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

Sodium in PDB 6ndg: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound, PDB code: 6ndg 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) 46.94 / 3.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 130.846, 130.846, 251.167, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.1

Other elements in 6ndg:

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

Yttrium (Y) 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 Yttrium Bound (pdb code 6ndg). 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 Yttrium Bound, PDB code: 6ndg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:32.0
occ:1.00
 O3 B:SO4201 2.0 83.8 1.0
OG C:SER184 2.7 42.6 1.0
N C:SER184 3.3 51.7 1.0
S B:SO4201 3.4 1.0 1.0
Y C:Y1401 3.4 93.2 1.0
CB C:SER184 3.6 42.2 1.0
O1 B:SO4201 3.7 64.7 1.0
OG C:SER182 3.9 47.9 1.0
CA C:SER184 4.0 45.6 1.0
N C:ASN183 4.0 47.4 1.0
O C:GLY247 4.2 55.0 1.0
O4 B:SO4201 4.2 0.1 1.0
CB C:SER182 4.2 41.0 1.0
O2 B:SO4201 4.3 77.0 1.0
C C:ASN183 4.3 51.4 1.0
CB C:ASN183 4.4 48.0 1.0
CA C:ASN183 4.4 48.8 1.0
CA C:ASP248 4.8 48.6 1.0
C C:SER182 4.8 45.7 1.0

Sodium binding site 2 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:27.7
occ:1.00
 O3 E:SO4203 2.1 90.8 1.0
OG F:SER184 3.0 68.6 1.0
OG F:SER182 3.3 31.3 1.0
Y F:Y1401 3.3 78.9 1.0
S E:SO4203 3.4 0.1 1.0
N F:SER184 3.6 54.8 1.0
N F:ASN183 3.7 45.5 1.0
CB F:SER182 3.8 34.0 1.0
O F:GLY247 3.8 30.5 1.0
O4 E:SO4203 3.9 87.8 1.0
CB F:SER184 3.9 55.8 1.0
O2 E:SO4203 4.0 59.7 1.0
CA F:SER184 4.4 51.9 1.0
CB F:ASN183 4.4 49.8 1.0
CA F:ASN183 4.4 50.7 1.0
O1 E:SO4203 4.5 74.6 1.0
C F:ASN183 4.5 59.3 1.0
C F:SER182 4.5 34.9 1.0
CA F:ASP248 4.6 39.4 1.0
CA F:SER182 4.7 33.3 1.0
C F:GLY247 4.9 36.9 1.0
C F:ASP248 5.0 33.3 1.0

Sodium binding site 3 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na402

b:23.9
occ:1.00
 O3 H:SO4202 2.0 90.0 1.0
OG I:SER184 3.0 74.6 1.0
OG I:SER182 3.2 30.5 1.0
S H:SO4202 3.3 98.8 1.0
Y I:Y1401 3.3 79.8 1.0
N I:SER184 3.7 52.0 1.0
O4 H:SO4202 3.7 95.2 1.0
O2 H:SO4202 3.7 55.8 1.0
CB I:SER182 3.7 34.7 1.0
N I:ASN183 3.7 44.0 1.0
CB I:SER184 3.9 57.4 1.0
O I:GLY247 3.9 34.8 1.0
CA I:SER184 4.3 51.0 1.0
O1 H:SO4202 4.4 75.5 1.0
CA I:ASN183 4.5 48.1 1.0
CB I:ASN183 4.5 47.7 1.0
C I:SER182 4.5 33.5 1.0
C I:ASN183 4.5 53.1 1.0
CA I:ASP248 4.6 37.9 1.0
CA I:SER182 4.7 32.5 1.0
C I:GLY247 4.9 36.9 1.0
C I:ASP248 4.9 33.2 1.0

Sodium binding site 4 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na402

b:32.9
occ:1.00
 O3 K:SO4202 1.9 90.2 1.0
OG L:SER184 2.6 36.9 1.0
S K:SO4202 3.2 0.8 1.0
Y L:Y1401 3.3 90.2 1.0
N L:SER184 3.5 48.9 1.0
CB L:SER184 3.6 39.9 1.0
O1 K:SO4202 3.7 78.4 1.0
OG L:SER182 3.7 51.8 1.0
O4 K:SO4202 3.8 97.2 1.0
CA L:SER184 4.0 42.4 1.0
N L:ASN183 4.1 44.7 1.0
CB L:SER182 4.1 42.4 1.0
O L:GLY247 4.1 60.9 1.0
O2 K:SO4202 4.2 63.6 1.0
C L:ASN183 4.4 50.4 1.0
CB L:ASN183 4.5 45.8 1.0
CA L:ASN183 4.5 47.2 1.0
C L:SER182 4.8 43.5 1.0
CA L:ASP248 4.8 49.7 1.0

Sodium binding site 5 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na402

b:43.2
occ:1.00
 O4 N:SO4201 1.9 0.7 1.0
S N:SO4201 3.1 0.7 1.0
Y O:Y1401 3.4 1.0 1.0
O3 N:SO4201 3.5 0.7 1.0
N O:SER184 3.5 46.8 1.0
OG O:SER184 3.7 48.5 1.0
O1 N:SO4201 3.7 87.9 1.0
OG O:SER182 3.8 57.0 1.0
CB O:SER184 3.8 55.6 1.0
N O:ASN183 3.9 54.4 1.0
O O:GLY247 3.9 58.0 1.0
CB O:SER182 4.0 55.9 1.0
CA O:SER184 4.2 54.2 1.0
O2 N:SO4201 4.2 0.4 1.0
CB O:ASN183 4.3 55.8 1.0
CA O:ASN183 4.4 55.9 1.0
C O:ASN183 4.4 48.5 1.0
CA O:ASP248 4.6 60.0 1.0
C O:SER182 4.7 52.9 1.0
O O:ASP248 4.8 57.5 1.0
C O:ASP248 4.8 58.6 1.0
C O:GLY247 4.9 67.1 1.0
CA O:SER182 4.9 56.9 1.0
CG O:ASN183 5.0 44.6 1.0

Sodium binding site 6 out of 6 in 6ndg

Go back to Sodium Binding Sites List in 6ndg
Sodium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium 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 Yttrium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na404

b:35.6
occ:1.00
 O3 Q:SO4202 2.1 96.0 1.0
N R:SER184 3.3 42.3 1.0
S Q:SO4202 3.4 0.5 1.0
OG R:SER184 3.4 44.6 1.0
Y R:Y1401 3.4 0.5 1.0
CB R:SER184 3.6 50.7 1.0
OG R:SER182 3.7 59.5 1.0
N R:ASN183 3.7 51.2 1.0
O1 Q:SO4202 3.8 99.0 1.0
O4 Q:SO4202 3.9 0.9 1.0
O R:GLY247 3.9 49.9 1.0
CA R:SER184 4.0 49.3 1.0
CB R:SER182 4.0 51.7 1.0
CB R:ASN183 4.2 50.1 1.0
C R:ASN183 4.2 45.8 1.0
CA R:ASN183 4.2 52.5 1.0
O2 Q:SO4202 4.4 1.0 1.0
C R:SER182 4.5 47.3 1.0
CA R:ASP248 4.7 57.8 1.0
O R:ASP248 4.8 62.6 1.0
CG R:ASN183 4.8 40.7 1.0
CA R:SER182 4.9 51.1 1.0
C R:ASP248 4.9 54.1 1.0
C R:GLY247 5.0 62.6 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound To Be Published.
Page generated: Tue Oct 8 12:14:41 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy