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Sodium in PDB 6ndb: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt, PDB code: 6ndb 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) 47.07 / 3.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.836, 131.836, 251.702, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 29.2

Other elements in 6ndb:

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

Cobalt (Co) 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 Cobalt (pdb code 6ndb). 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 Cobalt, PDB code: 6ndb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndb

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


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:35.8
occ:1.00
 O3 B:SO4201 2.1 74.7 1.0
OG C:SER184 2.6 50.3 1.0
N C:SER184 3.3 59.1 1.0
CO C:CO401 3.4 63.6 1.0
S B:SO4201 3.5 0.6 1.0
CB C:SER184 3.6 51.5 1.0
OG C:SER182 3.7 47.0 1.0
N C:ASN183 3.9 58.3 1.0
CA C:SER184 3.9 55.8 1.0
O1 B:SO4201 4.0 65.0 1.0
CB C:SER182 4.1 42.1 1.0
O C:GLY247 4.2 66.0 1.0
O4 B:SO4201 4.2 0.4 1.0
C C:ASN183 4.2 60.3 1.0
CB C:ASN183 4.3 53.5 1.0
CA C:ASN183 4.3 58.2 1.0
O2 B:SO4201 4.4 70.3 1.0
C C:SER182 4.7 54.0 1.0
CA C:ASP248 4.9 54.0 1.0

Sodium binding site 2 out of 6 in 6ndb

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


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 Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:21.1
occ:1.00
 O3 E:SO4203 2.1 83.4 1.0
OG F:SER184 2.7 57.1 1.0
OG F:SER182 3.2 25.6 1.0
CO F:CO401 3.3 63.2 1.0
S E:SO4203 3.4 98.7 1.0
O4 E:SO4203 3.5 85.0 1.0
N F:SER184 3.6 48.3 1.0
CB F:SER182 3.7 30.9 1.0
CB F:SER184 3.7 46.0 1.0
N F:ASN183 3.9 46.3 1.0
O F:GLY247 3.9 41.7 1.0
O2 E:SO4203 4.1 68.1 1.0
CA F:SER184 4.3 44.6 1.0
O1 E:SO4203 4.4 72.9 1.0
C F:SER182 4.5 36.0 1.0
CA F:ASN183 4.5 47.0 1.0
CB F:ASN183 4.6 47.1 1.0
C F:ASN183 4.6 50.6 1.0
CA F:SER182 4.6 35.3 1.0
CA F:ASP248 4.7 37.3 1.0
C F:GLY247 4.9 46.2 1.0

Sodium binding site 3 out of 6 in 6ndb

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


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

b:24.2
occ:1.00
 O3 H:SO4202 2.1 97.1 1.0
OG I:SER184 2.8 70.2 1.0
OG I:SER182 3.1 24.6 1.0
CO I:CO401 3.3 60.1 1.0
S H:SO4202 3.3 0.1 1.0
O4 H:SO4202 3.5 0.4 1.0
N I:SER184 3.6 51.7 1.0
CB I:SER184 3.7 51.2 1.0
CB I:SER182 3.7 29.3 1.0
N I:ASN183 3.9 45.3 1.0
O2 H:SO4202 4.0 66.0 1.0
O I:GLY247 4.0 47.7 1.0
CA I:SER184 4.2 49.2 1.0
O1 H:SO4202 4.4 77.9 1.0
C I:SER182 4.5 34.9 1.0
CA I:ASN183 4.6 47.8 1.0
C I:ASN183 4.6 53.7 1.0
CB I:ASN183 4.6 45.6 1.0
CA I:SER182 4.7 34.4 1.0
CA I:ASP248 4.8 37.4 1.0

Sodium binding site 4 out of 6 in 6ndb

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


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

b:28.5
occ:1.00
 O3 K:SO4202 2.1 76.9 1.0
OG L:SER184 2.8 41.4 1.0
CO L:CO401 3.3 63.0 1.0
N L:SER184 3.3 55.7 1.0
OG L:SER182 3.4 48.4 1.0
S K:SO4202 3.5 99.6 1.0
CB L:SER184 3.6 42.8 1.0
N L:ASN183 3.8 52.5 1.0
CA L:SER184 4.0 48.0 1.0
CB L:SER182 4.0 42.3 1.0
O1 K:SO4202 4.1 75.4 1.0
O L:GLY247 4.1 63.7 1.0
O4 K:SO4202 4.1 97.4 1.0
C L:ASN183 4.2 55.5 1.0
CA L:ASN183 4.3 53.7 1.0
CB L:ASN183 4.3 52.1 1.0
O2 K:SO4202 4.4 69.4 1.0
C L:SER182 4.6 49.9 1.0
CA L:ASP248 4.8 50.9 1.0
CA L:SER182 4.9 46.1 1.0

Sodium binding site 5 out of 6 in 6ndb

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


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

b:49.7
occ:1.00
 O4 N:SO4201 2.2 99.8 1.0
S N:SO4201 3.4 0.3 1.0
N O:SER184 3.5 57.7 1.0
O3 N:SO4201 3.6 0.9 1.0
CB O:SER184 3.6 68.0 1.0
CO O:CO401 3.6 89.4 1.0
OG O:SER184 3.6 53.7 1.0
OG O:SER182 3.8 71.3 1.0
O O:GLY247 3.8 59.3 1.0
N O:ASN183 3.9 58.9 1.0
CA O:SER184 4.0 60.4 1.0
CB O:SER182 4.0 61.7 1.0
O1 N:SO4201 4.1 99.0 1.0
CB O:ASN183 4.3 56.8 1.0
C O:ASN183 4.4 53.0 1.0
CA O:ASN183 4.4 56.5 1.0
O2 N:SO4201 4.5 0.8 1.0
CA O:ASP248 4.6 72.4 1.0
C O:SER182 4.6 61.0 1.0
CG O:ASN183 4.9 51.0 1.0
C O:GLY247 4.9 75.4 1.0
C O:ASP248 4.9 71.4 1.0
O O:ASP248 4.9 72.3 1.0
CA O:SER182 4.9 59.4 1.0

Sodium binding site 6 out of 6 in 6ndb

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


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

b:50.5
occ:1.00
 O3 Q:SO4202 2.2 96.2 1.0
OG R:SER184 3.2 51.3 1.0
N R:SER184 3.4 49.5 1.0
CB R:SER184 3.6 57.1 1.0
CO R:CO401 3.6 88.3 1.0
S Q:SO4202 3.6 0.8 1.0
N R:ASN183 3.8 52.5 1.0
OG R:SER182 3.8 62.8 1.0
O R:GLY247 3.9 54.8 1.0
CA R:SER184 4.0 54.2 1.0
O1 Q:SO4202 4.0 0.5 1.0
CB R:SER182 4.1 56.9 1.0
CB R:ASN183 4.2 45.0 1.0
C R:ASN183 4.2 46.3 1.0
CA R:ASN183 4.3 47.4 1.0
O2 Q:SO4202 4.3 0.8 1.0
O4 Q:SO4202 4.4 0.8 1.0
C R:SER182 4.5 55.5 1.0
CA R:ASP248 4.7 71.7 1.0
CG R:ASN183 4.9 39.5 1.0
CA R:SER182 4.9 57.0 1.0
C R:GLY247 5.0 69.7 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt To Be Published.
Page generated: Tue Oct 8 12:11:51 2024

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