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Chlorine in PDB 5thp: Rhodocetin in Complex with the Integrin ALPHA2-A Domain

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain, PDB code: 5thp was solved by M.Mcdougall, G.L.Orriss, J.Stetefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 3.01
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.763, 130.763, 251.351, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27

Other elements in 5thp:

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

Magnesium (Mg) 6 atoms
Sodium (Na) 31 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Chlorine atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain (pdb code 5thp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 35 binding sites of Chlorine where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain, PDB code: 5thp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 35 in 5thp

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Chlorine binding site 1 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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

b:89.4
occ:1.00
 O I:HOH514 2.7 59.2 1.0
OH I:TYR258 2.9 76.6 1.0
O A:HOH310 3.1 55.5 1.0
NE2 A:GLN55 3.4 97.5 1.0
N I:VAL222 3.7 76.2 1.0
CG2 I:VAL222 3.9 80.8 1.0
CZ I:TYR258 3.9 73.1 1.0
CD A:GLN55 4.1 0.0 1.0
OE1 A:GLN55 4.1 0.0 1.0
CB I:VAL222 4.1 66.3 1.0
CA I:ARG221 4.2 73.5 1.0
C I:ARG221 4.4 74.5 1.0
CA I:VAL222 4.5 67.4 1.0
CE2 I:TYR258 4.6 74.0 1.0
O I:PRO220 4.6 67.1 1.0
CE1 I:TYR258 4.7 62.4 1.0
OD1 A:ASN59 4.8 87.0 1.0
CG I:ARG221 5.0 68.9 1.0

Chlorine binding site 2 out of 35 in 5thp

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Chlorine binding site 2 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:0.1
occ:1.00
 CB C:SER334 3.2 77.2 1.0
CA C:SER334 3.2 67.9 1.0
N C:ILE335 3.3 66.4 1.0
O O:HOH501 3.3 65.2 1.0
OG C:SER334 3.6 75.2 1.0
CG2 C:ILE335 3.6 69.1 1.0
C C:SER334 3.7 70.6 1.0
CG2 O:ILE335 3.8 0.8 1.0
NH2 C:ARG306 4.1 59.7 1.0
NH1 C:ARG306 4.1 59.5 1.0
CZ C:ARG306 4.3 59.2 1.0
O C:ILE335 4.3 89.0 1.0
CA C:ILE335 4.4 69.3 1.0
OD1 C:ASN300 4.5 83.1 1.0
CB C:ILE335 4.5 68.5 1.0
N C:SER334 4.6 63.3 1.0
O C:SER334 4.8 84.7 1.0
C C:ILE335 4.8 75.1 1.0

Chlorine binding site 3 out of 35 in 5thp

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Chlorine binding site 3 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl406

b:82.4
occ:1.00
 N C:TRP188 3.1 98.6 1.0
OD1 C:ASP189 3.4 0.1 1.0
CB C:TRP188 3.6 0.6 1.0
CA C:TRP188 3.8 96.3 1.0
N C:ASP189 4.0 87.7 1.0
C C:TRP188 4.4 88.7 1.0
CG C:ASP189 4.5 0.3 1.0
CG C:TRP188 4.9 0.9 1.0

Chlorine binding site 4 out of 35 in 5thp

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Chlorine binding site 4 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl407

b:84.7
occ:1.00
 NH2 C:ARG339 2.8 0.4 1.0
O O:PHE362 2.9 89.3 1.0
C O:PHE362 3.6 90.8 1.0
CZ C:ARG339 3.9 99.4 1.0
CD1 O:PHE362 3.9 0.5 1.0
CE1 O:PHE362 4.0 98.9 1.0
NE C:ARG339 4.2 91.0 1.0
CG O:PHE362 4.4 0.8 1.0
CA O:PHE362 4.4 99.2 1.0
CZ O:PHE362 4.5 99.0 1.0
O O:GLN360 4.7 0.1 1.0
CD2 O:PHE362 4.8 98.3 1.0
CG C:PRO336 4.8 68.0 1.0
NE2 O:GLN360 4.8 0.6 1.0
CE2 O:PHE362 4.9 95.1 1.0
OE1 O:GLN360 5.0 0.0 1.0
NH1 C:ARG339 5.0 97.6 1.0
CB O:PHE362 5.0 0.0 1.0

Chlorine binding site 5 out of 35 in 5thp

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Chlorine binding site 5 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl408

b:76.2
occ:1.00
 N C:SER184 3.2 0.7 1.0
CB C:SER184 3.2 87.4 1.0
OG C:SER184 3.5 74.9 1.0
CA C:SER184 3.6 99.7 1.0
O3 C:SO4409 4.0 0.5 1.0
C C:ASN183 4.0 0.1 1.0
O C:HOH503 4.2 22.0 1.0
O1 C:SO4409 4.3 0.3 1.0
O C:GLY247 4.3 0.8 1.0
OG C:SER182 4.3 83.1 1.0
N C:ASN183 4.3 93.7 1.0
CB C:ASN183 4.4 0.4 1.0
CA C:ASN183 4.5 0.5 1.0
CB C:SER182 4.5 80.8 1.0
S C:SO4409 4.7 1.0 1.0
O C:ASP248 4.9 0.5 1.0
O C:ASN183 4.9 0.1 1.0
C C:SER182 4.9 90.9 1.0

Chlorine binding site 6 out of 35 in 5thp

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Chlorine binding site 6 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:83.1
occ:1.00
 O D:HOH316 2.7 39.8 1.0
OE1 D:GLN13 2.9 0.9 1.0
OD1 D:ASN3 3.0 0.1 1.0
CD D:GLN13 3.7 0.8 1.0
NE2 D:GLN13 3.8 0.0 1.0
CG D:ASN3 3.8 86.8 1.0
CB D:ASN3 4.1 84.8 1.0
CA D:ASN3 4.2 89.6 1.0
CB D:PHE2 4.3 0.8 1.0
CB D:SER133 4.5 89.2 1.0
ND2 D:ASN3 4.9 87.2 1.0
CA D:PHE2 4.9 0.5 1.0

Chlorine binding site 7 out of 35 in 5thp

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Chlorine binding site 7 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl204

b:82.0
occ:1.00
 NZ D:LYS23 2.7 65.9 1.0
CE D:LYS23 3.3 69.7 1.0
O D:HOH314 3.7 51.4 1.0
CL D:CL205 4.5 80.8 1.0
O D:HOH309 4.6 81.6 1.0
CD D:LYS23 4.8 61.1 1.0
CD2 D:PHE31 4.9 93.5 1.0

Chlorine binding site 8 out of 35 in 5thp

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Chlorine binding site 8 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl205

b:80.8
occ:1.00
 NZ D:LYS23 2.8 65.9 1.0
O D:HOH309 3.3 81.6 1.0
CE D:LYS23 3.7 69.7 1.0
CB D:GLU27 3.7 89.8 1.0
CD D:LYS23 3.9 61.1 1.0
OE1 D:GLU27 3.9 0.5 1.0
CD D:GLU27 4.0 0.0 1.0
CG D:GLU27 4.0 0.8 1.0
CG D:LYS23 4.4 78.1 1.0
CL D:CL204 4.5 82.0 1.0
O D:GLU27 4.5 70.9 1.0
OE2 D:GLU27 4.5 0.8 1.0
CA D:GLU27 4.6 68.1 1.0
O D:HOH314 4.7 51.4 1.0
NA D:NA202 4.8 52.1 1.0
CD D:ARG30 4.8 72.2 1.0
C D:GLU27 4.8 67.5 1.0
NE D:ARG30 4.9 0.6 1.0

Chlorine binding site 9 out of 35 in 5thp

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Chlorine binding site 9 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl206

b:68.7
occ:1.00
 OE1 D:GLN122 3.2 88.6 1.0
NE2 D:GLN122 3.7 91.3 1.0
CD D:GLN122 3.7 88.3 1.0
CB D:CYS121 4.2 0.1 1.0
SG D:CYS121 4.3 1.0 1.0

Chlorine binding site 10 out of 35 in 5thp

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Chlorine binding site 10 out of 35 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl207

b:71.6
occ:1.00
 NH2 D:ARG114 3.1 93.8 1.0
O D:ASP51 3.6 91.4 1.0
CB D:ASP51 3.9 90.5 1.0
CZ D:ARG114 4.0 85.9 1.0
C D:ASP51 4.3 94.2 1.0
NE D:ARG114 4.3 74.4 1.0
CA D:ASP51 4.4 91.3 1.0
CB D:GLN55 4.6 69.4 1.0
CG D:ASP51 4.6 94.0 1.0
OD1 D:ASP51 4.8 0.9 1.0
CD D:GLN55 4.8 85.5 1.0
CG D:GLN55 4.9 85.9 1.0
N D:GLN55 4.9 66.5 1.0

Reference:

J.A.Eble, M.Mcdougall, G.L.Orriss, S.Niland, B.Johanningmeier, G.Pohlentz, M.Meier, S.Karrasch, M.I.Estevao-Costa, A.Martins Lima, J.Stetefeld. Dramatic and Concerted Conformational Changes Enable Rhodocetin to Block Alpha 2 Beta 1 Integrin Selectively. Plos Biol. V. 15 01492 2017.
ISSN: ESSN 1545-7885
PubMed: 28704364
DOI: 10.1371/JOURNAL.PBIO.2001492
Page generated: Fri Jul 26 17:30:01 2024

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