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Barium in PDB 6nd8: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium, PDB code: 6nd8 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) 45.64 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.134, 131.134, 251.522, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 30.6

Other elements in 6nd8:

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

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

Barium Binding Sites:

The binding sites of Barium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium (pdb code 6nd8). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium, PDB code: 6nd8:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba401

b:0.2
occ:1.00
OG C:SER184 2.2 49.9 1.0
OD1 C:ASP283 2.5 44.8 1.0
OG C:SER182 2.8 40.1 1.0
CG C:ASP283 3.4 44.6 1.0
O2 B:SO4201 3.4 67.6 1.0
CB C:SER184 3.4 42.5 1.0
NA C:NA402 3.5 25.0 1.0
OD2 C:ASP283 3.6 39.4 1.0
O4 B:SO4201 3.7 97.8 1.0
OG1 C:THR250 3.9 38.1 1.0
S B:SO4201 3.9 95.6 1.0
OD2 C:ASP180 4.0 46.9 1.0
CB C:SER182 4.0 37.0 1.0
O C:ASP283 4.1 30.0 1.0
O1 B:SO4201 4.1 61.6 1.0
C C:ASP283 4.3 35.1 1.0
CA C:GLY284 4.3 38.8 1.0
N C:SER184 4.5 48.2 1.0
CA C:SER184 4.5 47.8 1.0
N C:GLY284 4.5 34.9 1.0
OD1 C:ASP180 4.7 39.6 1.0
CG C:ASP180 4.7 43.3 1.0
CB C:ASP283 4.7 41.2 1.0

Barium binding site 2 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ba401

b:99.2
occ:1.00
OG F:SER184 2.6 44.5 1.0
OG F:SER182 2.7 33.0 1.0
OD1 F:ASP283 3.1 43.9 1.0
O1 E:SO4203 3.3 48.0 1.0
O2 E:SO4203 3.3 73.0 1.0
NA F:NA402 3.6 26.2 1.0
OD2 F:ASP180 3.8 32.2 1.0
S E:SO4203 3.8 81.6 1.0
OG1 F:THR250 3.8 35.8 1.0
CB F:SER182 3.9 32.4 1.0
CB F:SER184 3.9 33.3 1.0
CG F:ASP283 3.9 45.5 1.0
O F:ASP283 4.0 29.4 1.0
C F:ASP283 4.1 32.2 1.0
O4 E:SO4203 4.2 38.1 1.0
CA F:GLY284 4.2 33.9 1.0
N F:GLY284 4.2 29.3 1.0
OD2 F:ASP283 4.4 53.0 1.0
OD1 F:ASP180 4.5 41.0 1.0
CG F:ASP180 4.5 38.2 1.0
CA F:ASP283 4.8 36.9 1.0
N F:SER184 4.9 38.7 1.0
CB F:ASP283 4.9 40.4 1.0
N F:ASP283 5.0 36.4 1.0
CA F:SER184 5.0 36.8 1.0

Barium binding site 3 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ba401

b:0.6
occ:1.00
OG I:SER184 2.5 51.8 1.0
OG I:SER182 2.7 34.9 1.0
OD1 I:ASP283 3.0 42.4 1.0
O1 H:SO4202 3.1 82.4 1.0
O3 H:SO4202 3.3 54.9 1.0
NA I:NA402 3.5 28.2 1.0
S H:SO4202 3.8 91.5 1.0
CB I:SER184 3.8 35.6 1.0
OD2 I:ASP180 3.8 32.9 1.0
CB I:SER182 3.9 32.9 1.0
CG I:ASP283 3.9 42.3 1.0
OG1 I:THR250 3.9 39.1 1.0
O I:ASP283 4.1 33.4 1.0
C I:ASP283 4.1 33.4 1.0
N I:GLY284 4.2 31.4 1.0
O2 H:SO4202 4.3 43.5 1.0
CA I:GLY284 4.3 37.6 1.0
OD2 I:ASP283 4.5 49.7 1.0
OD1 I:ASP180 4.6 37.9 1.0
CG I:ASP180 4.6 37.1 1.0
N I:SER184 4.8 41.1 1.0
CA I:SER184 4.9 38.4 1.0
CA I:ASP283 4.9 36.2 1.0
CB I:ASP283 4.9 39.6 1.0

Barium binding site 4 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ba401

b:0.5
occ:1.00
OG L:SER184 2.1 46.1 1.0
OD1 L:ASP283 2.5 40.8 1.0
OG L:SER182 2.8 45.0 1.0
CG L:ASP283 3.3 43.2 1.0
CB L:SER184 3.4 40.8 1.0
NA L:NA402 3.6 29.2 1.0
OD2 L:ASP283 3.6 42.1 1.0
O3 K:SO4202 3.6 72.1 1.0
O1 K:SO4202 3.9 89.8 1.0
O L:ASP283 3.9 27.2 1.0
OG1 L:THR250 3.9 38.5 1.0
OD2 L:ASP180 4.0 46.8 1.0
CB L:SER182 4.1 38.7 1.0
S K:SO4202 4.1 92.5 1.0
O4 K:SO4202 4.2 65.4 1.0
C L:ASP283 4.2 35.1 1.0
CA L:GLY284 4.3 39.3 1.0
N L:GLY284 4.5 34.8 1.0
N L:SER184 4.5 47.9 1.0
CA L:SER184 4.5 45.2 1.0
CB L:ASP283 4.7 38.9 1.0
OD1 L:ASP180 4.7 40.6 1.0
CG L:ASP180 4.7 43.6 1.0
CA L:ASP283 4.9 36.3 1.0

Barium binding site 5 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ba401

b:0.1
occ:1.00
OG O:SER184 2.4 57.5 1.0
OD1 O:ASP283 2.7 42.2 1.0
OG O:SER182 2.9 56.5 1.0
O1 N:SO4201 3.4 0.2 1.0
CB O:SER184 3.4 59.3 1.0
OG1 O:THR250 3.6 36.9 1.0
NA O:NA402 3.7 48.0 1.0
CG O:ASP283 3.8 47.9 1.0
OD2 O:ASP180 4.0 55.0 1.0
O2 N:SO4201 4.1 0.8 1.0
CB O:SER182 4.1 49.6 1.0
S N:SO4201 4.2 0.6 1.0
OD2 O:ASP283 4.3 62.8 1.0
CA O:GLY284 4.3 54.2 1.0
O4 N:SO4201 4.4 92.7 1.0
N O:GLY284 4.5 45.9 1.0
C O:ASP283 4.5 50.2 1.0
OD1 O:ASP180 4.6 50.8 1.0
N O:SER184 4.6 40.9 1.0
CA O:SER184 4.6 47.9 1.0
O O:ASP283 4.6 55.5 1.0
CG O:ASP180 4.6 48.9 1.0
CB O:THR250 5.0 36.3 1.0

Barium binding site 6 out of 6 in 6nd8

Go back to Barium Binding Sites List in 6nd8
Barium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ba401

b:0.3
occ:1.00
OG R:SER184 2.4 52.1 1.0
OD1 R:ASP283 2.8 39.3 1.0
OG R:SER182 3.0 51.6 1.0
O3 Q:SO4202 3.5 0.6 1.0
CB R:SER184 3.5 53.6 1.0
OG1 R:THR250 3.5 33.9 1.0
O4 Q:SO4202 3.6 0.4 1.0
NA R:NA404 3.7 48.8 1.0
CG R:ASP283 3.9 45.8 1.0
OD2 R:ASP180 3.9 58.0 1.0
S Q:SO4202 4.1 0.1 1.0
CB R:SER182 4.2 46.5 1.0
CA R:GLY284 4.2 51.4 1.0
N R:GLY284 4.3 46.8 1.0
C R:ASP283 4.4 52.6 1.0
OD2 R:ASP283 4.5 56.8 1.0
OD1 R:ASP180 4.5 47.2 1.0
O R:ASP283 4.6 56.1 1.0
CG R:ASP180 4.6 48.1 1.0
O1 Q:SO4202 4.6 0.9 1.0
N R:SER184 4.7 42.4 1.0
CA R:SER184 4.7 46.3 1.0
CB R:THR250 4.9 35.1 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium To Be Published.
Page generated: Wed Jul 10 15:59:48 2024

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