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Chromium in PDB 6ndc: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound, PDB code: 6ndc 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) 92.90 / 3.35
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.140, 131.140, 251.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.6

Other elements in 6ndc:

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

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

Chromium Binding Sites:

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

Chromium binding site 1 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cr401

b:52.6
occ:1.00
OG C:SER184 1.9 47.2 1.0
OD1 C:ASP283 2.7 57.1 1.0
OG C:SER182 2.8 35.3 1.0
O4 C:SO4402 2.9 0.3 1.0
CB C:SER184 2.9 42.0 1.0
O3 C:SO4402 3.2 82.3 1.0
CG C:ASP283 3.2 55.0 1.0
OD2 C:ASP283 3.3 56.0 1.0
S C:SO4402 3.4 96.2 1.0
O C:ASP283 3.6 31.1 1.0
O1 C:SO4402 3.7 78.5 1.0
CB C:SER182 3.9 39.1 1.0
NA C:NA403 3.9 31.6 1.0
OG1 C:THR250 3.9 38.5 1.0
OD2 C:ASP180 3.9 27.9 1.0
C C:ASP283 4.1 34.6 1.0
CA C:SER184 4.2 40.6 1.0
N C:SER184 4.3 41.1 1.0
CA C:GLY284 4.5 34.5 1.0
CB C:ASP283 4.5 48.5 1.0
N C:GLY284 4.6 32.0 1.0
CG C:ASP180 4.8 34.5 1.0
O2 C:SO4402 4.8 72.8 1.0
CA C:ASP283 4.9 39.1 1.0
OD1 C:ASP180 4.9 34.3 1.0

Chromium binding site 2 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cr402

b:47.4
occ:1.00
OG F:SER182 2.4 28.6 1.0
OG F:SER184 2.4 27.3 1.0
OD1 F:ASP283 2.7 42.7 1.0
O4 E:SO4202 2.8 81.6 1.0
CB F:SER182 3.4 30.1 1.0
OD2 F:ASP180 3.5 24.8 1.0
O3 E:SO4202 3.5 79.9 1.0
NA F:NA403 3.6 5.7 1.0
OG1 F:THR250 3.6 27.0 1.0
CB F:SER184 3.6 27.3 1.0
S E:SO4202 3.6 89.0 1.0
O F:ASP283 3.6 41.1 1.0
C F:ASP283 3.9 44.5 1.0
CG F:ASP283 3.9 50.7 1.0
O2 E:SO4202 4.0 70.0 1.0
OD1 F:ASP180 4.1 24.3 1.0
CG F:ASP180 4.2 25.7 1.0
CA F:GLY284 4.2 41.2 1.0
N F:GLY284 4.2 41.4 1.0
CA F:ASP283 4.7 44.6 1.0
CA F:SER182 4.7 30.2 1.0
CB F:ASP283 4.7 51.6 1.0
N F:SER184 4.8 31.3 1.0
CB F:THR250 4.8 33.3 1.0
CG2 F:THR250 4.8 35.6 1.0
CA F:SER184 4.8 28.7 1.0
OD2 F:ASP283 4.8 50.6 1.0
N F:ASP283 4.9 41.2 1.0
O1 E:SO4202 5.0 62.0 1.0

Chromium binding site 3 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cr402

b:44.2
occ:1.00
OG I:SER182 2.2 20.7 1.0
OG I:SER184 2.4 26.4 1.0
O4 H:SO4201 2.7 70.5 1.0
OD1 I:ASP283 2.8 58.8 1.0
CB I:SER182 3.3 22.6 1.0
OD2 I:ASP180 3.4 26.1 1.0
NA I:NA403 3.5 9.0 1.0
OG1 I:THR250 3.6 37.6 1.0
CB I:SER184 3.6 27.1 1.0
S H:SO4201 3.6 81.2 1.0
O3 H:SO4201 3.6 69.8 1.0
O I:ASP283 3.6 35.5 1.0
C I:ASP283 3.9 39.4 1.0
O2 H:SO4201 4.0 57.5 1.0
CG I:ASP283 4.1 54.5 1.0
N I:GLY284 4.1 37.6 1.0
CA I:GLY284 4.2 39.1 1.0
CG I:ASP180 4.2 24.7 1.0
OD1 I:ASP180 4.2 22.8 1.0
CA I:SER182 4.6 23.6 1.0
N I:SER184 4.7 31.3 1.0
CA I:SER184 4.7 28.2 1.0
CB I:THR250 4.8 42.8 1.0
CA I:ASP283 4.8 39.4 1.0
O1 H:SO4201 4.9 61.2 1.0
CG2 I:THR250 4.9 45.9 1.0
OD2 I:ASP283 4.9 52.8 1.0
CB I:ASP283 4.9 49.9 1.0
C I:SER182 4.9 25.1 1.0
N I:ASP283 5.0 35.0 1.0

Chromium binding site 4 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cr401

b:53.6
occ:1.00
OG L:SER184 2.0 32.5 1.0
OD1 L:ASP283 2.6 57.4 1.0
OG L:SER182 3.0 44.0 1.0
NA L:NA402 3.0 38.1 1.0
CB L:SER184 3.1 30.2 1.0
CG L:ASP283 3.2 54.3 1.0
O3 K:SO4202 3.3 84.7 1.0
OD2 L:ASP283 3.3 53.1 1.0
O4 K:SO4202 3.3 1.0 1.0
O L:ASP283 3.5 38.2 1.0
S K:SO4202 3.7 0.6 1.0
O1 K:SO4202 3.7 93.9 1.0
OG1 L:THR250 3.9 47.1 1.0
C L:ASP283 4.0 41.2 1.0
OD2 L:ASP180 4.0 28.9 1.0
CB L:SER182 4.1 43.7 1.0
CA L:GLY284 4.3 48.0 1.0
CA L:SER184 4.4 31.1 1.0
N L:SER184 4.4 35.5 1.0
N L:GLY284 4.4 42.5 1.0
CB L:ASP283 4.6 51.5 1.0
CG L:ASP180 4.9 34.2 1.0
CA L:ASP283 4.9 42.2 1.0
OD1 L:ASP180 4.9 35.7 1.0

Chromium binding site 5 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cr401

b:76.7
occ:1.00
OG O:SER184 2.3 43.7 1.0
OD1 O:ASP283 2.4 41.6 1.0
O4 N:SO4201 2.5 0.7 1.0
OG O:SER182 2.8 39.7 1.0
CG O:ASP283 3.3 43.1 1.0
CB O:SER184 3.4 45.8 1.0
OG1 O:THR250 3.5 34.0 1.0
OD2 O:ASP283 3.6 41.3 1.0
S N:SO4201 3.7 95.5 1.0
OD2 O:ASP180 3.8 45.6 1.0
NA O:NA402 3.9 32.0 1.0
CB O:SER182 4.0 39.4 1.0
O2 N:SO4201 4.0 0.2 1.0
CA O:GLY284 4.1 51.1 1.0
O1 N:SO4201 4.1 89.5 1.0
N O:GLY284 4.2 46.2 1.0
C O:ASP283 4.4 47.0 1.0
OD1 O:ASP180 4.5 44.6 1.0
CG O:ASP180 4.5 43.8 1.0
CA O:SER184 4.6 44.0 1.0
O O:ASP283 4.7 45.7 1.0
CB O:ASP283 4.7 45.4 1.0
N O:SER184 4.7 42.1 1.0
O3 N:SO4201 4.8 84.5 1.0
CB O:THR250 4.9 34.5 1.0
CA O:ASP283 5.0 45.0 1.0

Chromium binding site 6 out of 6 in 6ndc

Go back to Chromium Binding Sites List in 6ndc
Chromium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound


Mono view


Stereo pair view

A full contact list of Chromium with other atoms in the Cr binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cr401

b:76.3
occ:1.00
OG R:SER184 2.1 45.5 1.0
OD1 R:ASP283 2.4 43.7 1.0
OG R:SER182 2.6 45.3 1.0
O4 Q:SO4202 2.8 0.3 1.0
CB R:SER184 3.3 45.9 1.0
O3 Q:SO4202 3.4 96.3 1.0
CG R:ASP283 3.4 44.1 1.0
OG1 R:THR250 3.5 22.3 1.0
S Q:SO4202 3.6 0.4 1.0
NA R:NA404 3.7 35.2 1.0
OD2 R:ASP283 3.8 43.2 1.0
CB R:SER182 3.9 44.1 1.0
OD2 R:ASP180 3.9 46.6 1.0
CA R:GLY284 4.1 46.4 1.0
O1 Q:SO4202 4.3 90.1 1.0
N R:GLY284 4.3 39.7 1.0
OD1 R:ASP180 4.4 44.2 1.0
C R:ASP283 4.4 39.2 1.0
CA R:SER184 4.5 41.4 1.0
O R:ASP283 4.5 38.7 1.0
CG R:ASP180 4.5 43.2 1.0
N R:SER184 4.5 37.7 1.0
CB R:ASP283 4.8 43.1 1.0
O2 Q:SO4202 4.8 0.5 1.0
CB R:THR250 4.9 26.8 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound To Be Published.
Page generated: Sun Dec 13 10:55:17 2020

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