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Sodium in PDB 6nda: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium, PDB code: 6nda 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) 92.47 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.530, 130.530, 250.919, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 6nda:

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

Cadmium (Cd) 6 atoms
Chlorine (Cl) 9 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 6 in 6nda

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Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:8.1
occ:1.00
 O2 C:SO4402 1.7 57.7 1.0
OG C:SER184 2.6 31.9 1.0
CD C:CD401 2.9 40.0 1.0
S C:SO4402 3.1 83.2 1.0
CB C:SER184 3.1 33.1 1.0
N C:SER184 3.2 37.2 1.0
OG C:SER182 3.4 42.1 1.0
O1 C:SO4402 3.6 59.9 1.0
CA C:SER184 3.6 35.0 1.0
O4 C:SO4402 3.7 96.8 1.0
CB C:SER182 4.0 36.3 1.0
O3 C:SO4402 4.0 47.3 1.0
N C:ASN183 4.2 38.7 1.0
C C:ASN183 4.3 37.5 1.0
O C:GLY247 4.5 47.8 1.0
CA C:ASN183 4.6 36.7 1.0
CB C:ASN183 4.8 35.2 1.0
C C:SER182 4.8 38.4 1.0
OD2 C:ASP283 4.9 36.5 1.0

Sodium binding site 2 out of 6 in 6nda

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Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:19.3
occ:1.00
 O3 F:SO4402 2.0 85.0 1.0
OG F:SER184 2.6 39.5 1.0
CD F:CD401 3.0 35.7 1.0
S F:SO4402 3.1 83.4 1.0
O2 F:SO4402 3.2 56.4 1.0
OG F:SER182 3.4 14.4 1.0
CB F:SER182 3.5 19.3 1.0
N F:SER184 3.6 38.5 1.0
CB F:SER184 3.6 36.9 1.0
O4 F:SO4402 3.7 48.0 1.0
N F:ASN183 3.8 27.8 1.0
O F:GLY247 4.1 31.3 1.0
CA F:SER184 4.2 34.8 1.0
O1 F:SO4402 4.2 52.5 1.0
C F:SER182 4.5 22.8 1.0
C F:ASN183 4.5 36.0 1.0
CA F:SER182 4.6 20.9 1.0
CA F:ASN183 4.6 30.8 1.0
CB F:ASN183 4.7 32.7 1.0
CA F:ASP248 4.8 29.6 1.0
OD1 F:ASP283 5.0 55.0 1.0

Sodium binding site 3 out of 6 in 6nda

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Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na402

b:13.9
occ:1.00
 O3 H:SO4202 2.0 82.9 1.0
OG I:SER184 3.0 37.0 1.0
S H:SO4202 3.2 85.8 1.0
CD I:CD401 3.3 33.9 1.0
O2 H:SO4202 3.6 51.0 1.0
O1 H:SO4202 3.6 57.3 1.0
N I:SER184 3.6 42.0 1.0
CB I:SER182 3.7 24.3 1.0
OG I:SER182 3.7 20.8 1.0
N I:ASN183 3.8 33.5 1.0
CB I:SER184 3.9 36.2 1.0
O I:GLY247 4.1 33.7 1.0
CA I:SER184 4.3 36.5 1.0
O4 H:SO4202 4.3 62.1 1.0
CA I:ASN183 4.5 37.6 1.0
CB I:ASN183 4.5 37.0 1.0
C I:ASN183 4.5 42.9 1.0
CA I:ASP248 4.5 31.4 1.0
C I:SER182 4.6 26.8 1.0
CA I:SER182 4.7 24.2 1.0
C I:ASP248 4.9 30.8 1.0

Sodium binding site 4 out of 6 in 6nda

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Sodium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na402

b:14.7
occ:1.00
 O3 K:SO4202 1.8 75.1 1.0
OG L:SER184 2.2 23.9 1.0
CD L:CD401 2.7 42.7 1.0
CB L:SER184 2.9 27.5 1.0
S K:SO4202 3.0 91.3 1.0
OG L:SER182 3.3 41.2 1.0
N L:SER184 3.3 32.7 1.0
O1 K:SO4202 3.3 90.7 1.0
O4 K:SO4202 3.5 64.1 1.0
CA L:SER184 3.6 29.3 1.0
CB L:SER182 3.8 35.6 1.0
O2 K:SO4202 4.2 60.6 1.0
N L:ASN183 4.3 33.6 1.0
O L:GLY247 4.4 52.3 1.0
C L:ASN183 4.4 33.5 1.0
OD2 L:ASP283 4.7 29.6 1.0
C L:SER182 4.8 34.2 1.0
OD1 L:ASP283 4.8 25.3 1.0
CA L:ASN183 4.8 33.4 1.0
CA L:SER182 4.9 32.8 1.0
CB L:ASN183 4.9 35.2 1.0
C L:SER184 5.0 30.9 1.0

Sodium binding site 5 out of 6 in 6nda

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Sodium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na402

b:19.1
occ:1.00
 O1 N:SO4201 2.0 86.7 1.0
CD O:CD401 3.0 45.2 1.0
S N:SO4201 3.2 99.0 1.0
OG O:SER184 3.2 21.0 1.0
O3 N:SO4201 3.4 76.6 1.0
OG O:SER182 3.4 53.3 1.0
N O:SER184 3.4 33.5 1.0
CB O:SER184 3.5 31.0 1.0
CB O:SER182 3.7 48.9 1.0
O4 N:SO4201 3.8 63.4 1.0
N O:ASN183 4.0 41.7 1.0
CA O:SER184 4.0 34.4 1.0
O O:GLY247 4.1 43.1 1.0
O2 N:SO4201 4.3 85.0 1.0
C O:ASN183 4.5 35.8 1.0
C O:SER182 4.5 42.9 1.0
CA O:ASN183 4.6 42.0 1.0
CB O:ASN183 4.6 41.6 1.0
CA O:SER182 4.7 48.5 1.0
OG1 O:THR250 4.8 26.0 1.0
CA O:ASP248 4.9 59.2 1.0
O O:ASP248 4.9 61.5 1.0

Sodium binding site 6 out of 6 in 6nda

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


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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na404

b:11.9
occ:1.00
 O3 Q:SO4202 1.7 81.1 1.0
OG R:SER184 2.9 21.9 1.0
CD R:CD401 3.0 45.9 1.0
S Q:SO4202 3.1 98.0 1.0
N R:SER184 3.3 34.6 1.0
OG R:SER182 3.3 50.9 1.0
CB R:SER184 3.4 28.4 1.0
O1 Q:SO4202 3.6 71.2 1.0
CB R:SER182 3.7 46.3 1.0
O4 Q:SO4202 3.8 92.0 1.0
CA R:SER184 3.9 31.6 1.0
N R:ASN183 3.9 47.1 1.0
O2 Q:SO4202 4.0 69.4 1.0
O R:GLY247 4.1 37.0 1.0
C R:ASN183 4.3 38.7 1.0
CA R:ASN183 4.5 45.2 1.0
C R:SER182 4.5 43.4 1.0
CB R:ASN183 4.6 46.2 1.0
CA R:SER182 4.7 45.6 1.0
CA R:ASP248 4.9 49.5 1.0
OG1 R:THR250 4.9 29.7 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium To Be Published.
Page generated: Tue Oct 8 12:11:42 2024

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