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

Other elements in 8vs6:

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

Magnesium (Mg) 1 atom

Calcium Binding Sites:

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 8vs6

Go back to Calcium Binding Sites List in 8vs6
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 8vs6

Go back to Calcium Binding Sites List in 8vs6
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 8vs6

Go back to Calcium Binding Sites List in 8vs6
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 8vs6

Go back to Calcium Binding Sites List in 8vs6
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 8vs6

Go back to Calcium Binding Sites List in 8vs6
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

Reference:

M.Jin, Y.Cheng, S.L.Nishimura. Dynamic Allostery Drives Autocrine and Paracrine Tgf-Beta Signaling Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674
Page generated: Sat Sep 28 09:15:32 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy