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Sodium in PDB 6ndg: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound, PDB code: 6ndg 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) 46.94 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.846, 130.846, 251.167, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.1

Other elements in 6ndg:

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

Yttrium (Y) 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 with Yttrium Bound (pdb code 6ndg). 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 with Yttrium Bound, PDB code: 6ndg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndg

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


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:32.0
occ:1.00
 O3 B:SO4201 2.0 83.8 1.0
OG C:SER184 2.7 42.6 1.0
N C:SER184 3.3 51.7 1.0
S B:SO4201 3.4 1.0 1.0
Y C:Y1401 3.4 93.2 1.0
CB C:SER184 3.6 42.2 1.0
O1 B:SO4201 3.7 64.7 1.0
OG C:SER182 3.9 47.9 1.0
CA C:SER184 4.0 45.6 1.0
N C:ASN183 4.0 47.4 1.0
O C:GLY247 4.2 55.0 1.0
O4 B:SO4201 4.2 0.1 1.0
CB C:SER182 4.2 41.0 1.0
O2 B:SO4201 4.3 77.0 1.0
C C:ASN183 4.3 51.4 1.0
CB C:ASN183 4.4 48.0 1.0
CA C:ASN183 4.4 48.8 1.0
CA C:ASP248 4.8 48.6 1.0
C C:SER182 4.8 45.7 1.0

Sodium binding site 2 out of 6 in 6ndg

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


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:27.7
occ:1.00
 O3 E:SO4203 2.1 90.8 1.0
OG F:SER184 3.0 68.6 1.0
OG F:SER182 3.3 31.3 1.0
Y F:Y1401 3.3 78.9 1.0
S E:SO4203 3.4 0.1 1.0
N F:SER184 3.6 54.8 1.0
N F:ASN183 3.7 45.5 1.0
CB F:SER182 3.8 34.0 1.0
O F:GLY247 3.8 30.5 1.0
O4 E:SO4203 3.9 87.8 1.0
CB F:SER184 3.9 55.8 1.0
O2 E:SO4203 4.0 59.7 1.0
CA F:SER184 4.4 51.9 1.0
CB F:ASN183 4.4 49.8 1.0
CA F:ASN183 4.4 50.7 1.0
O1 E:SO4203 4.5 74.6 1.0
C F:ASN183 4.5 59.3 1.0
C F:SER182 4.5 34.9 1.0
CA F:ASP248 4.6 39.4 1.0
CA F:SER182 4.7 33.3 1.0
C F:GLY247 4.9 36.9 1.0
C F:ASP248 5.0 33.3 1.0

Sodium binding site 3 out of 6 in 6ndg

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


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na402

b:23.9
occ:1.00
 O3 H:SO4202 2.0 90.0 1.0
OG I:SER184 3.0 74.6 1.0
OG I:SER182 3.2 30.5 1.0
S H:SO4202 3.3 98.8 1.0
Y I:Y1401 3.3 79.8 1.0
N I:SER184 3.7 52.0 1.0
O4 H:SO4202 3.7 95.2 1.0
O2 H:SO4202 3.7 55.8 1.0
CB I:SER182 3.7 34.7 1.0
N I:ASN183 3.7 44.0 1.0
CB I:SER184 3.9 57.4 1.0
O I:GLY247 3.9 34.8 1.0
CA I:SER184 4.3 51.0 1.0
O1 H:SO4202 4.4 75.5 1.0
CA I:ASN183 4.5 48.1 1.0
CB I:ASN183 4.5 47.7 1.0
C I:SER182 4.5 33.5 1.0
C I:ASN183 4.5 53.1 1.0
CA I:ASP248 4.6 37.9 1.0
CA I:SER182 4.7 32.5 1.0
C I:GLY247 4.9 36.9 1.0
C I:ASP248 4.9 33.2 1.0

Sodium binding site 4 out of 6 in 6ndg

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


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na402

b:32.9
occ:1.00
 O3 K:SO4202 1.9 90.2 1.0
OG L:SER184 2.6 36.9 1.0
S K:SO4202 3.2 0.8 1.0
Y L:Y1401 3.3 90.2 1.0
N L:SER184 3.5 48.9 1.0
CB L:SER184 3.6 39.9 1.0
O1 K:SO4202 3.7 78.4 1.0
OG L:SER182 3.7 51.8 1.0
O4 K:SO4202 3.8 97.2 1.0
CA L:SER184 4.0 42.4 1.0
N L:ASN183 4.1 44.7 1.0
CB L:SER182 4.1 42.4 1.0
O L:GLY247 4.1 60.9 1.0
O2 K:SO4202 4.2 63.6 1.0
C L:ASN183 4.4 50.4 1.0
CB L:ASN183 4.5 45.8 1.0
CA L:ASN183 4.5 47.2 1.0
C L:SER182 4.8 43.5 1.0
CA L:ASP248 4.8 49.7 1.0

Sodium binding site 5 out of 6 in 6ndg

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


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na402

b:43.2
occ:1.00
 O4 N:SO4201 1.9 0.7 1.0
S N:SO4201 3.1 0.7 1.0
Y O:Y1401 3.4 1.0 1.0
O3 N:SO4201 3.5 0.7 1.0
N O:SER184 3.5 46.8 1.0
OG O:SER184 3.7 48.5 1.0
O1 N:SO4201 3.7 87.9 1.0
OG O:SER182 3.8 57.0 1.0
CB O:SER184 3.8 55.6 1.0
N O:ASN183 3.9 54.4 1.0
O O:GLY247 3.9 58.0 1.0
CB O:SER182 4.0 55.9 1.0
CA O:SER184 4.2 54.2 1.0
O2 N:SO4201 4.2 0.4 1.0
CB O:ASN183 4.3 55.8 1.0
CA O:ASN183 4.4 55.9 1.0
C O:ASN183 4.4 48.5 1.0
CA O:ASP248 4.6 60.0 1.0
C O:SER182 4.7 52.9 1.0
O O:ASP248 4.8 57.5 1.0
C O:ASP248 4.8 58.6 1.0
C O:GLY247 4.9 67.1 1.0
CA O:SER182 4.9 56.9 1.0
CG O:ASN183 5.0 44.6 1.0

Sodium binding site 6 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound


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 with Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na404

b:35.6
occ:1.00
 O3 Q:SO4202 2.1 96.0 1.0
N R:SER184 3.3 42.3 1.0
S Q:SO4202 3.4 0.5 1.0
OG R:SER184 3.4 44.6 1.0
Y R:Y1401 3.4 0.5 1.0
CB R:SER184 3.6 50.7 1.0
OG R:SER182 3.7 59.5 1.0
N R:ASN183 3.7 51.2 1.0
O1 Q:SO4202 3.8 99.0 1.0
O4 Q:SO4202 3.9 0.9 1.0
O R:GLY247 3.9 49.9 1.0
CA R:SER184 4.0 49.3 1.0
CB R:SER182 4.0 51.7 1.0
CB R:ASN183 4.2 50.1 1.0
C R:ASN183 4.2 45.8 1.0
CA R:ASN183 4.2 52.5 1.0
O2 Q:SO4202 4.4 1.0 1.0
C R:SER182 4.5 47.3 1.0
CA R:ASP248 4.7 57.8 1.0
O R:ASP248 4.8 62.6 1.0
CG R:ASN183 4.8 40.7 1.0
CA R:SER182 4.9 51.1 1.0
C R:ASP248 4.9 54.1 1.0
C R:GLY247 5.0 62.6 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound To Be Published.
Page generated: Mon Aug 18 06:13:48 2025

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