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Chlorine in PDB 6ndd: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound, PDB code: 6ndd 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) 48.01 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.712, 130.712, 251.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.4

Other elements in 6ndd:

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

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

Chlorine binding site 1 out of 9 in 6ndd

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Chlorine binding site 1 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:66.9
occ:1.00
 NH2 C:ARG339 3.1 94.6 1.0
NH2 O:ARG339 3.6 95.7 1.0
CZ C:ARG339 4.3 83.4 1.0
CZ O:ARG339 4.6 0.1 1.0
NH1 O:ARG339 4.9 0.1 1.0
NE C:ARG339 4.9 70.9 1.0

Chlorine binding site 2 out of 9 in 6ndd

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Chlorine binding site 2 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:65.5
occ:1.00
 N E:LYS59 3.1 66.3 1.0
N E:TYR60 3.8 61.5 1.0
CB E:LYS59 3.8 71.1 1.0
CA E:LEU58 3.8 63.2 1.0
CD2 E:LEU58 3.9 75.3 1.0
CA E:LYS59 3.9 73.3 1.0
C E:LEU58 4.0 57.7 1.0
OD1 F:ASP321 4.1 70.9 1.0
CB E:LEU58 4.3 75.1 1.0
CD2 E:TYR60 4.4 52.3 1.0
C E:LYS59 4.4 77.3 1.0
CB E:SER17 4.7 68.1 1.0
CG E:LEU58 4.8 75.2 1.0
CB E:TYR60 4.8 44.7 1.0
CA E:TYR60 4.8 48.7 1.0
O E:TYR60 4.8 56.8 1.0
O E:THR57 4.9 59.0 1.0

Chlorine binding site 3 out of 9 in 6ndd

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Chlorine binding site 3 out of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:70.7
occ:1.00
 N G:GLY7 3.3 76.8 1.0
CA G:GLY7 3.5 79.8 1.0
NH2 C:ARG260 3.5 76.0 1.0
NH1 C:ARG260 3.9 56.1 1.0
C G:GLY7 4.1 77.5 1.0
CZ C:ARG260 4.2 65.0 1.0
O G:TRP8 4.3 47.8 1.0
CE C:LYS261 4.3 62.0 1.0
C G:PRO6 4.5 68.6 1.0
O G:GLY7 4.5 89.6 1.0
N G:TRP8 4.8 65.9 1.0
CA G:PRO6 4.9 67.8 1.0
NZ C:LYS261 5.0 74.6 1.0

Chlorine binding site 4 out of 9 in 6ndd

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

b:71.1
occ:1.00
 N H:LYS59 3.2 69.8 1.0
CB H:LYS59 3.8 74.9 1.0
CA H:LEU58 3.9 58.0 1.0
N H:TYR60 3.9 61.9 1.0
CD2 H:LEU58 4.0 75.2 1.0
CA H:LYS59 4.0 75.6 1.0
C H:LEU58 4.0 55.3 1.0
OD2 I:ASP321 4.1 69.3 1.0
OG H:SER17 4.2 62.1 1.0
CB H:LEU58 4.3 68.2 1.0
CD2 H:TYR60 4.4 57.6 1.0
C H:LYS59 4.5 74.4 1.0
CB H:TYR60 4.8 47.7 1.0
CG H:LEU58 4.8 72.1 1.0
O H:THR57 4.8 59.7 1.0
CA H:TYR60 4.9 48.5 1.0
OD1 I:ASP321 4.9 58.9 1.0
CG I:ASP321 4.9 74.0 1.0

Chlorine binding site 5 out of 9 in 6ndd

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

b:87.4
occ:1.00
 NH2 J:ARG73 2.8 0.3 1.0
CD J:ARG75 3.7 87.4 1.0
NH1 J:ARG75 3.7 0.8 1.0
CZ J:ARG73 4.1 0.5 1.0
CG J:ARG75 4.2 80.9 1.0
CB J:ARG75 4.4 69.0 1.0
NE J:ARG75 4.4 98.0 1.0
CZ J:ARG75 4.4 0.8 1.0
NE J:ARG73 4.7 1.0 1.0
O J:ARG75 4.9 46.8 1.0
CA J:ARG75 4.9 57.6 1.0

Chlorine binding site 6 out of 9 in 6ndd

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

b:64.6
occ:1.00
 NH2 K:ARG14 3.0 90.0 1.0
NH1 K:ARG14 3.8 69.7 1.0
CZ K:ARG14 3.9 78.3 1.0
ND1 K:HIS4 4.8 0.7 1.0

Chlorine binding site 7 out of 9 in 6ndd

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

b:72.1
occ:1.00
 NH2 L:ARG260 3.5 78.3 1.0
NH1 L:ARG260 4.0 57.2 1.0
CZ L:ARG260 4.2 64.3 1.0
CE L:LYS261 4.6 66.8 1.0

Chlorine binding site 8 out of 9 in 6ndd

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

b:61.4
occ:1.00
 NH1 N:ARG91 2.9 67.1 1.0
NE2 M:GLN102 3.0 40.7 1.0
OE1 M:GLN102 3.8 59.5 1.0
CD M:GLN102 3.8 50.8 1.0
CZ N:ARG91 3.9 70.8 1.0
NH2 N:ARG91 4.2 75.1 1.0
OE1 M:GLU100 4.3 50.1 1.0
CE2 N:TYR94 4.7 45.6 1.0
OE2 M:GLU100 4.7 38.8 1.0
CD M:GLU100 4.9 41.8 1.0

Chlorine binding site 9 out of 9 in 6ndd

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

b:57.7
occ:1.00
 NH2 R:ARG339 3.7 0.7 1.0
CZ R:ARG339 4.8 0.8 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound To Be Published.
Page generated: Sat Jul 12 17:10:04 2025

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