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Sodium in PDB 6ndf: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium, PDB code: 6ndf 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) 48.50 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.395, 132.395, 252.991, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 31.7

Other elements in 6ndf:

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

Strontium (Sr) 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 Strontium (pdb code 6ndf). 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 Strontium, PDB code: 6ndf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndf

Go back to Sodium Binding Sites List in 6ndf
Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium


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

b:46.0
occ:1.00
 O3 B:SO4201 2.5 82.9 1.0
OG C:SER184 3.0 59.6 1.0
N C:SER184 3.2 63.6 1.0
SR C:SR401 3.7 0.2 1.0
CB C:SER184 3.7 61.7 1.0
N C:ASN183 3.8 60.9 1.0
S B:SO4201 3.9 0.8 1.0
OG C:SER182 3.9 69.6 1.0
CA C:SER184 4.0 63.1 1.0
O C:GLY247 4.0 78.2 1.0
CB C:ASN183 4.0 65.6 1.0
C C:ASN183 4.1 66.9 1.0
CB C:SER182 4.1 53.3 1.0
CA C:ASN183 4.1 63.8 1.0
O1 B:SO4201 4.5 89.0 1.0
C C:SER182 4.6 54.6 1.0
O4 B:SO4201 4.6 0.2 1.0
ND2 C:ASN183 4.7 51.1 1.0
CA C:ASP248 4.8 64.2 1.0
CG C:ASN183 4.8 70.1 1.0
O2 B:SO4201 4.8 80.5 1.0
CA C:SER182 4.9 53.4 1.0

Sodium binding site 2 out of 6 in 6ndf

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


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

b:41.4
occ:1.00
 O3 E:SO4203 2.5 76.1 1.0
OG F:SER184 2.9 67.0 1.0
N F:SER184 3.5 64.7 1.0
OG F:SER182 3.6 43.8 1.0
SR F:SR401 3.7 95.8 1.0
O F:GLY247 3.7 60.4 1.0
N F:ASN183 3.8 56.5 1.0
CB F:SER184 3.8 55.2 1.0
S E:SO4203 3.9 0.6 1.0
CB F:SER182 3.9 43.5 1.0
CB F:ASN183 4.1 59.6 1.0
CA F:SER184 4.2 57.3 1.0
CA F:ASN183 4.3 58.2 1.0
O4 E:SO4203 4.4 0.9 1.0
C F:ASN183 4.4 63.5 1.0
C F:SER182 4.5 48.2 1.0
CA F:ASP248 4.5 41.8 1.0
O2 E:SO4203 4.6 78.8 1.0
O1 E:SO4203 4.7 63.3 1.0
CA F:SER182 4.8 45.2 1.0
C F:GLY247 4.8 51.8 1.0
CG F:ASN183 4.8 56.3 1.0

Sodium binding site 3 out of 6 in 6ndf

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


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

b:50.6
occ:1.00
 O3 H:SO4202 2.4 89.9 1.0
OG I:SER184 2.7 59.0 1.0
N I:SER184 3.5 62.2 1.0
SR I:SR401 3.6 97.2 1.0
CB I:SER184 3.7 53.5 1.0
S H:SO4202 3.8 0.2 1.0
OG I:SER182 3.8 47.5 1.0
N I:ASN183 3.9 53.0 1.0
O I:GLY247 3.9 54.8 1.0
CB I:SER182 3.9 45.2 1.0
CA I:SER184 4.2 53.9 1.0
CB I:ASN183 4.3 57.2 1.0
O2 H:SO4202 4.3 91.3 1.0
CA I:ASN183 4.4 54.1 1.0
C I:ASN183 4.5 59.4 1.0
O4 H:SO4202 4.5 0.0 1.0
CA I:ASP248 4.5 42.8 1.0
C I:SER182 4.6 46.0 1.0
O1 H:SO4202 4.7 75.0 1.0
CA I:SER182 4.8 44.4 1.0
C I:GLY247 4.9 50.8 1.0
C I:ASP248 5.0 50.1 1.0

Sodium binding site 4 out of 6 in 6ndf

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


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

b:46.7
occ:1.00
 O3 K:SO4202 2.3 82.3 1.0
OG L:SER184 3.3 62.0 1.0
N L:SER184 3.4 63.8 1.0
SR L:SR401 3.6 0.8 1.0
OG L:SER182 3.6 64.1 1.0
S K:SO4202 3.7 1.0 1.0
N L:ASN183 3.9 60.7 1.0
CB L:SER184 3.9 61.7 1.0
O L:GLY247 4.0 65.5 1.0
CB L:SER182 4.1 50.7 1.0
CB L:ASN183 4.2 64.0 1.0
CA L:SER184 4.2 63.4 1.0
CA L:ASN183 4.3 62.8 1.0
O4 K:SO4202 4.3 0.2 1.0
O1 K:SO4202 4.4 92.2 1.0
C L:ASN183 4.4 68.7 1.0
O2 K:SO4202 4.6 82.4 1.0
C L:SER182 4.7 54.0 1.0
CA L:ASP248 4.7 61.9 1.0
ND2 L:ASN183 4.9 61.0 1.0
CG L:ASN183 4.9 68.2 1.0
CA L:SER182 5.0 49.9 1.0
C L:ASP248 5.0 62.5 1.0

Sodium binding site 5 out of 6 in 6ndf

Go back to Sodium Binding Sites List in 6ndf
Sodium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium


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

b:65.5
occ:1.00
 O4 N:SO4201 2.1 0.2 1.0
S N:SO4201 3.4 0.0 1.0
O O:GLY247 3.6 54.2 1.0
O3 N:SO4201 3.6 0.3 1.0
SR O:SR401 3.8 0.1 1.0
CB O:SER182 4.0 63.3 1.0
OG O:SER182 4.0 68.2 1.0
O O:ASP248 4.0 84.8 1.0
CA O:ASP248 4.1 64.5 1.0
OG O:SER184 4.1 70.0 1.0
N O:SER184 4.1 66.5 1.0
C O:ASP248 4.2 69.8 1.0
N O:ASN183 4.3 60.1 1.0
O2 N:SO4201 4.3 97.3 1.0
CB O:SER184 4.3 79.6 1.0
O1 N:SO4201 4.3 0.9 1.0
CB O:ASN183 4.5 60.5 1.0
C O:GLY247 4.5 61.6 1.0
N O:ASP248 4.7 65.8 1.0
CA O:SER184 4.8 68.3 1.0
CA O:ASN183 4.8 55.0 1.0
CG O:ASN183 4.9 56.5 1.0
C O:SER182 4.9 61.9 1.0
N O:LEU249 4.9 53.1 1.0
CA O:SER182 5.0 63.7 1.0

Sodium binding site 6 out of 6 in 6ndf

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


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

b:72.4
occ:1.00
 O3 Q:SO4202 2.2 0.7 1.0
O R:GLY247 3.6 54.6 1.0
SR R:SR401 3.6 0.7 1.0
S Q:SO4202 3.6 1.0 1.0
N R:SER184 3.7 63.4 1.0
OG R:SER182 3.8 67.7 1.0
N R:ASN183 3.9 61.3 1.0
CB R:SER182 4.0 63.7 1.0
CB R:SER184 4.0 76.8 1.0
OG R:SER184 4.0 81.9 1.0
O2 Q:SO4202 4.1 0.5 1.0
CB R:ASN183 4.2 58.1 1.0
CA R:ASP248 4.3 65.4 1.0
O1 Q:SO4202 4.3 0.7 1.0
CA R:SER184 4.4 66.7 1.0
O4 Q:SO4202 4.4 0.0 1.0
CA R:ASN183 4.4 52.6 1.0
C R:ASN183 4.5 57.5 1.0
C R:GLY247 4.6 64.5 1.0
C R:ASP248 4.6 71.7 1.0
O R:ASP248 4.6 95.5 1.0
C R:SER182 4.7 61.2 1.0
CG R:ASN183 4.7 54.3 1.0
ND2 R:ASN183 4.9 65.0 1.0
N R:ASP248 4.9 70.1 1.0
CA R:SER182 4.9 61.1 1.0

Reference:

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

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