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Sodium in PDB 6ndd: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound, PDB code: 6ndd 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) 48.01 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.712, 130.712, 251.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.4

Other elements in 6ndd:

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

Manganese (Mn) 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 Manganese Bound (pdb code 6ndd). 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 Manganese Bound, PDB code: 6ndd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndd

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Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:32.6
occ:1.00
 O2 C:SO4402 1.7 87.2 1.0
OG C:SER184 2.3 41.3 1.0
MN C:MN401 3.0 47.4 1.0
S C:SO4402 3.1 0.1 1.0
CB C:SER184 3.3 41.3 1.0
N C:SER184 3.3 53.3 1.0
OG C:SER182 3.3 40.8 1.0
O4 C:SO4402 3.6 1.0 1.0
O1 C:SO4402 3.8 68.6 1.0
CA C:SER184 3.8 43.3 1.0
CB C:SER182 3.9 43.9 1.0
O3 C:SO4402 4.1 73.4 1.0
N C:ASN183 4.1 46.8 1.0
O C:GLY247 4.3 59.2 1.0
C C:ASN183 4.4 51.9 1.0
CA C:ASN183 4.6 46.4 1.0
CB C:ASN183 4.6 48.7 1.0
C C:SER182 4.7 46.5 1.0
CA C:SER182 4.9 40.3 1.0

Sodium binding site 2 out of 6 in 6ndd

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Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:26.4
occ:1.00
 O2 F:SO4402 1.9 85.5 1.0
OG F:SER184 2.7 50.3 1.0
S F:SO4402 3.1 0.0 1.0
MN F:MN401 3.1 41.5 1.0
O4 F:SO4402 3.3 76.1 1.0
OG F:SER182 3.3 26.4 1.0
N F:SER184 3.6 47.2 1.0
O3 F:SO4402 3.6 57.3 1.0
CB F:SER184 3.6 44.1 1.0
CB F:SER182 3.7 29.8 1.0
N F:ASN183 4.0 44.3 1.0
O F:GLY247 4.0 36.5 1.0
CA F:SER184 4.2 42.7 1.0
O1 F:SO4402 4.3 54.9 1.0
C F:ASN183 4.5 52.5 1.0
CA F:ASN183 4.6 49.2 1.0
C F:SER182 4.6 33.5 1.0
CB F:ASN183 4.7 52.6 1.0
CA F:SER182 4.7 29.6 1.0
CA F:ASP248 4.8 33.3 1.0

Sodium binding site 3 out of 6 in 6ndd

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Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na403

b:30.1
occ:1.00
 O3 I:SO4402 1.9 92.5 1.0
OG I:SER184 2.6 53.2 1.0
S I:SO4402 3.0 0.8 1.0
MN I:MN401 3.1 41.2 1.0
OG I:SER182 3.2 29.8 1.0
O1 I:SO4402 3.4 77.5 1.0
O2 I:SO4402 3.4 66.6 1.0
CB I:SER184 3.6 45.6 1.0
CB I:SER182 3.6 34.0 1.0
N I:SER184 3.6 48.7 1.0
N I:ASN183 4.0 45.0 1.0
O I:GLY247 4.1 45.9 1.0
CA I:SER184 4.2 43.2 1.0
O4 I:SO4402 4.2 61.7 1.0
C I:ASN183 4.6 53.7 1.0
C I:SER182 4.7 37.8 1.0
CA I:ASN183 4.7 48.8 1.0
CA I:SER182 4.7 33.0 1.0
CA I:ASP248 4.7 36.7 1.0
CB I:ASN183 4.8 47.5 1.0
OG1 I:THR250 4.9 53.4 1.0

Sodium binding site 4 out of 6 in 6ndd

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Sodium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na402

b:32.3
occ:1.00
 O3 K:SO4202 1.9 93.6 1.0
OG L:SER184 2.4 36.5 1.0
MN L:MN401 2.8 47.0 1.0
S K:SO4202 3.1 0.8 1.0
CB L:SER184 3.2 39.4 1.0
OG L:SER182 3.3 44.1 1.0
N L:SER184 3.4 48.1 1.0
O1 K:SO4202 3.5 0.3 1.0
O4 K:SO4202 3.6 89.7 1.0
CA L:SER184 3.8 41.1 1.0
CB L:SER182 4.0 42.8 1.0
N L:ASN183 4.3 47.5 1.0
O2 K:SO4202 4.3 68.6 1.0
O L:GLY247 4.5 57.5 1.0
C L:ASN183 4.5 46.6 1.0
CA L:ASN183 4.8 44.8 1.0
OD1 L:ASP283 4.8 36.5 1.0
C L:SER182 4.8 45.6 1.0
CB L:ASN183 4.9 44.4 1.0
OD2 L:ASP283 5.0 41.1 1.0

Sodium binding site 5 out of 6 in 6ndd

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Sodium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na402

b:40.3
occ:1.00
 O1 N:SO4201 2.0 0.9 1.0
S N:SO4201 3.0 0.6 1.0
O3 N:SO4201 3.2 99.3 1.0
OG O:SER184 3.2 51.2 1.0
MN O:MN401 3.3 63.0 1.0
N O:SER184 3.5 43.6 1.0
CB O:SER184 3.6 57.4 1.0
OG O:SER182 3.6 58.0 1.0
O4 N:SO4201 3.8 94.5 1.0
CB O:SER182 3.8 57.4 1.0
O O:GLY247 4.0 50.0 1.0
CA O:SER184 4.0 52.6 1.0
N O:ASN183 4.1 54.3 1.0
O2 N:SO4201 4.2 0.8 1.0
CB O:ASN183 4.5 51.2 1.0
C O:ASN183 4.5 44.8 1.0
CA O:ASN183 4.6 51.5 1.0
C O:SER182 4.7 52.2 1.0
O O:ASP248 4.7 64.5 1.0
CA O:ASP248 4.9 58.7 1.0
CA O:SER182 4.9 56.8 1.0
C O:ASP248 4.9 61.8 1.0
OG1 O:THR250 5.0 39.5 1.0

Sodium binding site 6 out of 6 in 6ndd

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Sodium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese 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 Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na404

b:35.2
occ:1.00
 O3 Q:SO4202 1.7 95.1 1.0
OG R:SER184 3.0 39.3 1.0
MN R:MN401 3.1 62.6 1.0
S Q:SO4202 3.1 0.3 1.0
N R:SER184 3.3 40.6 1.0
CB R:SER184 3.3 44.9 1.0
OG R:SER182 3.5 56.9 1.0
O1 Q:SO4202 3.7 92.8 1.0
O4 Q:SO4202 3.8 0.4 1.0
CA R:SER184 3.8 46.1 1.0
CB R:SER182 3.8 52.9 1.0
N R:ASN183 3.9 51.5 1.0
O2 Q:SO4202 4.1 85.7 1.0
O R:GLY247 4.1 54.6 1.0
C R:ASN183 4.2 40.6 1.0
CA R:ASN183 4.4 45.9 1.0
CB R:ASN183 4.4 44.7 1.0
C R:SER182 4.6 52.3 1.0
CA R:SER182 4.8 54.8 1.0
CA R:ASP248 5.0 57.2 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Manganese Bound To Be Published.
Page generated: Tue Oct 8 12:12:07 2024

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