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Sodium in PDB 6ndh: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc, PDB code: 6ndh 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) 47.00 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.399, 131.399, 251.358, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.5

Other elements in 6ndh:

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

Chlorine (Cl) 9 atoms
Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Zinc (pdb code 6ndh). 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 Zinc, PDB code: 6ndh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndh

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


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

b:40.1
occ:1.00
 O3 B:SO4201 2.0 64.8 1.0
OG C:SER184 2.9 47.2 1.0
ZN C:ZN401 3.4 73.5 1.0
N C:SER184 3.4 49.9 1.0
S B:SO4201 3.4 0.1 1.0
CB C:SER184 3.6 43.0 1.0
OG C:SER182 3.7 39.1 1.0
N C:ASN183 4.0 44.3 1.0
CA C:SER184 4.0 47.0 1.0
O1 B:SO4201 4.1 77.0 1.0
CB C:SER182 4.1 38.6 1.0
O C:GLY247 4.2 54.4 1.0
O2 B:SO4201 4.2 63.7 1.0
O4 B:SO4201 4.2 0.5 1.0
CB C:ASN183 4.3 45.5 1.0
C C:ASN183 4.3 46.9 1.0
CA C:ASN183 4.4 44.6 1.0
C C:SER182 4.6 42.9 1.0
CA C:ASP248 4.8 44.6 1.0
CA C:SER182 5.0 38.5 1.0

Sodium binding site 2 out of 6 in 6ndh

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


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

b:30.2
occ:1.00
 O3 E:SO4203 2.0 59.9 1.0
OG F:SER184 2.9 42.4 1.0
OG F:SER182 3.2 32.1 1.0
S E:SO4203 3.4 87.2 1.0
ZN F:ZN401 3.4 58.1 1.0
N F:SER184 3.6 43.2 1.0
CB F:SER182 3.6 35.7 1.0
O4 E:SO4203 3.7 89.8 1.0
N F:ASN183 3.7 37.0 1.0
O F:GLY247 3.9 39.9 1.0
CB F:SER184 3.9 35.9 1.0
O2 E:SO4203 4.1 53.0 1.0
O1 E:SO4203 4.3 63.9 1.0
C F:SER182 4.3 33.4 1.0
CA F:SER184 4.4 38.0 1.0
CA F:ASN183 4.4 42.9 1.0
CB F:ASN183 4.5 43.0 1.0
C F:ASN183 4.5 47.1 1.0
CA F:SER182 4.6 31.7 1.0
CA F:ASP248 4.6 34.8 1.0
C F:GLY247 4.9 35.0 1.0
C F:ASP248 5.0 35.6 1.0

Sodium binding site 3 out of 6 in 6ndh

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


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

b:33.8
occ:1.00
 O3 H:SO4202 1.9 69.0 1.0
OG I:SER184 2.9 47.3 1.0
S H:SO4202 3.2 95.1 1.0
OG I:SER182 3.2 30.8 1.0
ZN I:ZN401 3.3 55.2 1.0
O4 H:SO4202 3.6 95.4 1.0
CB I:SER182 3.7 33.8 1.0
N I:SER184 3.8 42.2 1.0
O2 H:SO4202 3.8 57.4 1.0
N I:ASN183 3.9 36.4 1.0
CB I:SER184 3.9 37.1 1.0
O I:GLY247 4.0 39.7 1.0
O1 H:SO4202 4.2 62.5 1.0
CA I:SER184 4.4 38.1 1.0
C I:SER182 4.5 33.7 1.0
CA I:ASP248 4.6 35.3 1.0
CA I:ASN183 4.6 40.2 1.0
CB I:ASN183 4.6 40.4 1.0
C I:ASN183 4.7 44.0 1.0
CA I:SER182 4.7 31.4 1.0
C I:ASP248 4.9 36.4 1.0
C I:GLY247 5.0 33.8 1.0

Sodium binding site 4 out of 6 in 6ndh

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


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

b:36.6
occ:1.00
 O3 K:SO4202 2.0 72.3 1.0
OG L:SER184 2.9 42.6 1.0
ZN L:ZN401 3.1 73.0 1.0
S K:SO4202 3.4 99.3 1.0
OG L:SER182 3.4 42.6 1.0
N L:SER184 3.5 48.3 1.0
CB L:SER184 3.5 38.9 1.0
O1 K:SO4202 3.9 81.7 1.0
CB L:SER182 3.9 41.8 1.0
CA L:SER184 4.0 43.8 1.0
O4 K:SO4202 4.1 92.5 1.0
N L:ASN183 4.1 43.4 1.0
O2 K:SO4202 4.3 62.8 1.0
O L:GLY247 4.3 52.8 1.0
C L:ASN183 4.4 45.4 1.0
CB L:ASN183 4.5 46.6 1.0
CA L:ASN183 4.5 44.0 1.0
C L:SER182 4.6 42.6 1.0
CA L:ASP248 4.9 43.7 1.0
CA L:SER182 4.9 39.5 1.0

Sodium binding site 5 out of 6 in 6ndh

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


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

b:49.0
occ:1.00
 O4 N:SO4201 2.0 0.7 1.0
S N:SO4201 3.3 0.8 1.0
OG O:SER184 3.4 47.4 1.0
ZN O:ZN401 3.6 94.3 1.0
N O:SER184 3.6 46.7 1.0
O3 N:SO4201 3.7 98.4 1.0
CB O:SER184 3.8 56.6 1.0
OG O:SER182 3.8 49.2 1.0
O O:GLY247 3.9 38.7 1.0
N O:ASN183 3.9 46.3 1.0
CB O:SER182 4.0 49.4 1.0
O1 N:SO4201 4.0 94.0 1.0
CA O:SER184 4.3 49.4 1.0
O2 N:SO4201 4.4 97.4 1.0
CB O:ASN183 4.4 48.7 1.0
CA O:ASN183 4.5 47.4 1.0
C O:ASN183 4.5 47.6 1.0
CA O:ASP248 4.5 54.7 1.0
C O:SER182 4.6 50.9 1.0
C O:ASP248 4.8 57.8 1.0
O O:ASP248 4.8 60.4 1.0
CA O:SER182 4.9 50.6 1.0
C O:GLY247 4.9 53.2 1.0
CG O:ASN183 4.9 43.5 1.0

Sodium binding site 6 out of 6 in 6ndh

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


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

b:48.8
occ:1.00
 O3 Q:SO4202 1.9 0.8 1.0
OG R:SER184 3.2 50.2 1.0
S Q:SO4202 3.4 0.9 1.0
ZN R:ZN401 3.5 91.9 1.0
N R:SER184 3.5 43.5 1.0
CB R:SER184 3.8 55.5 1.0
OG R:SER182 3.8 48.6 1.0
N R:ASN183 3.9 47.9 1.0
O R:GLY247 3.9 42.3 1.0
O1 Q:SO4202 4.0 97.0 1.0
CB R:SER182 4.0 48.4 1.0
O4 Q:SO4202 4.0 0.5 1.0
CA R:SER184 4.2 47.7 1.0
O2 Q:SO4202 4.2 0.9 1.0
CB R:ASN183 4.3 48.1 1.0
CA R:ASN183 4.4 47.0 1.0
C R:ASN183 4.4 45.8 1.0
C R:SER182 4.6 51.4 1.0
CA R:ASP248 4.6 51.5 1.0
C R:ASP248 4.9 54.3 1.0
CG R:ASN183 4.9 44.4 1.0
CA R:SER182 4.9 47.6 1.0
O R:ASP248 4.9 59.2 1.0
C R:GLY247 4.9 50.5 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Zinc Bound To Be Published.
Page generated: Tue Oct 8 12:15:00 2024

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