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Sodium 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
Chlorine (Cl) 35 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 31 binding sites of Sodium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain, PDB code: 5thp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 31 in 5thp

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Sodium binding site 1 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na201

b:87.5
occ:1.00
OE2 A:GLU27 2.5 0.5 1.0
O A:HOH316 2.5 65.4 1.0
CD A:GLU27 3.7 0.9 1.0
N A:GLU27 4.3 0.7 1.0
CB A:GLU27 4.3 0.2 1.0
OE1 A:GLU27 4.5 0.0 1.0
CB A:ASP26 4.6 0.7 1.0
CG A:GLU27 4.6 0.4 1.0
CA A:GLU27 4.6 0.3 1.0

Sodium binding site 2 out of 31 in 5thp

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Sodium binding site 2 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
B:Na201

b:62.1
occ:1.00
OE2 B:GLU18 2.5 85.8 1.0
OE1 B:GLU18 2.7 0.5 1.0
CD B:GLU18 2.9 93.0 1.0
OG B:SER17 3.7 83.6 1.0
N B:SER17 4.1 81.4 1.0
CD1 B:PHE16 4.4 84.8 1.0
CG B:GLU18 4.4 83.0 1.0
CA B:PHE16 4.6 81.8 1.0
N B:GLU18 4.6 94.0 1.0
NH1 B:ARG14 4.6 0.1 1.0
NH2 B:ARG14 4.7 0.8 1.0
CB B:SER17 4.8 82.0 1.0
C B:PHE16 4.8 80.5 1.0
CA B:SER17 4.9 86.2 1.0
CB B:PHE16 4.9 81.5 1.0

Sodium binding site 3 out of 31 in 5thp

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Sodium binding site 3 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na401

b:78.8
occ:1.00
OD1 C:ASN303 2.6 0.2 1.0
CG2 O:THR337 2.7 66.0 1.0
CG C:ASN303 3.4 0.5 1.0
CB O:THR337 3.7 93.5 1.0
ND2 C:ASN303 3.8 99.3 1.0
OG1 O:THR337 4.2 0.9 1.0
CB C:ASN303 4.5 1.0 1.0
CD O:LYS330 4.8 76.5 1.0

Sodium binding site 4 out of 31 in 5thp

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Sodium binding site 4 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na402

b:61.2
occ:1.00
O C:ASP321 2.4 0.8 1.0
OE2 C:GLU285 2.4 0.4 1.0
C C:ASP321 3.6 0.6 1.0
CD C:GLU285 3.7 0.4 1.0
ND2 C:ASN324 3.9 0.9 1.0
CB C:ASN324 4.1 0.9 1.0
N C:ASN324 4.3 99.5 1.0
CG C:ASN324 4.4 99.8 1.0
O B:THR115 4.4 79.6 1.0
OE1 C:GLU285 4.4 98.8 1.0
N C:THR322 4.4 0.8 1.0
CA C:THR322 4.5 0.9 1.0
CA C:ASP321 4.5 0.6 1.0
CG2 B:THR115 4.5 69.3 1.0
CB C:ASP321 4.5 0.3 1.0
CG C:GLU285 4.6 95.3 1.0
N C:LYS323 4.6 0.8 1.0
C C:THR322 4.6 0.2 1.0
CA C:ASN324 4.7 95.0 1.0
N C:LEU325 4.8 79.8 1.0
N C:ASP321 4.8 0.8 1.0
CD1 B:LEU19 4.9 84.0 1.0

Sodium binding site 5 out of 31 in 5thp

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Sodium binding site 5 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na403

b:67.1
occ:1.00
NE2 C:HIS287 2.6 94.4 1.0
CD2 C:HIS287 3.1 96.2 1.0
CE1 C:HIS287 3.3 88.0 1.0
CG B:GLU113 3.9 61.0 1.0
O C:HIS287 3.9 77.1 1.0
CG C:HIS287 4.0 89.1 1.0
CB B:GLU113 4.1 61.7 1.0
ND1 C:HIS287 4.1 85.7 1.0
C C:HIS287 4.9 78.4 1.0

Sodium binding site 6 out of 31 in 5thp

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Sodium binding site 6 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na411

b:0.3
occ:1.00
OD1 C:ASP297 2.3 64.6 1.0
OD1 O:ASP297 2.4 73.6 1.0
ND2 O:ASN300 2.5 0.1 1.0
ND2 C:ASN300 2.6 86.9 1.0
CB O:ASN300 2.7 0.4 1.0
CG O:ASN300 2.9 0.7 1.0
CG C:ASP297 3.3 65.7 1.0
CG O:ASP297 3.4 73.3 1.0
CA O:ASP297 3.5 86.6 1.0
CG C:ASN300 3.6 85.3 1.0
CB O:ASP297 3.8 84.8 1.0
CB C:ASN300 4.0 86.7 1.0
CB C:ASP297 4.0 55.5 1.0
OD1 O:ASN300 4.1 90.8 1.0
O O:ASP297 4.1 88.2 1.0
CA C:ASP297 4.1 56.5 1.0
OD2 C:ASP297 4.1 85.0 1.0
CA O:ASN300 4.1 0.7 1.0
C O:ASP297 4.3 88.8 1.0
O O:ILE296 4.4 75.8 1.0
CE1 C:HIS301 4.5 0.6 1.0
OD2 O:ASP297 4.5 70.9 1.0
N O:ASP297 4.5 86.6 1.0
OD1 C:ASN300 4.7 83.1 1.0
C O:ASN300 4.7 0.7 1.0
NE2 C:HIS301 4.7 0.9 1.0
C O:ILE296 4.8 79.0 1.0
N O:ASN300 4.8 0.4 1.0
N C:ASP297 5.0 57.5 1.0
N O:HIS301 5.0 0.6 1.0

Sodium binding site 7 out of 31 in 5thp

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Sodium binding site 7 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na201

b:90.3
occ:1.00
OE1 J:GLU34 2.5 98.3 1.0
OE1 D:GLU27 2.5 0.5 1.0
OE2 D:GLU27 2.5 0.8 1.0
OE2 J:GLU34 2.5 95.9 1.0
CD J:GLU34 2.8 96.3 1.0
CD D:GLU27 2.8 0.0 1.0
NA D:NA202 3.8 52.1 1.0
CG J:GLU34 4.1 94.6 1.0
CG D:GLU27 4.3 0.8 1.0
O J:HOH304 4.4 37.5 1.0
O D:HOH309 4.4 81.6 1.0
CG2 D:THR24 4.7 66.6 1.0
CB J:GLU34 4.7 94.0 1.0

Sodium binding site 8 out of 31 in 5thp

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Sodium binding site 8 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na202

b:52.1
occ:1.00
O D:HOH309 2.4 81.6 1.0
O D:PRO22 2.6 66.6 1.0
CA D:LYS23 2.7 57.0 1.0
CG D:LYS23 2.8 78.1 1.0
OE1 D:GLU27 2.9 0.5 1.0
CB D:LYS23 3.1 71.0 1.0
C D:PRO22 3.4 58.0 1.0
N D:LYS23 3.5 54.5 1.0
NA D:NA201 3.8 90.3 1.0
C D:LYS23 3.8 54.3 1.0
N D:THR24 3.9 69.3 1.0
CD D:LYS23 4.1 61.1 1.0
NZ D:LYS23 4.1 65.9 1.0
CD D:GLU27 4.1 0.0 1.0
O D:HOH314 4.4 51.4 1.0
CE D:LYS23 4.6 69.7 1.0
CB D:GLU27 4.7 89.8 1.0
CB D:LYS124 4.7 0.2 1.0
CL D:CL205 4.8 80.8 1.0
CA D:PRO22 4.8 57.1 1.0
OE2 D:GLU27 4.8 0.8 1.0
O D:LYS23 5.0 51.8 1.0

Sodium binding site 9 out of 31 in 5thp

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Sodium binding site 9 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na209

b:0.4
occ:1.00
OD1 E:ASP80 2.3 0.4 1.0
OG D:SER43 2.4 0.7 1.0
N E:SER79 2.5 97.3 1.0
N E:ASP80 2.6 0.5 1.0
CB E:TRP78 2.7 84.8 1.0
OG E:SER79 2.8 0.6 1.0
CG E:ASP80 3.0 0.9 1.0
C E:TRP78 3.0 94.5 1.0
CA E:SER79 3.2 1.0 1.0
CA E:TRP78 3.3 93.7 1.0
C E:SER79 3.3 0.8 1.0
O D:GLY71 3.4 55.0 1.0
CB E:SER79 3.5 0.3 1.0
CB E:ASP80 3.6 0.8 1.0
CA E:ASP80 3.6 0.1 1.0
CG E:TRP78 3.7 79.4 1.0
CE3 E:TRP78 3.7 84.7 1.0
O D:LEU41 3.7 86.9 1.0
OD2 E:ASP80 3.8 0.9 1.0
CA D:GLY71 3.8 53.2 1.0
CB D:SER43 3.8 92.9 1.0
C D:GLY71 3.9 53.3 1.0
O E:TRP78 3.9 93.0 1.0
CD2 E:TRP78 4.0 76.8 1.0
N E:ASP81 4.4 0.3 1.0
C E:ASP80 4.4 0.4 1.0
O D:VAL42 4.5 71.4 1.0
O E:SER79 4.6 0.8 1.0
N E:TRP78 4.7 0.5 1.0
CA D:SER43 4.7 81.8 1.0
C D:LEU41 4.7 74.5 1.0
C D:VAL42 4.8 72.4 1.0
N D:GLY71 4.9 58.8 1.0
N D:SER43 4.9 80.6 1.0
CZ3 E:TRP78 4.9 89.4 1.0
N D:LEU72 4.9 52.0 1.0
CD1 E:TRP78 5.0 85.9 1.0

Sodium binding site 10 out of 31 in 5thp

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Sodium binding site 10 out of 31 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
E:Na201

b:0.6
occ:1.00
O E:LEU3 2.4 0.7 1.0
O E:HOH309 2.4 78.5 1.0
CA E:HIS4 2.7 98.5 1.0
C E:LEU3 3.0 0.7 1.0
N E:HIS4 3.2 0.3 1.0
C E:HIS4 3.4 99.5 1.0
O E:HIS4 3.6 1.0 1.0
CD2 E:HIS4 3.8 0.4 1.0
CB E:HIS4 3.9 0.1 1.0
CG E:HIS4 4.2 0.1 1.0
CA E:LEU3 4.3 0.2 1.0
N E:TRP5 4.3 86.0 1.0
O E:TRP5 4.5 88.4 1.0
CD2 E:LEU3 4.8 0.8 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: Tue Dec 15 11:37:28 2020

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