Calcium in PDB 5ffo: Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta

Protein crystallography data

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo was solved by X.Dong, B.Zhao, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 3.49
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.440, 91.440, 131.030, 89.98, 86.25, 89.85
R / Rfree (%) 22.4 / 27.7

Other elements in 5ffo:

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta (pdb code 5ffo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 1 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:0.8
occ:1.00
O A:TYR290 2.2 0.2 1.0
OD1 A:ASP292 2.3 0.4 1.0
OD1 A:ASP284 2.3 0.5 1.0
OD2 A:ASP292 2.4 0.7 1.0
OD1 A:ASN286 2.4 0.1 1.0
OD1 A:ASP288 2.4 0.8 1.0
CG A:ASP292 2.6 0.8 1.0
CG A:ASP288 3.2 0.2 1.0
OD2 A:ASP288 3.2 0.4 1.0
C A:TYR290 3.4 0.1 1.0
CG A:ASP284 3.5 0.6 1.0
CG A:ASN286 3.5 0.9 1.0
CA A:ASP284 3.9 1.0 1.0
ND2 A:ASN286 4.0 0.2 1.0
N A:ILE285 4.0 0.5 1.0
CB A:TYR290 4.1 0.4 1.0
CB A:ASP284 4.1 0.9 1.0
CA A:TYR290 4.1 0.8 1.0
CB A:ASP292 4.1 0.8 1.0
N A:TYR290 4.2 0.7 1.0
N A:ASN286 4.3 0.8 1.0
C A:ASP284 4.4 0.1 1.0
OD2 A:ASP284 4.5 0.2 1.0
C A:ALA291 4.5 0.4 1.0
N A:ASP292 4.5 0.5 1.0
N A:ALA291 4.5 0.8 1.0
O A:GLN320 4.6 0.2 1.0
CB A:ASP288 4.6 0.1 1.0
N A:ASP288 4.7 0.7 1.0
N A:GLN320 4.7 0.5 1.0
CA A:ALA291 4.7 0.8 1.0
O A:ALA291 4.7 0.2 1.0
CA A:ASP292 4.8 0.2 1.0
CB A:ASN286 4.8 0.2 1.0
CA A:ASN286 5.0 0.6 1.0

Calcium binding site 2 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 2 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:0.5
occ:1.00
OD1 A:ASP353 2.3 1.0 1.0
OD1 A:ASP357 2.4 0.4 1.0
OD2 A:ASP357 2.4 0.3 1.0
OD2 A:ASP353 2.5 0.5 1.0
OD1 A:ASP351 2.5 0.2 1.0
O A:PHE355 2.5 0.0 1.0
OD1 A:ASP349 2.6 0.8 1.0
CG A:ASP353 2.6 0.6 1.0
CG A:ASP357 2.7 0.8 1.0
CG A:ASP351 3.3 0.5 1.0
OD2 A:ASP351 3.5 0.9 1.0
C A:PHE355 3.7 0.6 1.0
CG A:ASP349 3.7 0.0 1.0
ND2 A:ASN377 3.9 0.5 1.0
CB A:ASP353 4.0 0.9 1.0
CB A:ASP357 4.2 0.7 1.0
N A:ASP353 4.3 1.0 1.0
OD2 A:ASP349 4.3 0.8 1.0
N A:PHE355 4.4 0.3 1.0
N A:ASP351 4.4 0.2 1.0
CA A:PHE355 4.4 0.8 1.0
C A:ASN356 4.5 0.8 1.0
CA A:ASP349 4.6 0.9 1.0
O A:ASN356 4.6 0.5 1.0
CB A:PHE355 4.6 0.6 1.0
N A:ASP357 4.6 0.3 1.0
N A:LEU350 4.7 0.3 1.0
CB A:ASP351 4.7 0.4 1.0
N A:GLY378 4.7 0.3 1.0
CA A:ASP353 4.7 0.3 1.0
N A:ASN356 4.7 0.8 1.0
N A:GLN352 4.7 0.3 1.0
CB A:ASP349 4.7 0.3 1.0
CB A:ASN377 4.8 0.8 1.0
C A:ASP349 4.8 0.8 1.0
CA A:ASN356 4.8 0.5 1.0
CG A:ASN377 4.9 0.8 1.0
CA A:ASP351 4.9 0.8 1.0
O A:GLY378 4.9 0.2 1.0
CA A:ASP357 4.9 0.8 1.0
C A:ASP351 5.0 1.0 1.0

Calcium binding site 3 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 3 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:0.9
occ:1.00
OD1 A:ASN418 2.2 0.2 1.0
ND2 A:ASN418 2.3 0.8 1.0
OD2 A:ASP422 2.4 0.6 1.0
O A:TYR420 2.4 0.4 1.0
OD1 A:ASP422 2.4 0.1 1.0
CG A:ASN418 2.4 0.8 1.0
OD1 A:ASP416 2.6 0.5 1.0
OD1 A:ASP414 2.6 0.2 1.0
CG A:ASP422 2.7 0.3 1.0
C A:TYR420 3.4 0.3 1.0
CG A:ASP416 3.5 0.8 1.0
CB A:ASN418 3.7 0.4 1.0
OD2 A:ASP416 3.7 0.3 1.0
CG A:ASP414 3.8 0.7 1.0
CB A:TYR420 4.0 0.7 1.0
CA A:TYR420 4.1 0.5 1.0
N A:TYR420 4.1 0.5 1.0
N A:ALA438 4.1 0.9 1.0
CB A:ASP422 4.2 0.4 1.0
O A:ALA438 4.2 0.6 1.0
CB A:ALA438 4.3 0.5 1.0
C A:PRO421 4.4 0.5 1.0
N A:ASP422 4.4 0.6 1.0
N A:PRO421 4.5 0.7 1.0
OD2 A:ASP414 4.5 0.9 1.0
O A:PRO421 4.6 0.5 1.0
CA A:ASN418 4.7 0.4 1.0
N A:ASN418 4.7 0.6 1.0
CA A:ASP422 4.7 0.1 1.0
CA A:ALA438 4.7 0.2 1.0
CA A:PRO421 4.7 0.1 1.0
CA A:ASP414 4.7 1.0 1.0
CB A:ASP414 4.8 0.4 1.0
CB A:ASP416 4.9 0.6 1.0
N A:ASP416 4.9 0.2 1.0
C A:ALA438 4.9 0.2 1.0
N A:ILE415 5.0 0.4 1.0
C A:ASN418 5.0 0.8 1.0

Calcium binding site 4 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 4 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2004

b:0.9
occ:1.00
O A:ILE236 2.2 0.4 1.0
OD1 A:ASN232 2.3 0.7 1.0
OD1 A:ASP234 2.3 0.3 1.0
OD1 A:ASP238 2.3 0.4 1.0
OD2 A:ASP238 2.4 0.8 1.0
OD1 A:ASP230 2.6 0.2 1.0
CG A:ASP238 2.6 0.1 1.0
CG A:ASN232 3.2 0.2 1.0
CG A:ASP234 3.2 0.2 1.0
C A:ILE236 3.3 0.8 1.0
ND2 A:ASN232 3.5 0.5 1.0
OD2 A:ASP234 3.5 0.1 1.0
CG A:ASP230 3.7 0.4 1.0
N A:ILE236 3.8 1.0 1.0
CA A:ILE236 3.9 0.3 1.0
CB A:ILE236 4.0 0.1 1.0
CB A:ASP238 4.1 0.3 1.0
OD1 A:ASP257 4.2 0.9 1.0
N A:ASP238 4.3 0.0 1.0
N A:PHE231 4.4 0.5 1.0
CA A:ASP230 4.4 0.2 1.0
N A:ASP237 4.4 0.4 1.0
N A:ASN232 4.5 0.8 1.0
C A:ASP237 4.5 0.8 1.0
CB A:ASP234 4.5 0.4 1.0
N A:GLY235 4.5 0.4 1.0
OD2 A:ASP230 4.5 0.2 1.0
CB A:ASP230 4.5 0.0 1.0
CB A:ASN232 4.6 0.6 1.0
CA A:ASP238 4.6 0.4 1.0
N A:ASP234 4.7 0.5 1.0
CG2 A:ILE236 4.8 0.5 1.0
CA A:ASP237 4.8 0.7 1.0
C A:GLY235 4.9 0.2 1.0
C A:ASP230 4.9 0.3 1.0
O A:ASP237 5.0 0.8 1.0
CA A:ASN232 5.0 0.6 1.0

Calcium binding site 5 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 5 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2001

b:0.8
occ:1.00
O E:TYR290 2.3 0.8 1.0
OD1 E:ASP292 2.3 0.5 1.0
OD1 E:ASN286 2.4 0.8 1.0
OD2 E:ASP292 2.4 0.1 1.0
OD1 E:ASP284 2.4 0.5 1.0
OD1 E:ASP288 2.4 0.4 1.0
CG E:ASP292 2.6 0.9 1.0
CG E:ASP288 3.1 0.6 1.0
OD2 E:ASP288 3.2 0.7 1.0
CG E:ASN286 3.5 0.7 1.0
C E:TYR290 3.5 0.7 1.0
CG E:ASP284 3.5 0.2 1.0
ND2 E:ASN286 3.9 0.7 1.0
CA E:ASP284 4.0 0.5 1.0
N E:ILE285 4.0 0.9 1.0
CB E:TYR290 4.1 0.2 1.0
CB E:ASP292 4.1 0.0 1.0
CB E:ASP284 4.1 0.1 1.0
CA E:TYR290 4.2 0.3 1.0
N E:TYR290 4.3 0.0 1.0
N E:ASN286 4.3 0.7 1.0
C E:ASP284 4.4 0.7 1.0
N E:ASP292 4.5 0.3 1.0
C E:ALA291 4.5 0.5 1.0
OD2 E:ASP284 4.5 0.7 1.0
O E:GLN320 4.5 0.6 1.0
N E:ALA291 4.6 0.9 1.0
CB E:ASP288 4.6 0.2 1.0
N E:GLN320 4.7 0.4 1.0
CB E:ASN286 4.7 0.9 1.0
N E:ASP288 4.7 0.9 1.0
CA E:ASP292 4.7 0.7 1.0
O E:ALA291 4.8 0.5 1.0
CA E:ALA291 4.8 0.4 1.0
CA E:ASN286 4.9 0.2 1.0

Calcium binding site 6 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 6 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2002

b:0.4
occ:1.00
OD1 E:ASP353 2.4 0.2 1.0
OD2 E:ASP357 2.4 0.4 1.0
OD1 E:ASP357 2.4 0.9 1.0
OD1 E:ASP349 2.4 0.1 1.0
OD1 E:ASP351 2.4 0.2 1.0
OD2 E:ASP353 2.5 0.2 1.0
O E:PHE355 2.5 0.6 1.0
CG E:ASP353 2.7 0.7 1.0
CG E:ASP357 2.7 0.8 1.0
CG E:ASP351 3.3 0.5 1.0
OD2 E:ASP351 3.5 0.9 1.0
CG E:ASP349 3.6 0.9 1.0
C E:PHE355 3.7 1.0 1.0
ND2 E:ASN377 3.9 0.1 1.0
CB E:ASP353 4.0 0.2 1.0
OD2 E:ASP349 4.2 0.0 1.0
CB E:ASP357 4.2 0.6 1.0
N E:ASP353 4.2 0.5 1.0
N E:ASP351 4.3 0.0 1.0
N E:PHE355 4.4 0.3 1.0
CA E:ASP349 4.4 0.5 1.0
CA E:PHE355 4.5 0.5 1.0
C E:ASN356 4.5 0.2 1.0
N E:LEU350 4.5 0.1 1.0
O E:ASN356 4.6 0.3 1.0
CB E:ASP349 4.6 0.8 1.0
C E:ASP349 4.6 0.8 1.0
N E:ASP357 4.6 0.9 1.0
CB E:ASP351 4.6 0.3 1.0
CB E:PHE355 4.6 0.5 1.0
CA E:ASP353 4.7 0.2 1.0
N E:GLN352 4.7 0.9 1.0
N E:ASN356 4.7 0.3 1.0
N E:GLY378 4.7 0.4 1.0
CB E:ASN377 4.8 0.0 1.0
CA E:ASN356 4.8 0.8 1.0
CA E:ASP351 4.8 0.1 1.0
CG E:ASN377 4.9 1.0 1.0
CA E:ASP357 4.9 0.9 1.0
C E:ASP351 4.9 0.7 1.0
O E:GLY378 5.0 0.6 1.0

Calcium binding site 7 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 7 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2003

b:0.9
occ:1.00
OD1 E:ASP422 2.3 0.4 1.0
OD1 E:ASP416 2.3 0.9 1.0
O E:TYR420 2.3 0.7 1.0
OD1 E:ASN418 2.4 1.0 1.0
OD2 E:ASP422 2.5 0.7 1.0
OD1 E:ASP414 2.5 0.5 1.0
CG E:ASP422 2.7 0.4 1.0
CG E:ASN418 3.2 0.4 1.0
CG E:ASP416 3.4 0.3 1.0
C E:TYR420 3.5 0.8 1.0
CG E:ASP414 3.7 0.6 1.0
ND2 E:ASN418 3.7 0.1 1.0
OD2 E:ASP416 3.7 0.5 1.0
CB E:ASP422 4.2 0.4 1.0
N E:TYR420 4.2 0.9 1.0
CA E:TYR420 4.2 0.9 1.0
CB E:ASN418 4.3 0.9 1.0
CB E:TYR420 4.3 0.6 1.0
N E:ASP422 4.4 0.7 1.0
CA E:ASP414 4.4 0.8 1.0
C E:PRO421 4.4 0.6 1.0
N E:ASP416 4.4 0.3 1.0
N E:PRO421 4.5 0.4 1.0
N E:ILE415 4.5 0.6 1.0
N E:ASN418 4.5 0.3 1.0
OD2 E:ASP414 4.5 0.6 1.0
CB E:ASP414 4.5 0.1 1.0
CB E:ASP416 4.6 0.3 1.0
CA E:PRO421 4.6 0.4 1.0
N E:ALA438 4.6 0.9 1.0
CA E:ASP422 4.7 0.9 1.0
C E:ASP414 4.7 1.0 1.0
O E:PRO421 4.7 0.4 1.0
O E:ALA438 4.8 0.9 1.0
CA E:ASN418 4.9 0.1 1.0
CB E:ALA438 4.9 0.5 1.0
CA E:ASP416 4.9 0.1 1.0

Calcium binding site 8 out of 8 in 5ffo

Go back to Calcium Binding Sites List in 5ffo
Calcium binding site 8 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2004

b:0.6
occ:1.00
OD1 E:ASN232 2.3 0.2 1.0
OD1 E:ASP238 2.3 0.8 1.0
OD1 E:ASP234 2.4 0.1 1.0
O E:ILE236 2.4 0.1 1.0
OD2 E:ASP238 2.4 0.0 1.0
CG E:ASP238 2.7 0.9 1.0
CG E:ASN232 3.1 0.6 1.0
CG E:ASP234 3.1 0.0 1.0
ND2 E:ASN232 3.1 0.7 1.0
OD2 E:ASP234 3.3 0.2 1.0
OD1 E:ASP230 3.4 0.3 1.0
C E:ILE236 3.5 0.6 1.0
OD1 E:ASP257 3.7 0.2 1.0
CB E:ILE236 3.9 0.8 1.0
N E:ILE236 3.9 0.4 1.0
CA E:ILE236 3.9 0.3 1.0
CB E:ASP238 4.1 0.1 1.0
CB E:ASP234 4.4 0.9 1.0
N E:ASP238 4.5 0.3 1.0
CG E:ASP230 4.5 0.2 1.0
CB E:ASN232 4.5 0.3 1.0
N E:ASP237 4.6 0.2 1.0
CG2 E:ILE236 4.6 0.6 1.0
C E:ASP237 4.6 0.1 1.0
N E:ASN232 4.7 0.7 1.0
CA E:ASP238 4.7 0.3 1.0
N E:GLY235 4.7 0.3 1.0
N E:GLY258 4.8 0.4 1.0
N E:PHE231 4.9 0.0 1.0
CG E:ASP257 4.9 0.9 1.0
N E:ASP234 4.9 0.7 1.0
CG1 E:ILE236 5.0 0.2 1.0
CA E:ASP237 5.0 0.2 1.0
O E:ASP237 5.0 0.2 1.0

Reference:

X.Dong, B.Zhao, R.E.Iacob, J.Zhu, A.C.Koksal, C.Lu, J.R.Engen, T.A.Springer. Force Interacts with Macromolecular Structure in Activation of Tgf-Beta. Nature V. 542 55 2017.
ISSN: ESSN 1476-4687
PubMed: 28117447
DOI: 10.1038/NATURE21035
Page generated: Sat Dec 12 05:25:05 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