 1.0
O G:GLY7 4.5 0.0 1.0
C G:PRO6 4.6 1.0 1.0
O G:TRP8 4.8 0.4 1.0
CA G:PRO6 5.0 0.9 1.0

Chlorine binding site 4 out of 9 in 6nde

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


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

b:91.8
occ:1.00
 N H:LYS59 3.4 0.5 1.0
OD2 I:ASP321 3.8 0.7 1.0
N H:TYR60 3.9 0.9 1.0
CB H:LYS59 4.0 0.0 1.0
CA H:LEU58 4.1 0.3 1.0
CA H:LYS59 4.2 0.6 1.0
CD2 H:TYR60 4.2 0.8 1.0
CD2 H:LEU58 4.2 0.6 1.0
C H:LEU58 4.3 0.4 1.0
OG H:SER17 4.3 94.8 1.0
OD1 I:ASP321 4.5 0.2 1.0
C H:LYS59 4.5 0.4 1.0
CB H:LEU58 4.5 1.0 1.0
CG I:ASP321 4.6 0.6 1.0
CB H:TYR60 4.7 0.2 1.0
CA H:TYR60 4.8 0.0 1.0
CG H:TYR60 4.9 0.6 1.0
O H:TYR60 5.0 0.1 1.0

Chlorine binding site 5 out of 9 in 6nde

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


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

b:0.3
occ:1.00
 NH1 J:ARG75 3.3 0.5 1.0
NH2 J:ARG73 3.6 0.4 1.0
CD J:ARG75 3.9 0.5 1.0
CZ J:ARG75 3.9 0.6 1.0
NE J:ARG75 4.2 0.7 1.0
NH2 J:ARG75 4.8 0.2 1.0
CZ J:ARG73 4.8 0.1 1.0
CG J:ARG75 4.8 0.1 1.0

Chlorine binding site 6 out of 9 in 6nde

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


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

b:0.6
occ:1.00
 NH2 K:ARG14 4.0 0.9 1.0
NH1 K:ARG14 4.8 0.5 1.0
CZ K:ARG14 4.9 0.3 1.0

Chlorine binding site 7 out of 9 in 6nde

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


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

b:91.0
occ:1.00
 NH2 L:ARG260 3.7 0.2 1.0
NH1 L:ARG260 4.0 0.6 1.0
CZ L:ARG260 4.3 0.3 1.0
CE L:LYS261 4.5 0.3 1.0

Chlorine binding site 8 out of 9 in 6nde

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


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

b:91.9
occ:1.00
 NE2 M:GLN102 2.9 0.7 1.0
NH1 N:ARG91 3.4 0.5 1.0
OE1 M:GLN102 3.6 0.7 1.0
CD M:GLN102 3.7 0.3 1.0
CZ N:ARG91 4.2 0.9 1.0
NH2 N:ARG91 4.3 0.9 1.0
OE1 M:GLU100 4.3 98.6 1.0
OE2 M:GLU100 4.3 81.4 1.0
CD M:GLU100 4.7 85.7 1.0
O M:GLY99 5.0 0.2 1.0

Chlorine binding site 9 out of 9 in 6nde

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


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

b:89.5
occ:1.00
 NH2 R:ARG339 3.9 0.1 1.0
CZ R:ARG339 4.9 0.8 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium Bound To Be Published.
Page generated: Sat Jul 12 17:10:40 2025

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