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Yttrium 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:

Chlorine (Cl) 9 atoms
Sodium (Na) 6 atoms

Yttrium Binding Sites:

The binding sites of Yttrium 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 Yttrium atom.
In total 6 binding sites of Yttrium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Yttrium Bound, PDB code: 6ndg:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6;

Yttrium binding site 1 out of 6 in 6ndg

Go back to Yttrium Binding Sites List in 6ndg
Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:93.2
occ:1.00
OG C:SER184 1.9 42.6 1.0
OD1 C:ASP283 2.3 40.8 1.0
OG C:SER182 2.8 47.9 1.0
CB C:SER184 3.1 42.2 1.0
CG C:ASP283 3.2 48.6 1.0
O3 B:SO4201 3.3 83.8 1.0
O4 B:SO4201 3.4 0.1 1.0
NA C:NA402 3.4 32.0 1.0
OD2 C:ASP283 3.5 44.4 1.0
S B:SO4201 3.7 1.0 1.0
O C:ASP283 3.8 54.4 1.0
OD2 C:ASP180 3.8 59.2 1.0
OG1 C:THR250 3.9 54.4 1.0
O1 B:SO4201 3.9 64.7 1.0
CB C:SER182 4.0 41.0 1.0
C C:ASP283 4.2 51.4 1.0
CA C:SER184 4.3 45.6 1.0
CA C:GLY284 4.4 52.3 1.0
N C:SER184 4.4 51.7 1.0
CB C:ASP283 4.6 49.2 1.0
N C:GLY284 4.6 49.3 1.0
CG C:ASP180 4.7 58.8 1.0
OD1 C:ASP180 4.7 60.6 1.0
CA C:ASP283 4.9 47.1 1.0

Yttrium binding site 2 out of 6 in 6ndg

Go back to Yttrium Binding Sites List in 6ndg
Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:78.9
occ:1.00
OG F:SER184 2.4 68.6 1.0
OG F:SER182 2.5 31.3 1.0
OD1 F:ASP283 2.8 48.5 1.0
O4 E:SO4203 3.0 87.8 1.0
NA F:NA402 3.3 27.7 1.0
O3 E:SO4203 3.5 90.8 1.0
CB F:SER182 3.6 34.0 1.0
OD2 F:ASP180 3.6 44.4 1.0
CB F:SER184 3.6 55.8 1.0
S E:SO4203 3.7 0.1 1.0
OG1 F:THR250 3.7 48.1 1.0
CG F:ASP283 3.8 58.5 1.0
O F:ASP283 4.0 38.1 1.0
O2 E:SO4203 4.1 59.7 1.0
C F:ASP283 4.2 46.6 1.0
CA F:GLY284 4.3 50.0 1.0
OD2 F:ASP283 4.4 68.2 1.0
CG F:ASP180 4.4 37.9 1.0
OD1 F:ASP180 4.4 32.8 1.0
N F:GLY284 4.4 44.9 1.0
N F:SER184 4.7 54.8 1.0
CA F:SER184 4.8 51.9 1.0
CA F:SER182 4.9 33.3 1.0
CA F:ASP283 4.9 45.4 1.0
CB F:ASP283 4.9 54.4 1.0
CB F:THR250 5.0 55.8 1.0

Yttrium binding site 3 out of 6 in 6ndg

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Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:79.8
occ:1.00
OG I:SER184 2.3 74.6 1.0
OG I:SER182 2.5 30.5 1.0
O4 H:SO4202 2.6 95.2 1.0
OD1 I:ASP283 2.8 48.9 1.0
NA I:NA402 3.3 23.9 1.0
S H:SO4202 3.5 98.8 1.0
O3 H:SO4202 3.5 90.0 1.0
OD2 I:ASP180 3.6 37.0 1.0
CB I:SER184 3.6 57.4 1.0
CB I:SER182 3.6 34.7 1.0
OG1 I:THR250 3.7 50.9 1.0
O2 H:SO4202 3.9 55.8 1.0
CG I:ASP283 3.9 54.0 1.0
O I:ASP283 4.0 37.2 1.0
C I:ASP283 4.1 42.2 1.0
CA I:GLY284 4.3 42.2 1.0
N I:GLY284 4.3 38.1 1.0
CG I:ASP180 4.4 35.0 1.0
OD1 I:ASP180 4.4 31.3 1.0
OD2 I:ASP283 4.6 62.9 1.0
N I:SER184 4.7 52.0 1.0
CA I:SER184 4.7 51.0 1.0
O1 H:SO4202 4.8 75.5 1.0
CA I:ASP283 4.9 43.5 1.0
CA I:SER182 4.9 32.5 1.0
CB I:ASP283 4.9 49.4 1.0
CB I:THR250 4.9 54.5 1.0

Yttrium binding site 4 out of 6 in 6ndg

Go back to Yttrium Binding Sites List in 6ndg
Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:90.2
occ:1.00
OG L:SER184 2.0 36.9 1.0
OD1 L:ASP283 2.2 42.0 1.0
OG L:SER182 2.8 51.8 1.0
CB L:SER184 3.1 39.9 1.0
CG L:ASP283 3.2 49.6 1.0
NA L:NA402 3.3 32.9 1.0
OD2 L:ASP283 3.4 47.3 1.0
O4 K:SO4202 3.5 97.2 1.0
O3 K:SO4202 3.6 90.2 1.0
O L:ASP283 3.7 55.7 1.0
OD2 L:ASP180 3.9 62.1 1.0
OG1 L:THR250 3.9 50.9 1.0
S K:SO4202 3.9 0.8 1.0
O1 K:SO4202 4.0 78.4 1.0
CB L:SER182 4.0 42.4 1.0
C L:ASP283 4.1 56.5 1.0
CA L:GLY284 4.3 55.5 1.0
CA L:SER184 4.4 42.4 1.0
N L:SER184 4.5 48.9 1.0
CB L:ASP283 4.5 48.8 1.0
N L:GLY284 4.5 53.7 1.0
CG L:ASP180 4.7 58.4 1.0
OD1 L:ASP180 4.7 63.7 1.0
CA L:ASP283 4.9 48.0 1.0

Yttrium binding site 5 out of 6 in 6ndg

Go back to Yttrium Binding Sites List in 6ndg
Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:1.0
occ:1.00
OG O:SER184 2.3 48.5 1.0
OG O:SER182 2.6 57.0 1.0
OD1 O:ASP283 2.7 41.6 1.0
O4 N:SO4201 2.9 0.7 1.0
CB O:SER184 3.3 55.6 1.0
NA O:NA402 3.4 43.2 1.0
OG1 O:THR250 3.5 37.2 1.0
CG O:ASP283 3.7 46.9 1.0
CB O:SER182 3.8 55.9 1.0
OD2 O:ASP180 3.8 61.0 1.0
S N:SO4201 3.9 0.7 1.0
OD2 O:ASP283 4.0 60.4 1.0
O2 N:SO4201 4.1 0.4 1.0
O1 N:SO4201 4.2 87.9 1.0
CA O:GLY284 4.3 63.6 1.0
OD1 O:ASP180 4.3 58.5 1.0
O O:ASP283 4.4 78.0 1.0
CG O:ASP180 4.5 52.0 1.0
C O:ASP283 4.5 61.8 1.0
CA O:SER184 4.5 54.2 1.0
N O:SER184 4.5 46.8 1.0
N O:GLY284 4.6 57.5 1.0
CB O:THR250 4.9 36.1 1.0
CB O:ASP283 5.0 43.2 1.0
CA O:SER182 5.0 56.9 1.0

Yttrium binding site 6 out of 6 in 6ndg

Go back to Yttrium Binding Sites List in 6ndg
Yttrium 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 Yttrium with other atoms in the Y 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:Y401

b:0.5
occ:1.00
OG R:SER184 2.3 44.6 1.0
OG R:SER182 2.6 59.5 1.0
OD1 R:ASP283 2.7 43.1 1.0
O4 Q:SO4202 3.2 0.9 1.0
OG1 R:THR250 3.4 38.5 1.0
NA R:NA404 3.4 35.6 1.0
CB R:SER184 3.5 50.7 1.0
O3 Q:SO4202 3.7 96.0 1.0
CB R:SER182 3.8 51.7 1.0
CG R:ASP283 3.8 49.1 1.0
OD2 R:ASP180 3.8 64.0 1.0
S Q:SO4202 3.9 0.5 1.0
CA R:GLY284 4.2 61.6 1.0
OD1 R:ASP180 4.2 56.9 1.0
OD2 R:ASP283 4.2 60.5 1.0
O1 Q:SO4202 4.3 99.0 1.0
O R:ASP283 4.4 81.3 1.0
C R:ASP283 4.4 67.2 1.0
CG R:ASP180 4.4 54.1 1.0
N R:GLY284 4.5 59.6 1.0
N R:SER184 4.6 42.3 1.0
CA R:SER184 4.6 49.3 1.0
CB R:THR250 4.8 36.0 1.0
CA R:SER182 5.0 51.1 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: Wed Dec 16 02:41:20 2020

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