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

Sodium in PDB 6ndc: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound, PDB code: 6ndc 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) 92.90 / 3.35
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.140, 131.140, 251.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.6

Other elements in 6ndc:

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

Chromium (Cr) 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 Chromium Bound (pdb code 6ndc). 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 Chromium Bound, PDB code: 6ndc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndc

Go back to Sodium Binding Sites List in 6ndc
Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium 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 Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:31.6
occ:1.00
 O3 C:SO4402 2.6 82.3 1.0
N C:SER184 3.1 41.1 1.0
N C:ASN183 3.5 40.4 1.0
OG C:SER184 3.6 47.2 1.0
CB C:ASN183 3.7 36.8 1.0
C C:ASN183 3.7 41.6 1.0
CA C:ASN183 3.8 39.5 1.0
CB C:SER184 3.8 42.0 1.0
CR C:CR401 3.9 52.6 1.0
CA C:SER184 3.9 40.6 1.0
O C:GLY247 3.9 33.3 1.0
S C:SO4402 3.9 96.2 1.0
CB C:SER182 4.1 39.1 1.0
OG C:SER182 4.2 35.3 1.0
CG C:ASN183 4.4 35.2 1.0
O1 C:SO4402 4.4 78.5 1.0
C C:SER182 4.5 44.3 1.0
ND2 C:ASN183 4.6 38.9 1.0
O4 C:SO4402 4.6 0.3 1.0
CA C:ASP248 4.7 39.3 1.0
O C:ASN183 4.8 42.4 1.0
O2 C:SO4402 4.8 72.8 1.0
CA C:SER182 4.9 40.3 1.0
C C:GLY247 4.9 33.8 1.0

Sodium binding site 2 out of 6 in 6ndc

Go back to Sodium Binding Sites List in 6ndc
Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium 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 Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:5.7
occ:1.00
 O3 E:SO4202 2.0 79.9 1.0
OG F:SER184 2.9 27.3 1.0
S E:SO4202 3.4 89.0 1.0
OG F:SER182 3.5 28.6 1.0
CR F:CR402 3.6 47.4 1.0
N F:SER184 3.6 31.3 1.0
CB F:SER182 3.7 30.1 1.0
N F:ASN183 3.8 31.5 1.0
O4 E:SO4202 3.9 81.6 1.0
O F:GLY247 3.9 29.5 1.0
CB F:SER184 3.9 27.3 1.0
O2 E:SO4202 4.0 70.0 1.0
CB F:ASN183 4.3 31.8 1.0
O1 E:SO4202 4.3 62.0 1.0
CA F:SER184 4.3 28.7 1.0
CA F:ASP248 4.4 27.9 1.0
CA F:ASN183 4.4 33.2 1.0
C F:ASN183 4.5 35.3 1.0
C F:SER182 4.5 30.9 1.0
CA F:SER182 4.6 30.2 1.0
C F:ASP248 4.9 28.1 1.0
C F:GLY247 4.9 29.8 1.0

Sodium binding site 3 out of 6 in 6ndc

Go back to Sodium Binding Sites List in 6ndc
Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium 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 Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na403

b:9.0
occ:1.00
 O3 H:SO4201 2.0 69.8 1.0
OG I:SER184 2.8 26.4 1.0
S H:SO4201 3.3 81.2 1.0
OG I:SER182 3.4 20.7 1.0
CR I:CR402 3.5 44.2 1.0
N I:SER184 3.6 31.3 1.0
O4 H:SO4201 3.6 70.5 1.0
CB I:SER182 3.7 22.6 1.0
N I:ASN183 3.8 28.2 1.0
CB I:SER184 3.8 27.1 1.0
O I:GLY247 4.0 31.6 1.0
O2 H:SO4201 4.0 57.5 1.0
O1 H:SO4201 4.2 61.2 1.0
CB I:ASN183 4.3 32.7 1.0
CA I:SER184 4.3 28.2 1.0
CA I:ASP248 4.3 28.6 1.0
CA I:ASN183 4.4 31.3 1.0
C I:ASN183 4.5 32.2 1.0
C I:SER182 4.5 25.1 1.0
CA I:SER182 4.7 23.6 1.0
C I:ASP248 4.7 28.4 1.0
O I:ASP248 4.9 28.1 1.0
C I:GLY247 4.9 31.7 1.0

Sodium binding site 4 out of 6 in 6ndc

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

b:38.1
occ:1.00
 O3 K:SO4202 2.0 84.7 1.0
CR L:CR401 3.0 53.6 1.0
OG L:SER184 3.1 32.5 1.0
S K:SO4202 3.3 0.6 1.0
N L:SER184 3.5 35.5 1.0
CB L:SER184 3.7 30.2 1.0
OG L:SER182 3.7 44.0 1.0
O1 K:SO4202 3.8 93.9 1.0
N L:ASN183 3.8 38.0 1.0
CB L:SER182 3.9 43.7 1.0
O4 K:SO4202 4.0 1.0 1.0
CA L:SER184 4.1 31.1 1.0
O L:GLY247 4.2 33.9 1.0
O2 K:SO4202 4.3 83.0 1.0
C L:ASN183 4.4 38.5 1.0
CA L:ASN183 4.4 39.4 1.0
CB L:ASN183 4.5 41.9 1.0
C L:SER182 4.6 42.2 1.0
CA L:ASP248 4.7 39.3 1.0
CA L:SER182 4.8 40.9 1.0
C L:ASP248 5.0 40.2 1.0

Sodium binding site 5 out of 6 in 6ndc

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

b:32.0
occ:1.00
 O4 N:SO4201 2.4 0.7 1.0
O3 N:SO4201 3.3 84.5 1.0
S N:SO4201 3.4 95.5 1.0
OG O:SER182 3.6 39.7 1.0
O O:GLY247 3.6 49.9 1.0
N O:SER184 3.9 42.1 1.0
OG O:SER184 3.9 43.7 1.0
CR O:CR401 3.9 76.7 1.0
N O:ASN183 3.9 36.1 1.0
CB O:SER182 3.9 39.4 1.0
CB O:SER184 4.1 45.8 1.0
CB O:ASN183 4.2 42.6 1.0
CA O:ASP248 4.3 50.5 1.0
O1 N:SO4201 4.4 89.5 1.0
O2 N:SO4201 4.4 0.2 1.0
CA O:ASN183 4.5 37.7 1.0
CA O:SER184 4.5 44.0 1.0
C O:ASP248 4.6 49.6 1.0
C O:ASN183 4.6 38.0 1.0
C O:GLY247 4.6 47.1 1.0
C O:SER182 4.7 37.6 1.0
O O:ASP248 4.8 48.1 1.0
CG O:ASN183 4.8 45.2 1.0
CA O:SER182 4.9 38.6 1.0
N O:ASP248 5.0 48.9 1.0

Sodium binding site 6 out of 6 in 6ndc

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

b:35.2
occ:1.00
 O3 Q:SO4202 2.1 96.3 1.0
O R:GLY247 3.4 51.9 1.0
OG R:SER182 3.5 45.3 1.0
OG R:SER184 3.5 45.5 1.0
S Q:SO4202 3.5 0.4 1.0
N R:ASN183 3.7 35.9 1.0
CR R:CR401 3.7 76.3 1.0
N R:SER184 3.8 37.7 1.0
CB R:SER182 3.8 44.1 1.0
CB R:SER184 4.0 45.9 1.0
O4 Q:SO4202 4.1 0.3 1.0
CB R:ASN183 4.1 40.5 1.0
CA R:ASP248 4.2 49.7 1.0
O1 Q:SO4202 4.3 90.1 1.0
CA R:ASN183 4.3 37.1 1.0
O2 Q:SO4202 4.3 0.5 1.0
O R:ASP248 4.4 48.8 1.0
C R:ASP248 4.4 47.5 1.0
C R:ASN183 4.5 35.3 1.0
C R:GLY247 4.5 51.5 1.0
C R:SER182 4.5 39.4 1.0
CA R:SER184 4.5 41.4 1.0
CA R:SER182 4.7 43.9 1.0
CG R:ASN183 4.8 45.0 1.0
N R:ASP248 4.8 52.4 1.0

Reference:

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

Last articles

K in 9ESI
K in 9ESH
K in 9ES4
K in 9ES5
K in 9ES2
K in 9ES0
K in 9ES1
K in 9EIO
K in 9ED1
K in 9EIE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy