Calcium in PDB 6nd9: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium

Protein crystallography data

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium, PDB code: 6nd9 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) 48.06 / 2.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 131.044, 131.044, 251.245, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.2

Other elements in 6nd9:

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

Chlorine (Cl) 3 atoms
Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium (pdb code 6nd9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium, PDB code: 6nd9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:45.9
occ:1.00
OG C:SER184 1.9 30.4 1.0
OD1 C:ASP283 2.1 33.2 1.0
OG C:SER182 2.6 31.7 1.0
O4 C:SO4402 2.9 0.1 1.0
O3 C:SO4402 3.1 60.5 1.0
CB C:SER184 3.1 30.0 1.0
CG C:ASP283 3.1 38.4 1.0
NA C:NA403 3.4 28.6 1.0
S C:SO4402 3.5 91.6 1.0
OD2 C:ASP283 3.5 38.0 1.0
O C:ASP283 3.8 33.0 1.0
OD2 C:ASP180 3.8 48.5 1.0
OG1 C:THR250 3.8 41.1 1.0
CB C:SER182 3.8 35.1 1.0
O1 C:SO4402 3.9 52.6 1.0
C C:ASP283 4.1 33.5 1.0
CA C:GLY284 4.3 37.9 1.0
N C:GLY284 4.4 33.9 1.0
CA C:SER184 4.4 37.5 1.0
CB C:ASP283 4.5 38.7 1.0
N C:SER184 4.5 44.0 1.0
CG C:ASP180 4.6 45.3 1.0
OD1 C:ASP180 4.6 47.4 1.0
CA C:ASP283 4.7 33.3 1.0
O2 C:SO4402 4.8 47.1 1.0

Calcium binding site 2 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:33.4
occ:1.00
OG F:SER184 2.2 30.4 1.0
O4 E:SO4203 2.3 96.5 1.0
OD1 F:ASP283 2.3 49.0 1.0
OG F:SER182 2.4 25.7 1.0
NA F:NA402 3.3 21.2 1.0
CG F:ASP283 3.4 38.1 1.0
CB F:SER184 3.4 27.8 1.0
S E:SO4203 3.4 91.0 1.0
O3 E:SO4203 3.5 65.6 1.0
OD2 F:ASP180 3.6 40.8 1.0
CB F:SER182 3.6 30.5 1.0
OG1 F:THR250 3.6 32.0 1.0
OD2 F:ASP283 3.9 42.3 1.0
O F:ASP283 4.1 31.0 1.0
C F:ASP283 4.2 30.5 1.0
O2 E:SO4203 4.2 46.2 1.0
CA F:GLY284 4.3 31.3 1.0
N F:GLY284 4.4 29.5 1.0
OD1 F:ASP180 4.4 41.5 1.0
CG F:ASP180 4.4 36.9 1.0
O1 E:SO4203 4.5 51.1 1.0
CA F:SER184 4.6 28.9 1.0
N F:SER184 4.6 38.1 1.0
CB F:ASP283 4.7 38.0 1.0
CA F:SER182 4.9 27.9 1.0
CA F:ASP283 4.9 34.1 1.0
CB F:THR250 5.0 35.1 1.0

Calcium binding site 3 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:34.3
occ:1.00
OG I:SER184 2.1 36.8 1.0
OD1 I:ASP283 2.3 51.5 1.0
O4 H:SO4202 2.3 83.7 1.0
OG I:SER182 2.4 27.0 1.0
NA I:NA402 3.2 26.9 1.0
CB I:SER184 3.4 30.3 1.0
CG I:ASP283 3.4 40.9 1.0
S H:SO4202 3.4 94.9 1.0
O3 H:SO4202 3.5 68.0 1.0
CB I:SER182 3.6 29.5 1.0
OD2 I:ASP180 3.6 38.6 1.0
OG1 I:THR250 3.6 40.5 1.0
OD2 I:ASP283 3.9 39.8 1.0
O I:ASP283 4.1 34.7 1.0
O2 H:SO4202 4.1 47.1 1.0
C I:ASP283 4.2 34.6 1.0
CA I:GLY284 4.3 35.6 1.0
N I:GLY284 4.4 34.9 1.0
OD1 I:ASP180 4.4 39.0 1.0
CG I:ASP180 4.4 36.6 1.0
CA I:SER184 4.5 30.2 1.0
O1 H:SO4202 4.6 51.6 1.0
N I:SER184 4.6 39.1 1.0
CB I:ASP283 4.7 41.2 1.0
CA I:SER182 4.9 26.0 1.0
CA I:ASP283 4.9 37.0 1.0

Calcium binding site 4 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca401

b:43.7
occ:1.00
OG L:SER184 1.9 33.0 1.0
OD1 L:ASP283 2.1 33.4 1.0
OG L:SER182 2.6 34.4 1.0
CG L:ASP283 3.1 35.6 1.0
CB L:SER184 3.1 30.7 1.0
O3 L:SO4402 3.2 59.0 1.0
NA L:NA403 3.3 26.7 1.0
O4 L:SO4402 3.4 86.1 1.0
OD2 L:ASP283 3.5 37.7 1.0
S L:SO4402 3.7 92.5 1.0
O L:ASP283 3.8 31.9 1.0
OD2 L:ASP180 3.8 47.2 1.0
O1 L:SO4402 3.8 60.9 1.0
CB L:SER182 3.8 35.4 1.0
OG1 L:THR250 3.9 39.9 1.0
C L:ASP283 4.1 34.6 1.0
CA L:GLY284 4.3 38.2 1.0
CA L:SER184 4.4 36.6 1.0
N L:GLY284 4.4 34.1 1.0
CB L:ASP283 4.4 37.9 1.0
N L:SER184 4.5 44.2 1.0
CG L:ASP180 4.6 45.8 1.0
OD1 L:ASP180 4.6 48.3 1.0
CA L:ASP283 4.7 34.7 1.0

Calcium binding site 5 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca401

b:46.6
occ:1.00
OG O:SER184 2.0 40.7 1.0
OD1 O:ASP283 2.3 34.4 1.0
OG O:SER182 2.5 50.2 1.0
O4 N:SO4201 2.7 72.6 1.0
CB O:SER184 3.3 43.2 1.0
NA O:NA402 3.3 26.6 1.0
CG O:ASP283 3.3 37.1 1.0
OG1 O:THR250 3.6 33.9 1.0
CB O:SER182 3.7 44.8 1.0
OD2 O:ASP180 3.7 49.7 1.0
OD2 O:ASP283 3.8 53.3 1.0
S N:SO4201 3.9 91.2 1.0
O O:ASP283 4.0 58.1 1.0
C O:ASP283 4.1 45.1 1.0
CA O:GLY284 4.2 48.6 1.0
O2 N:SO4201 4.3 72.5 1.0
O1 N:SO4201 4.3 68.2 1.0
N O:GLY284 4.3 42.9 1.0
OD1 O:ASP180 4.5 47.6 1.0
CG O:ASP180 4.5 41.5 1.0
CA O:SER184 4.5 37.8 1.0
N O:SER184 4.6 38.8 1.0
CB O:ASP283 4.6 33.3 1.0
CA O:ASP283 4.8 39.4 1.0
CA O:SER182 5.0 46.3 1.0

Calcium binding site 6 out of 6 in 6nd9

Go back to Calcium Binding Sites List in 6nd9
Calcium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca401

b:56.1
occ:1.00
OG R:SER184 2.0 40.3 1.0
OD1 R:ASP283 2.3 39.3 1.0
OG R:SER182 2.5 44.0 1.0
O4 Q:SO4202 2.8 0.2 1.0
O3 Q:SO4202 3.1 55.2 1.0
CB R:SER184 3.3 43.4 1.0
CG R:ASP283 3.4 39.9 1.0
S Q:SO4202 3.5 99.4 1.0
OG1 R:THR250 3.6 34.9 1.0
CB R:SER182 3.6 38.2 1.0
OD2 R:ASP180 3.7 48.1 1.0
OD2 R:ASP283 3.8 51.8 1.0
O R:ASP283 4.1 56.2 1.0
O1 Q:SO4202 4.2 62.7 1.0
C R:ASP283 4.2 45.6 1.0
CA R:GLY284 4.2 46.5 1.0
N R:GLY284 4.4 41.2 1.0
OD1 R:ASP180 4.5 42.0 1.0
CG R:ASP180 4.5 37.9 1.0
CA R:SER184 4.5 36.8 1.0
N R:SER184 4.5 41.0 1.0
CB R:ASP283 4.7 33.5 1.0
O2 Q:SO4202 4.7 57.2 1.0
CA R:ASP283 4.9 39.6 1.0
CA R:SER182 4.9 40.0 1.0

Reference:

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Calcium To Be Published.
Page generated: Sat Dec 12 07:22:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy