Atomistry » Sodium » PDB 6mz1-6nib » 6ndf
Atomistry »
  Sodium »
    PDB 6mz1-6nib »
      6ndf »

Sodium in PDB 6ndf: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium, PDB code: 6ndf 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) 48.50 / 3.05
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.395, 132.395, 252.991, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 31.7

Other elements in 6ndf:

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

Strontium (Sr) 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 Strontium (pdb code 6ndf). 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 Strontium, PDB code: 6ndf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ndf

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


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

b:46.0
occ:1.00
 O3 B:SO4201 2.5 82.9 1.0
OG C:SER184 3.0 59.6 1.0
N C:SER184 3.2 63.6 1.0
SR C:SR401 3.7 0.2 1.0
CB C:SER184 3.7 61.7 1.0
N C:ASN183 3.8 60.9 1.0
S B:SO4201 3.9 0.8 1.0
OG C:SER182 3.9 69.6 1.0
CA C:SER184 4.0 63.1 1.0
O C:GLY247 4.0 78.2 1.0
CB C:ASN183 4.0 65.6 1.0
C C:ASN183 4.1 66.9 1.0
CB C:SER182 4.1 53.3 1.0
CA C:ASN183 4.1 63.8 1.0
O1 B:SO4201 4.5 89.0 1.0
C C:SER182 4.6 54.6 1.0
O4 B:SO4201 4.6 0.2 1.0
ND2 C:ASN183 4.7 51.1 1.0
CA C:ASP248 4.8 64.2 1.0
CG C:ASN183 4.8 70.1 1.0
O2 B:SO4201 4.8 80.5 1.0
CA C:SER182 4.9 53.4 1.0

Sodium binding site 2 out of 6 in 6ndf

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


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

b:41.4
occ:1.00
 O3 E:SO4203 2.5 76.1 1.0
OG F:SER184 2.9 67.0 1.0
N F:SER184 3.5 64.7 1.0
OG F:SER182 3.6 43.8 1.0
SR F:SR401 3.7 95.8 1.0
O F:GLY247 3.7 60.4 1.0
N F:ASN183 3.8 56.5 1.0
CB F:SER184 3.8 55.2 1.0
S E:SO4203 3.9 0.6 1.0
CB F:SER182 3.9 43.5 1.0
CB F:ASN183 4.1 59.6 1.0
CA F:SER184 4.2 57.3 1.0
CA F:ASN183 4.3 58.2 1.0
O4 E:SO4203 4.4 0.9 1.0
C F:ASN183 4.4 63.5 1.0
C F:SER182 4.5 48.2 1.0
CA F:ASP248 4.5 41.8 1.0
O2 E:SO4203 4.6 78.8 1.0
O1 E:SO4203 4.7 63.3 1.0
CA F:SER182 4.8 45.2 1.0
C F:GLY247 4.8 51.8 1.0
CG F:ASN183 4.8 56.3 1.0

Sodium binding site 3 out of 6 in 6ndf

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


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

b:50.6
occ:1.00
 O3 H:SO4202 2.4 89.9 1.0
OG I:SER184 2.7 59.0 1.0
N I:SER184 3.5 62.2 1.0
SR I:SR401 3.6 97.2 1.0
CB I:SER184 3.7 53.5 1.0
S H:SO4202 3.8 0.2 1.0
OG I:SER182 3.8 47.5 1.0
N I:ASN183 3.9 53.0 1.0
O I:GLY247 3.9 54.8 1.0
CB I:SER182 3.9 45.2 1.0
CA I:SER184 4.2 53.9 1.0
CB I:ASN183 4.3 57.2 1.0
O2 H:SO4202 4.3 91.3 1.0
CA I:ASN183 4.4 54.1 1.0
C I:ASN183 4.5 59.4 1.0
O4 H:SO4202 4.5 0.0 1.0
CA I:ASP248 4.5 42.8 1.0
C I:SER182 4.6 46.0 1.0
O1 H:SO4202 4.7 75.0 1.0
CA I:SER182 4.8 44.4 1.0
C I:GLY247 4.9 50.8 1.0
C I:ASP248 5.0 50.1 1.0

Sodium binding site 4 out of 6 in 6ndf

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


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

b:46.7
occ:1.00
 O3 K:SO4202 2.3 82.3 1.0
OG L:SER184 3.3 62.0 1.0
N L:SER184 3.4 63.8 1.0
SR L:SR401 3.6 0.8 1.0
OG L:SER182 3.6 64.1 1.0
S K:SO4202 3.7 1.0 1.0
N L:ASN183 3.9 60.7 1.0
CB L:SER184 3.9 61.7 1.0
O L:GLY247 4.0 65.5 1.0
CB L:SER182 4.1 50.7 1.0
CB L:ASN183 4.2 64.0 1.0
CA L:SER184 4.2 63.4 1.0
CA L:ASN183 4.3 62.8 1.0
O4 K:SO4202 4.3 0.2 1.0
O1 K:SO4202 4.4 92.2 1.0
C L:ASN183 4.4 68.7 1.0
O2 K:SO4202 4.6 82.4 1.0
C L:SER182 4.7 54.0 1.0
CA L:ASP248 4.7 61.9 1.0
ND2 L:ASN183 4.9 61.0 1.0
CG L:ASN183 4.9 68.2 1.0
CA L:SER182 5.0 49.9 1.0
C L:ASP248 5.0 62.5 1.0

Sodium binding site 5 out of 6 in 6ndf

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


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

b:65.5
occ:1.00
 O4 N:SO4201 2.1 0.2 1.0
S N:SO4201 3.4 0.0 1.0
O O:GLY247 3.6 54.2 1.0
O3 N:SO4201 3.6 0.3 1.0
SR O:SR401 3.8 0.1 1.0
CB O:SER182 4.0 63.3 1.0
OG O:SER182 4.0 68.2 1.0
O O:ASP248 4.0 84.8 1.0
CA O:ASP248 4.1 64.5 1.0
OG O:SER184 4.1 70.0 1.0
N O:SER184 4.1 66.5 1.0
C O:ASP248 4.2 69.8 1.0
N O:ASN183 4.3 60.1 1.0
O2 N:SO4201 4.3 97.3 1.0
CB O:SER184 4.3 79.6 1.0
O1 N:SO4201 4.3 0.9 1.0
CB O:ASN183 4.5 60.5 1.0
C O:GLY247 4.5 61.6 1.0
N O:ASP248 4.7 65.8 1.0
CA O:SER184 4.8 68.3 1.0
CA O:ASN183 4.8 55.0 1.0
CG O:ASN183 4.9 56.5 1.0
C O:SER182 4.9 61.9 1.0
N O:LEU249 4.9 53.1 1.0
CA O:SER182 5.0 63.7 1.0

Sodium binding site 6 out of 6 in 6ndf

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


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

b:72.4
occ:1.00
 O3 Q:SO4202 2.2 0.7 1.0
O R:GLY247 3.6 54.6 1.0
SR R:SR401 3.6 0.7 1.0
S Q:SO4202 3.6 1.0 1.0
N R:SER184 3.7 63.4 1.0
OG R:SER182 3.8 67.7 1.0
N R:ASN183 3.9 61.3 1.0
CB R:SER182 4.0 63.7 1.0
CB R:SER184 4.0 76.8 1.0
OG R:SER184 4.0 81.9 1.0
O2 Q:SO4202 4.1 0.5 1.0
CB R:ASN183 4.2 58.1 1.0
CA R:ASP248 4.3 65.4 1.0
O1 Q:SO4202 4.3 0.7 1.0
CA R:SER184 4.4 66.7 1.0
O4 Q:SO4202 4.4 0.0 1.0
CA R:ASN183 4.4 52.6 1.0
C R:ASN183 4.5 57.5 1.0
C R:GLY247 4.6 64.5 1.0
C R:ASP248 4.6 71.7 1.0
O R:ASP248 4.6 95.5 1.0
C R:SER182 4.7 61.2 1.0
CG R:ASN183 4.7 54.3 1.0
ND2 R:ASN183 4.9 65.0 1.0
N R:ASP248 4.9 70.1 1.0
CA R:SER182 4.9 61.1 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium Bound To Be Published.
Page generated: Mon Aug 18 06:12:43 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy