Calcium in PDB 8vs6: L-Tgf-B3/AVB8

The structure of L-Tgf-B3/AVB8 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the L-Tgf-B3/AVB8 (pdb code 8vs6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the L-Tgf-B3/AVB8, PDB code: 8vs6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the L-Tgf-B3/AVB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L-Tgf-B3/AVB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:30.9 occ:1.00 OD1 A:ASP288 2.3 21.7 1.0 OD1 A:ASP292 2.3 12.1 1.0 OD1 A:ASN286 2.3 16.1 1.0 OD1 A:ASP284 2.4 20.9 1.0 O A:TYR290 2.4 12.5 1.0 OD2 A:ASP292 2.8 13.9 1.0 CG A:ASP292 2.9 12.5 1.0 HB2 A:TYR290 3.2 21.4 1.0 CG A:ASN286 3.3 16.9 1.0 CG A:ASP288 3.3 20.7 1.0 HA A:ASP284 3.4 18.7 1.0 H A:TYR290 3.4 22.1 1.0 C A:TYR290 3.4 15.1 1.0 HD22 A:ASN286 3.4 18.8 1.0 CG A:ASP284 3.5 23.7 1.0 H A:ASN286 3.6 17.3 1.0 H A:ASP288 3.7 20.7 1.0 ND2 A:ASN286 3.8 23.1 1.0 OD2 A:ASP288 3.8 22.2 1.0 H A:ILE285 3.9 15.6 1.0 CB A:TYR290 3.9 20.9 1.0 CA A:TYR290 4.0 15.1 1.0 H A:GLN320 4.0 17.8 1.0 N A:TYR290 4.0 22.4 1.0 CA A:ASP284 4.1 18.2 1.0 HB3 A:TYR290 4.2 21.9 1.0 CB A:ASP284 4.2 17.0 1.0 HD22 A:LEU319 4.2 17.4 1.0 HB2 A:ASP284 4.2 18.0 1.0 O A:GLN320 4.2 21.3 1.0 HB3 A:GLN320 4.2 18.9 1.0 CB A:ASP292 4.3 11.8 1.0 HB3 A:LEU319 4.4 17.6 1.0 N A:ILE285 4.4 13.5 1.0 N A:ASN286 4.4 14.1 1.0 OD2 A:ASP284 4.4 24.2 1.0 N A:ALA291 4.5 22.7 1.0 N A:ASP288 4.5 22.3 1.0 CB A:ASP288 4.5 23.3 1.0 N A:ASP292 4.5 14.2 1.0 C A:ALA291 4.6 14.7 1.0 CB A:ASN286 4.6 15.6 1.0 C A:ASP284 4.6 15.5 1.0 H A:GLY287 4.6 20.4 1.0 N A:GLN320 4.6 21.8 1.0 HD21 A:ASN286 4.6 18.5 1.0 HA A:LEU319 4.6 17.3 1.0 HA A:ALA291 4.6 16.2 1.0 H A:ASP292 4.7 15.7 1.0 HB3 A:ASP288 4.7 21.4 1.0 HG22 A:ILE285 4.7 15.9 1.0 HB3 A:ASP292 4.8 15.1 1.0 HB2 A:ASP292 4.8 14.7 1.0 CA A:ALA291 4.8 15.5 1.0 HB3 A:ASN286 4.9 17.2 1.0 CA A:ASP292 4.9 13.8 1.0 O A:ALA291 4.9 12.9 1.0 CA A:ASN286 4.9 13.5 1.0 CA A:ASP288 4.9 21.2 1.0 N A:GLY287 4.9 24.6 1.0 HA A:ASP292 4.9 15.4 1.0 HA A:TYR290 5.0 20.9 1.0 H A:ASP289 5.0 22.8 1.0 C A:ASP288 5.0 21.8 1.0

Calcium binding site 2 out of 5 in the L-Tgf-B3/AVB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L-Tgf-B3/AVB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:12.8 occ:1.00 OD1 A:ASP357 2.4 27.7 1.0 O A:PHE355 2.5 18.4 1.0 OD1 A:ASP351 2.5 22.0 1.0 OD1 A:ASP353 2.6 22.6 1.0 HD21 A:ASN377 2.6 17.6 1.0 OD1 A:ASP349 2.7 23.3 1.0 OD2 A:ASP357 3.0 22.9 1.0 CG A:ASP357 3.0 21.9 1.0 ND2 A:ASN377 3.4 20.3 1.0 H A:ASP351 3.4 21.1 1.0 H A:ASP353 3.4 22.1 1.0 H A:GLY378 3.6 17.2 1.0 CG A:ASP353 3.6 26.6 1.0 CG A:ASP351 3.6 23.2 1.0 HD22 A:ASN377 3.7 18.4 1.0 HA A:ASP349 3.7 19.6 1.0 C A:PHE355 3.7 21.4 1.0 HB2 A:ASP353 3.7 22.2 1.0 CG A:ASP349 3.9 19.9 1.0 H A:PHE355 3.9 20.0 1.0 HB2 A:PHE355 3.9 18.0 1.0 H A:LEU350 3.9 19.3 1.0 HB3 A:ASN377 4.1 16.9 1.0 OD2 A:ASP351 4.2 26.9 1.0 CB A:ASP353 4.2 20.9 1.0 H A:GLN352 4.2 21.9 1.0 N A:ASP351 4.3 21.0 1.0 N A:ASP353 4.3 19.7 1.0 N A:LEU350 4.3 23.8 1.0 HA A:ASN356 4.4 17.1 1.0 N A:GLY378 4.4 17.6 1.0 HA A:ASN377 4.4 16.5 1.0 CA A:ASP349 4.5 19.2 1.0 C A:ASN356 4.5 14.2 1.0 OD2 A:ASP353 4.5 31.7 1.0 CB A:ASP357 4.5 14.7 1.0 CA A:PHE355 4.5 18.8 1.0 CG A:ASN377 4.5 17.1 1.0 N A:PHE355 4.6 22.4 1.0 OD2 A:ASP349 4.6 18.5 1.0 N A:GLN352 4.6 24.1 1.0 CB A:PHE355 4.6 15.4 1.0 HB3 A:LEU350 4.6 18.6 1.0 N A:ASP357 4.6 15.4 1.0 C A:ASP349 4.6 20.2 1.0 N A:ASN356 4.7 17.9 1.0 O A:ASN356 4.7 13.5 1.0 CB A:ASN377 4.7 16.6 1.0 CA A:ASN356 4.7 15.1 1.0 CB A:ASP349 4.8 19.7 1.0 H A:ASP357 4.8 16.9 1.0 CB A:ASP351 4.8 20.5 1.0 CA A:ASP353 4.9 21.3 1.0 HB3 A:PHE355 4.9 18.5 1.0 CA A:ASP351 4.9 20.6 1.0 O A:GLY378 4.9 15.6 1.0 HB2 A:ASP357 4.9 16.3 1.0 C A:ASP351 4.9 22.0 1.0 CA A:ASN377 5.0 16.7 1.0 HB3 A:ASP353 5.0 21.7 1.0 HA3 A:GLY378 5.0 17.4 1.0

Calcium binding site 3 out of 5 in the L-Tgf-B3/AVB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L-Tgf-B3/AVB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:13.5 occ:1.00 OD1 A:ASN417 2.2 25.5 1.0 OD1 A:ASP421 2.2 19.6 1.0 OD1 A:ASP415 2.3 24.5 1.0 O A:TYR419 2.3 19.7 1.0 OD1 A:ASP413 2.9 18.8 1.0 CG A:ASP421 3.1 20.0 1.0 CG A:ASN417 3.1 25.5 1.0 CG A:ASP415 3.1 25.8 1.0 OD2 A:ASP421 3.2 29.2 1.0 OD2 A:ASP415 3.3 25.4 1.0 HD22 A:ASN417 3.3 23.8 1.0 HB2 A:TYR419 3.4 21.9 1.0 H A:TYR419 3.4 22.8 1.0 C A:TYR419 3.5 17.7 1.0 ND2 A:ASN417 3.6 26.5 1.0 HA A:ASP413 3.8 20.1 1.0 H A:ASN417 3.8 24.3 1.0 H A:ALA437 3.8 21.6 1.0 H A:ASP415 3.8 24.3 1.0 HB3 A:ALA437 3.9 21.3 1.0 CG A:ASP413 4.0 20.3 1.0 CB A:TYR419 4.0 18.5 1.0 N A:TYR419 4.1 25.8 1.0 O A:ALA437 4.1 25.6 1.0 CA A:TYR419 4.1 19.3 1.0 HB3 A:TYR419 4.2 22.1 1.0 HB3 A:ARG436 4.2 22.6 1.0 CB A:ASN417 4.3 17.5 1.0 N A:ALA437 4.4 21.1 1.0 HB3 A:ASN417 4.4 23.1 1.0 HD21 A:ASN417 4.4 24.1 1.0 C A:PRO420 4.4 16.1 1.0 CB A:ASP421 4.5 19.0 1.0 N A:ASP421 4.5 13.0 1.0 CA A:ASP413 4.5 13.8 1.0 H A:ILE414 4.5 22.5 1.0 CB A:ASP415 4.5 23.3 1.0 HA A:ARG436 4.5 22.0 1.0 N A:PRO420 4.6 19.2 1.0 N A:ASN417 4.6 26.7 1.0 O A:PRO420 4.6 23.2 1.0 HA A:PRO420 4.6 20.4 1.0 N A:ASP415 4.6 23.1 1.0 CB A:ASP413 4.7 16.2 1.0 HB2 A:ASP413 4.7 19.9 1.0 HG22 A:ILE414 4.7 23.0 1.0 H A:ASP421 4.7 19.0 1.0 HG2 A:ARG436 4.7 23.1 1.0 HA A:ASP421 4.8 20.7 1.0 CA A:PRO420 4.8 16.8 1.0 CB A:ALA437 4.8 16.2 1.0 H A:LYS416 4.8 25.1 1.0 H A:GLY418 4.8 22.7 1.0 N A:ILE414 4.8 21.8 1.0 CA A:ASN417 4.9 20.3 1.0 HB3 A:ASP415 4.9 24.7 1.0 CA A:ASP421 4.9 22.2 1.0 OD2 A:ASP413 4.9 18.9 1.0 C A:ASP413 4.9 21.6 1.0 CA A:ALA437 4.9 19.8 1.0 C A:ALA437 4.9 27.0 1.0 HB3 A:ASP421 5.0 20.1 1.0 HB2 A:ASP421 5.0 20.1 1.0 N A:GLY418 5.0 19.7 1.0

Calcium binding site 4 out of 5 in the L-Tgf-B3/AVB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L-Tgf-B3/AVB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:27.4 occ:1.00 OD1 A:ASN232 2.2 20.3 1.0 OD1 A:ASP238 2.2 13.9 1.0 O A:ILE236 2.2 21.0 1.0 OD1 A:ASP234 2.4 27.0 1.0 OD1 A:ASP230 2.5 18.2 1.0 CG A:ASP238 3.2 16.0 1.0 H A:ILE236 3.2 19.7 1.0 H A:ASN232 3.3 18.5 1.0 CG A:ASP234 3.3 23.8 1.0 CG A:ASN232 3.3 18.9 1.0 C A:ILE236 3.4 20.2 1.0 OD2 A:ASP238 3.4 23.7 1.0 H A:ASP234 3.4 20.6 1.0 H A:PHE231 3.4 13.8 1.0 HG21 A:ILE236 3.5 19.6 1.0 HA A:ASP230 3.5 16.2 1.0 OD2 A:ASP234 3.7 23.0 1.0 HD22 A:ASN232 3.7 19.1 1.0 CG A:ASP230 3.7 18.4 1.0 HB A:ILE236 3.7 19.0 1.0 N A:ILE236 3.8 21.7 1.0 ND2 A:ASN232 3.9 23.2 1.0 CA A:ILE236 4.0 20.4 1.0 OD1 A:ASP257 4.1 24.1 1.0 N A:ASN232 4.1 20.3 1.0 CB A:ILE236 4.2 16.8 1.0 H A:GLY233 4.2 18.5 1.0 N A:PHE231 4.2 8.4 1.0 CG2 A:ILE236 4.2 20.6 1.0 H A:GLY235 4.2 18.8 1.0 H A:GLY258 4.2 17.1 1.0 N A:ASP234 4.2 23.6 1.0 CA A:ASP230 4.3 12.4 1.0 H A:ASP238 4.4 14.3 1.0 N A:ASP238 4.4 10.8 1.0 N A:ASP237 4.5 16.4 1.0 CB A:ASP234 4.5 21.3 1.0 CB A:ASN232 4.5 16.7 1.0 CB A:ASP230 4.5 15.1 1.0 C A:ASP237 4.5 17.1 1.0 N A:GLY235 4.5 18.6 1.0 N A:GLY233 4.5 20.0 1.0 CB A:ASP238 4.5 13.7 1.0 HA A:ASP237 4.6 16.4 1.0 OD2 A:ASP230 4.6 18.8 1.0 CA A:ASN232 4.6 20.3 1.0 C A:ASN232 4.7 19.9 1.0 HB2 A:ASP230 4.7 15.7 1.0 CA A:ASP234 4.7 18.1 1.0 HG23 A:ILE236 4.8 19.8 1.0 HD21 A:ASN232 4.8 19.5 1.0 C A:ASP230 4.8 11.4 1.0 C A:ASP234 4.8 18.5 1.0 HB3 A:ASP234 4.8 20.6 1.0 CA A:ASP237 4.8 13.8 1.0 C A:GLY235 4.8 18.9 1.0 HB3 A:ASN232 4.8 17.8 1.0 HA A:ASP238 4.8 15.8 1.0 CA A:ASP238 4.9 10.8 1.0 HA A:ILE236 4.9 19.6 1.0 HG22 A:ILE236 4.9 19.4 1.0 CG A:ASP257 4.9 22.7 1.0 O A:ASP237 4.9 17.8 1.0 HA A:ASP257 4.9 17.4 1.0 HB2 A:ASP238 5.0 15.1 1.0

Calcium binding site 5 out of 5 in the L-Tgf-B3/AVB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of L-Tgf-B3/AVB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:15.5 occ:1.00 O B:PRO211 2.1 6.7 1.0 O B:ASP209 2.2 9.4 1.0 ND2 B:ASN207 2.3 4.5 1.0 OD2 B:ASP151 2.3 7.0 1.0 HD21 B:ASN207 2.5 10.5 1.0 OD2 B:ASP209 2.6 21.4 1.0 C B:PRO211 3.1 11.2 1.0 HG2 B:GLU212 3.1 11.8 1.0 HA B:GLU212 3.1 11.2 1.0 CD B:GLU212 3.3 8.2 1.0 C B:ASP209 3.3 11.7 1.0 OE2 B:GLU212 3.4 13.6 1.0 CG B:ASN207 3.4 14.7 1.0 CG B:ASP209 3.5 16.3 1.0 OE1 B:GLU212 3.5 10.1 1.0 CG B:ASP151 3.5 8.7 1.0 HE2 B:HIS247 3.6 10.0 1.0 CG B:GLU212 3.6 9.7 1.0 C B:THR210 3.8 4.9 1.0 CA B:GLU212 3.8 11.1 1.0 O B:THR210 3.8 22.3 1.0 N B:GLU212 3.8 10.4 1.0 OD1 B:ASN207 3.8 16.8 1.0 HB2 B:ASP151 3.9 11.2 1.0 N B:PRO211 3.9 15.8 1.0 HD2 B:PRO211 4.0 11.4 1.0 H B:ASP209 4.1 10.0 1.0 CA B:PRO211 4.1 7.1 1.0 CA B:ASP209 4.1 7.2 1.0 N B:THR210 4.1 9.7 1.0 OD1 B:ASP209 4.2 15.6 1.0 CB B:GLU212 4.2 7.5 1.0 HB2 E:ASP243 4.2 4.7 1.0 N B:ASP209 4.2 7.1 1.0 NE2 B:HIS247 4.3 7.3 1.0 CB B:ASP151 4.3 13.8 1.0 CB B:ASP209 4.3 7.1 1.0 CA B:THR210 4.3 0.0 1.0 HA B:THR210 4.4 9.0 1.0 HD2 B:HIS247 4.4 9.8 1.0 HB3 B:GLU212 4.5 8.6 1.0 OD1 B:ASP151 4.5 9.0 1.0 CD B:PRO211 4.5 16.5 1.0 HG3 B:GLU212 4.5 10.3 1.0 HB2 B:ASP209 4.5 9.9 1.0 HB2 B:ASN207 4.6 12.8 1.0 HB3 B:TYR157 4.6 10.0 1.0 HB3 B:ASP151 4.7 10.9 1.0 CB B:ASN207 4.7 11.8 1.0 H B:GLU212 4.7 9.6 1.0 CD2 B:HIS247 4.7 8.1 1.0 HA B:PRO211 4.8 8.4 1.0 HB2 B:PRO211 4.8 8.7 1.0 O B:VAL150 4.9 1.3 1.0 H B:THR210 4.9 10.2 1.0

M.Jin, Y.Cheng, S.L.Nishimura. Dynamic Allostery Drives Autocrine and Paracrine Tgf-Beta Signaling Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674