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Sodium in PDB 6nde: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium, PDB code: 6nde 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) 48.57 / 3.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 132.351, 132.351, 254.244, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 36.9

Other elements in 6nde:

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

Praseodymium (Pr) 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 Prasedymium (pdb code 6nde). 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 Prasedymium, PDB code: 6nde:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6nde

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


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

b:66.7
occ:1.00
O3 B:SO4201 2.4 0.1 1.0
OG C:SER184 3.4 92.7 1.0
O C:GLY247 3.6 90.0 1.0
N C:ASN183 3.7 97.9 1.0
S B:SO4201 3.7 0.4 1.0
N C:SER184 3.7 97.3 1.0
CB C:SER182 3.8 96.0 1.0
PR C:PR401 4.0 0.3 1.0
OG C:SER182 4.0 0.2 1.0
O1 B:SO4201 4.0 0.4 1.0
CB C:ASN183 4.2 0.1 1.0
CA C:ASN183 4.3 0.6 1.0
CB C:SER184 4.3 97.0 1.0
CA C:ASP248 4.3 98.1 1.0
C C:ASN183 4.3 0.1 1.0
O2 B:SO4201 4.5 1.0 1.0
CA C:SER184 4.5 96.3 1.0
C C:SER182 4.5 0.9 1.0
C C:GLY247 4.5 88.0 1.0
O4 B:SO4201 4.6 0.9 1.0
C C:ASP248 4.7 0.1 1.0
CG C:ASN183 4.7 0.2 1.0
CA C:SER182 4.7 92.8 1.0
O C:ASP248 4.8 0.8 1.0
N C:ASP248 4.9 71.0 1.0

Sodium binding site 2 out of 6 in 6nde

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


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

b:75.7
occ:1.00
OG F:SER184 2.6 0.3 1.0
O3 E:SO4203 2.9 0.4 1.0
N F:SER184 3.7 0.9 1.0
CB F:SER184 3.8 0.8 1.0
N F:ASN183 3.9 75.1 1.0
CB F:ASN183 3.9 0.5 1.0
O F:GLY247 3.9 92.2 1.0
PR F:PR401 4.1 0.8 1.0
CA F:ASN183 4.3 97.0 1.0
S E:SO4203 4.3 0.3 1.0
CA F:SER184 4.3 0.4 1.0
CB F:SER182 4.4 0.7 1.0
C F:ASN183 4.4 97.5 1.0
OG F:SER182 4.5 97.3 1.0
CA F:ASP248 4.5 83.5 1.0
CG F:ASN183 4.8 0.2 1.0
O2 E:SO4203 4.8 0.6 1.0
C F:SER182 4.9 73.8 1.0
OH E:TYR94 4.9 61.7 1.0
O F:ASP248 5.0 91.1 1.0
C F:ASP248 5.0 85.1 1.0
C F:GLY247 5.0 95.6 1.0
O4 E:SO4203 5.0 0.4 1.0

Sodium binding site 3 out of 6 in 6nde

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


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

b:75.8
occ:1.00
OG I:SER184 2.6 0.1 1.0
O3 H:SO4202 2.9 0.4 1.0
N I:SER184 3.7 0.7 1.0
CB I:SER184 3.8 0.7 1.0
CB I:ASN183 3.9 0.4 1.0
O I:GLY247 4.0 80.7 1.0
N I:ASN183 4.1 79.7 1.0
PR I:PR401 4.2 0.2 1.0
S H:SO4202 4.3 0.2 1.0
CA I:SER184 4.3 98.2 1.0
CA I:ASN183 4.3 96.2 1.0
C I:ASN183 4.4 95.8 1.0
OG I:SER182 4.5 97.8 1.0
CA I:ASP248 4.5 86.2 1.0
CB I:SER182 4.6 91.8 1.0
CG I:ASN183 4.8 95.0 1.0
OH H:TYR94 4.8 64.1 1.0
O2 H:SO4202 4.8 0.4 1.0
O4 H:SO4202 5.0 97.9 1.0
O I:ASP248 5.0 93.7 1.0

Sodium binding site 4 out of 6 in 6nde

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


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

b:55.8
occ:1.00
O3 K:SO4202 2.5 0.1 1.0
OG L:SER184 3.4 92.3 1.0
O L:GLY247 3.6 96.2 1.0
N L:ASN183 3.6 1.0 1.0
N L:SER184 3.6 90.8 1.0
S K:SO4202 3.8 0.5 1.0
CB L:SER182 3.8 0.4 1.0
OG L:SER182 3.9 0.3 1.0
PR L:PR401 4.0 0.8 1.0
O1 K:SO4202 4.0 0.1 1.0
CB L:ASN183 4.2 0.2 1.0
CA L:ASN183 4.2 0.0 1.0
CB L:SER184 4.2 92.6 1.0
C L:ASN183 4.3 0.2 1.0
CA L:ASP248 4.4 98.6 1.0
C L:SER182 4.4 0.8 1.0
CA L:SER184 4.5 97.6 1.0
O2 K:SO4202 4.6 0.9 1.0
C L:GLY247 4.6 92.3 1.0
CA L:SER182 4.7 98.8 1.0
CG L:ASN183 4.7 0.2 1.0
O4 K:SO4202 4.8 0.7 1.0
C L:ASP248 4.8 0.5 1.0
O L:ASP248 4.9 0.8 1.0
N L:ASP248 5.0 74.1 1.0

Sodium binding site 5 out of 6 in 6nde

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


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

b:73.5
occ:1.00
O4 N:SO4201 2.0 0.2 1.0
S N:SO4201 3.5 0.6 1.0
OG O:SER184 3.7 0.1 1.0
O O:GLY247 3.8 84.5 1.0
O O:ASP248 4.0 0.9 1.0
PR O:PR401 4.1 0.6 1.0
CA O:ASP248 4.1 0.2 1.0
O3 N:SO4201 4.1 0.8 1.0
O1 N:SO4201 4.1 0.0 1.0
CB O:SER182 4.2 0.1 1.0
C O:ASP248 4.2 0.9 1.0
O2 N:SO4201 4.3 0.5 1.0
CB O:SER184 4.4 0.6 1.0
OG O:SER182 4.4 0.2 1.0
N O:SER184 4.4 98.8 1.0
N O:ASN183 4.4 84.9 1.0
CB O:ASN183 4.7 89.7 1.0
C O:GLY247 4.7 96.5 1.0
N O:ASP248 4.9 89.1 1.0
OG1 O:THR250 4.9 64.9 1.0
N O:LEU249 5.0 0.1 1.0

Sodium binding site 6 out of 6 in 6nde

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


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

b:67.8
occ:1.00
O3 Q:SO4202 2.2 0.1 1.0
S Q:SO4202 3.6 0.8 1.0
O R:GLY247 3.7 92.7 1.0
O R:ASP248 3.9 0.2 1.0
CA R:ASP248 4.0 0.2 1.0
PR R:PR401 4.1 0.5 1.0
OG R:SER184 4.1 0.2 1.0
CB R:SER182 4.1 0.5 1.0
C R:ASP248 4.1 0.9 1.0
O1 Q:SO4202 4.2 0.0 1.0
N R:SER184 4.2 83.4 1.0
N R:ASN183 4.3 86.1 1.0
O2 Q:SO4202 4.4 0.6 1.0
CB R:SER184 4.4 0.9 1.0
OG R:SER182 4.4 0.3 1.0
O4 Q:SO4202 4.4 0.7 1.0
CB R:ASN183 4.5 92.1 1.0
C R:GLY247 4.6 0.7 1.0
N R:ASP248 4.8 95.6 1.0
CA R:ASN183 4.8 83.6 1.0
CA R:SER184 4.9 0.5 1.0
C R:SER182 5.0 0.7 1.0
N R:LEU249 5.0 0.5 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Prasedymium Bound To Be Published.
Page generated: Tue Dec 15 12:38:40 2020

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