Atomistry » Sodium » PDB 6myw-6nfx » 6nda
Atomistry »
  Sodium »
    PDB 6myw-6nfx »
      6nda »

Sodium in PDB 6nda: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium, PDB code: 6nda 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) 92.47 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.530, 130.530, 250.919, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 6nda:

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

Cadmium (Cd) 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 Cadmium (pdb code 6nda). 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 Cadmium, PDB code: 6nda:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6nda

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


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:8.1
occ:1.00
 O2 C:SO4402 1.7 57.7 1.0
OG C:SER184 2.6 31.9 1.0
CD C:CD401 2.9 40.0 1.0
S C:SO4402 3.1 83.2 1.0
CB C:SER184 3.1 33.1 1.0
N C:SER184 3.2 37.2 1.0
OG C:SER182 3.4 42.1 1.0
O1 C:SO4402 3.6 59.9 1.0
CA C:SER184 3.6 35.0 1.0
O4 C:SO4402 3.7 96.8 1.0
CB C:SER182 4.0 36.3 1.0
O3 C:SO4402 4.0 47.3 1.0
N C:ASN183 4.2 38.7 1.0
C C:ASN183 4.3 37.5 1.0
O C:GLY247 4.5 47.8 1.0
CA C:ASN183 4.6 36.7 1.0
CB C:ASN183 4.8 35.2 1.0
C C:SER182 4.8 38.4 1.0
OD2 C:ASP283 4.9 36.5 1.0

Sodium binding site 2 out of 6 in 6nda

Go back to Sodium Binding Sites List in 6nda
Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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 Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:19.3
occ:1.00
 O3 F:SO4402 2.0 85.0 1.0
OG F:SER184 2.6 39.5 1.0
CD F:CD401 3.0 35.7 1.0
S F:SO4402 3.1 83.4 1.0
O2 F:SO4402 3.2 56.4 1.0
OG F:SER182 3.4 14.4 1.0
CB F:SER182 3.5 19.3 1.0
N F:SER184 3.6 38.5 1.0
CB F:SER184 3.6 36.9 1.0
O4 F:SO4402 3.7 48.0 1.0
N F:ASN183 3.8 27.8 1.0
O F:GLY247 4.1 31.3 1.0
CA F:SER184 4.2 34.8 1.0
O1 F:SO4402 4.2 52.5 1.0
C F:SER182 4.5 22.8 1.0
C F:ASN183 4.5 36.0 1.0
CA F:SER182 4.6 20.9 1.0
CA F:ASN183 4.6 30.8 1.0
CB F:ASN183 4.7 32.7 1.0
CA F:ASP248 4.8 29.6 1.0
OD1 F:ASP283 5.0 55.0 1.0

Sodium binding site 3 out of 6 in 6nda

Go back to Sodium Binding Sites List in 6nda
Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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

b:13.9
occ:1.00
 O3 H:SO4202 2.0 82.9 1.0
OG I:SER184 3.0 37.0 1.0
S H:SO4202 3.2 85.8 1.0
CD I:CD401 3.3 33.9 1.0
O2 H:SO4202 3.6 51.0 1.0
O1 H:SO4202 3.6 57.3 1.0
N I:SER184 3.6 42.0 1.0
CB I:SER182 3.7 24.3 1.0
OG I:SER182 3.7 20.8 1.0
N I:ASN183 3.8 33.5 1.0
CB I:SER184 3.9 36.2 1.0
O I:GLY247 4.1 33.7 1.0
CA I:SER184 4.3 36.5 1.0
O4 H:SO4202 4.3 62.1 1.0
CA I:ASN183 4.5 37.6 1.0
CB I:ASN183 4.5 37.0 1.0
C I:ASN183 4.5 42.9 1.0
CA I:ASP248 4.5 31.4 1.0
C I:SER182 4.6 26.8 1.0
CA I:SER182 4.7 24.2 1.0
C I:ASP248 4.9 30.8 1.0

Sodium binding site 4 out of 6 in 6nda

Go back to Sodium Binding Sites List in 6nda
Sodium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium


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

b:14.7
occ:1.00
 O3 K:SO4202 1.8 75.1 1.0
OG L:SER184 2.2 23.9 1.0
CD L:CD401 2.7 42.7 1.0
CB L:SER184 2.9 27.5 1.0
S K:SO4202 3.0 91.3 1.0
OG L:SER182 3.3 41.2 1.0
N L:SER184 3.3 32.7 1.0
O1 K:SO4202 3.3 90.7 1.0
O4 K:SO4202 3.5 64.1 1.0
CA L:SER184 3.6 29.3 1.0
CB L:SER182 3.8 35.6 1.0
O2 K:SO4202 4.2 60.6 1.0
N L:ASN183 4.3 33.6 1.0
O L:GLY247 4.4 52.3 1.0
C L:ASN183 4.4 33.5 1.0
OD2 L:ASP283 4.7 29.6 1.0
C L:SER182 4.8 34.2 1.0
OD1 L:ASP283 4.8 25.3 1.0
CA L:ASN183 4.8 33.4 1.0
CA L:SER182 4.9 32.8 1.0
CB L:ASN183 4.9 35.2 1.0
C L:SER184 5.0 30.9 1.0

Sodium binding site 5 out of 6 in 6nda

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


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

b:19.1
occ:1.00
 O1 N:SO4201 2.0 86.7 1.0
CD O:CD401 3.0 45.2 1.0
S N:SO4201 3.2 99.0 1.0
OG O:SER184 3.2 21.0 1.0
O3 N:SO4201 3.4 76.6 1.0
OG O:SER182 3.4 53.3 1.0
N O:SER184 3.4 33.5 1.0
CB O:SER184 3.5 31.0 1.0
CB O:SER182 3.7 48.9 1.0
O4 N:SO4201 3.8 63.4 1.0
N O:ASN183 4.0 41.7 1.0
CA O:SER184 4.0 34.4 1.0
O O:GLY247 4.1 43.1 1.0
O2 N:SO4201 4.3 85.0 1.0
C O:ASN183 4.5 35.8 1.0
C O:SER182 4.5 42.9 1.0
CA O:ASN183 4.6 42.0 1.0
CB O:ASN183 4.6 41.6 1.0
CA O:SER182 4.7 48.5 1.0
OG1 O:THR250 4.8 26.0 1.0
CA O:ASP248 4.9 59.2 1.0
O O:ASP248 4.9 61.5 1.0

Sodium binding site 6 out of 6 in 6nda

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


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

b:11.9
occ:1.00
 O3 Q:SO4202 1.7 81.1 1.0
OG R:SER184 2.9 21.9 1.0
CD R:CD401 3.0 45.9 1.0
S Q:SO4202 3.1 98.0 1.0
N R:SER184 3.3 34.6 1.0
OG R:SER182 3.3 50.9 1.0
CB R:SER184 3.4 28.4 1.0
O1 Q:SO4202 3.6 71.2 1.0
CB R:SER182 3.7 46.3 1.0
O4 Q:SO4202 3.8 92.0 1.0
CA R:SER184 3.9 31.6 1.0
N R:ASN183 3.9 47.1 1.0
O2 Q:SO4202 4.0 69.4 1.0
O R:GLY247 4.1 37.0 1.0
C R:ASN183 4.3 38.7 1.0
CA R:ASN183 4.5 45.2 1.0
C R:SER182 4.5 43.4 1.0
CB R:ASN183 4.6 46.2 1.0
CA R:SER182 4.7 45.6 1.0
CA R:ASP248 4.9 49.5 1.0
OG1 R:THR250 4.9 29.7 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium To Be Published.
Page generated: Tue Oct 8 12:11:42 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy