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Strontium 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:

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

Strontium Binding Sites:

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

Strontium binding site 1 out of 6 in 6ndf

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Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:0.2
occ:1.00
 OG C:SER184 2.1 59.6 1.0
OD1 C:ASP283 2.3 53.5 1.0
OG C:SER182 2.8 69.6 1.0
O3 B:SO4201 3.3 82.9 1.0
CG C:ASP283 3.3 65.1 1.0
CB C:SER184 3.4 61.7 1.0
O4 B:SO4201 3.4 0.2 1.0
OG1 C:THR250 3.7 62.5 1.0
NA C:NA402 3.7 46.0 1.0
OD2 C:ASP283 3.7 70.0 1.0
S B:SO4201 3.8 0.8 1.0
CB C:SER182 3.9 53.3 1.0
OD2 C:ASP180 3.9 71.9 1.0
O C:ASP283 4.0 59.8 1.0
CA C:GLY284 4.2 48.1 1.0
O1 B:SO4201 4.2 89.0 1.0
C C:ASP283 4.2 57.7 1.0
N C:GLY284 4.4 44.6 1.0
CA C:SER184 4.5 63.1 1.0
N C:SER184 4.6 63.6 1.0
OD1 C:ASP180 4.6 82.6 1.0
CB C:ASP283 4.7 61.7 1.0
CG C:ASP180 4.7 74.5 1.0
CA C:ASP283 4.9 56.1 1.0

Strontium binding site 2 out of 6 in 6ndf

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Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:95.8
occ:1.00
 OG F:SER184 2.4 67.0 1.0
OG F:SER182 2.6 43.8 1.0
OD1 F:ASP283 2.8 74.9 1.0
O4 E:SO4203 2.9 0.9 1.0
O3 E:SO4203 3.3 76.1 1.0
CB F:SER184 3.6 55.2 1.0
NA F:NA402 3.7 41.4 1.0
S E:SO4203 3.7 0.6 1.0
OD2 F:ASP180 3.7 64.1 1.0
CB F:SER182 3.7 43.5 1.0
CG F:ASP283 3.9 69.8 1.0
O F:ASP283 4.0 53.3 1.0
OG1 F:THR250 4.1 55.5 1.0
C F:ASP283 4.3 53.9 1.0
O2 E:SO4203 4.3 78.8 1.0
CA F:GLY284 4.3 59.2 1.0
OD2 F:ASP283 4.5 64.9 1.0
N F:GLY284 4.5 61.0 1.0
CG F:ASP180 4.6 64.8 1.0
OD1 F:ASP180 4.6 55.8 1.0
CA F:SER184 4.8 57.3 1.0
N F:SER184 4.8 64.7 1.0
O1 E:SO4203 4.9 63.3 1.0
CA F:ASP283 5.0 49.6 1.0
CB F:ASP283 5.0 63.2 1.0
CA F:SER182 5.0 45.2 1.0

Strontium binding site 3 out of 6 in 6ndf

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Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:97.2
occ:1.00
 OG I:SER184 2.4 59.0 1.0
OG I:SER182 2.7 47.5 1.0
OD1 I:ASP283 2.8 75.1 1.0
O4 H:SO4202 2.9 0.0 1.0
O3 H:SO4202 3.2 89.9 1.0
CB I:SER184 3.4 53.5 1.0
S H:SO4202 3.6 0.2 1.0
NA I:NA402 3.6 50.6 1.0
CB I:SER182 3.8 45.2 1.0
OD2 I:ASP180 3.8 60.2 1.0
O I:ASP283 3.9 51.2 1.0
OG1 I:THR250 4.0 61.7 1.0
CG I:ASP283 4.0 68.3 1.0
C I:ASP283 4.1 52.5 1.0
O2 H:SO4202 4.2 91.3 1.0
CA I:GLY284 4.3 52.3 1.0
N I:GLY284 4.4 53.5 1.0
CG I:ASP180 4.6 61.6 1.0
OD1 I:ASP180 4.6 55.1 1.0
OD2 I:ASP283 4.7 64.5 1.0
CA I:SER184 4.7 53.9 1.0
N I:SER184 4.9 62.2 1.0
O1 H:SO4202 4.9 75.0 1.0
CA I:ASP283 4.9 52.7 1.0
CB I:ASP283 5.0 63.1 1.0

Strontium binding site 4 out of 6 in 6ndf

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Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:0.8
occ:1.00
 OG L:SER184 2.2 62.0 1.0
OD1 L:ASP283 2.3 55.1 1.0
OG L:SER182 2.8 64.1 1.0
CG L:ASP283 3.3 64.6 1.0
O4 K:SO4202 3.4 0.2 1.0
CB L:SER184 3.4 61.7 1.0
O3 K:SO4202 3.5 82.3 1.0
NA L:NA402 3.6 46.7 1.0
OD2 L:ASP283 3.7 75.1 1.0
OG1 L:THR250 3.7 57.0 1.0
S K:SO4202 3.9 1.0 1.0
OD2 L:ASP180 4.0 66.3 1.0
CB L:SER182 4.0 50.7 1.0
O L:ASP283 4.1 56.9 1.0
O1 K:SO4202 4.2 92.2 1.0
CA L:GLY284 4.2 54.1 1.0
C L:ASP283 4.2 57.3 1.0
N L:GLY284 4.4 47.4 1.0
CA L:SER184 4.6 63.4 1.0
N L:SER184 4.6 63.8 1.0
CB L:ASP283 4.7 62.9 1.0
OD1 L:ASP180 4.7 78.5 1.0
CG L:ASP180 4.7 68.1 1.0
CA L:ASP283 4.9 56.5 1.0

Strontium binding site 5 out of 6 in 6ndf

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Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:0.1
occ:1.00
 OG O:SER184 2.1 70.0 1.0
OD1 O:ASP283 2.4 62.8 1.0
OG O:SER182 2.7 68.2 1.0
O4 N:SO4201 3.3 0.2 1.0
CB O:SER184 3.3 79.6 1.0
CG O:ASP283 3.3 58.1 1.0
OD2 O:ASP283 3.6 74.5 1.0
OG1 O:THR250 3.8 44.3 1.0
NA O:NA402 3.8 65.5 1.0
CB O:SER182 3.8 63.3 1.0
OD2 O:ASP180 3.9 70.7 1.0
S N:SO4201 4.3 0.0 1.0
O2 N:SO4201 4.3 97.3 1.0
OD1 O:ASP180 4.4 58.5 1.0
O O:ASP283 4.4 80.5 1.0
CA O:GLY284 4.5 65.9 1.0
C O:ASP283 4.5 67.7 1.0
CA O:SER184 4.5 68.3 1.0
CG O:ASP180 4.5 55.2 1.0
N O:SER184 4.6 66.5 1.0
N O:GLY284 4.6 66.2 1.0
CB O:ASP283 4.7 53.0 1.0
O1 N:SO4201 4.7 0.9 1.0
CA O:ASP283 5.0 53.0 1.0

Strontium binding site 6 out of 6 in 6ndf

Go back to Strontium Binding Sites List in 6ndf
Strontium 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 Strontium with other atoms in the Sr 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:Sr401

b:0.7
occ:1.00
 OG R:SER184 2.1 81.9 1.0
OD1 R:ASP283 2.5 52.4 1.0
OG R:SER182 2.6 67.7 1.0
CB R:SER184 3.2 76.8 1.0
O3 Q:SO4202 3.2 0.7 1.0
CG R:ASP283 3.6 61.4 1.0
NA R:NA404 3.6 72.4 1.0
CB R:SER182 3.8 63.7 1.0
OG1 R:THR250 3.9 42.9 1.0
OD2 R:ASP283 3.9 79.3 1.0
O4 Q:SO4202 4.0 0.0 1.0
OD2 R:ASP180 4.0 71.9 1.0
S Q:SO4202 4.1 1.0 1.0
CA R:SER184 4.3 66.7 1.0
O R:ASP283 4.4 84.5 1.0
N R:SER184 4.4 63.4 1.0
OD1 R:ASP180 4.5 70.6 1.0
C R:ASP283 4.5 68.9 1.0
O1 Q:SO4202 4.6 0.7 1.0
CA R:GLY284 4.6 68.2 1.0
CG R:ASP180 4.7 62.1 1.0
N R:GLY284 4.7 69.5 1.0
CB R:ASP283 4.9 58.0 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: Fri Oct 11 06:44:19 2024

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