Calcium in PDB 7y1t: Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2

Other elements in 7y1t:

The structure of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 (pdb code 7y1t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2, PDB code: 7y1t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7y1t

Go back to Calcium Binding Sites List in 7y1t
Calcium binding site 1 out of 5 in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:68.4
occ:1.00
 OD1 A:ASP238 2.4 64.3 1.0
OD1 A:ASN232 2.4 66.7 1.0
O A:ILE236 2.4 70.8 1.0
OD1 A:ASP234 2.6 72.0 1.0
CG A:ASP238 2.9 64.3 1.0
OD2 A:ASP238 2.9 64.3 1.0
OD1 A:ASP230 3.4 66.0 1.0
CG A:ASP234 3.4 72.0 1.0
CG A:ASN232 3.5 66.7 1.0
OD2 A:ASP234 3.7 72.0 1.0
C A:ILE236 3.7 70.8 1.0
N A:PHE231 3.9 61.4 1.0
N A:ASP238 3.9 64.3 1.0
ND2 A:ASN232 4.0 66.7 1.0
CG A:ASP230 4.0 66.0 1.0
CA A:ASP230 4.1 66.0 1.0
N A:ASN232 4.2 66.7 1.0
CB A:ASP238 4.2 64.3 1.0
CG2 A:ILE236 4.3 70.8 1.0
C A:ASP237 4.3 68.3 1.0
N A:ASP234 4.5 72.0 1.0
CA A:ASP238 4.5 64.3 1.0
CA A:ASP237 4.5 68.3 1.0
CB A:ASP230 4.5 66.0 1.0
O A:GLY229 4.5 63.0 1.0
C A:ASP230 4.5 66.0 1.0
N A:ILE236 4.5 70.8 1.0
N A:GLY233 4.5 68.4 1.0
N A:ASP237 4.5 68.3 1.0
CA A:ILE236 4.6 70.8 1.0
OD1 A:ASP257 4.7 67.1 1.0
CB A:ASP234 4.7 72.0 1.0
CB A:ASN232 4.7 66.7 1.0
OD2 A:ASP230 4.8 66.0 1.0
CA A:ASN232 4.9 66.7 1.0
CA A:PHE231 4.9 61.4 1.0
C A:PHE231 5.0 61.4 1.0

Calcium binding site 2 out of 5 in 7y1t

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Calcium binding site 2 out of 5 in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:41.6
occ:1.00
 OD1 A:ASP292 2.4 49.0 1.0
OD1 A:ASP288 2.4 51.2 1.0
OD1 A:ASN286 2.5 51.0 1.0
OD1 A:ASP284 2.6 52.3 1.0
OD2 A:ASP292 2.6 49.0 1.0
O A:TYR290 2.8 54.4 1.0
CG A:ASP292 2.8 49.0 1.0
OD2 A:ASP288 2.8 51.2 1.0
CG A:ASP288 3.0 51.2 1.0
CG A:ASN286 3.5 51.0 1.0
CG A:ASP284 3.7 52.3 1.0
ND2 A:ASN286 3.7 51.0 1.0
C A:TYR290 3.8 54.4 1.0
CB A:TYR290 4.0 54.4 1.0
CA A:TYR290 4.3 54.4 1.0
CB A:ASP292 4.3 49.0 1.0
N A:TYR290 4.4 54.4 1.0
OD2 A:ASP284 4.4 52.3 1.0
N A:ASP292 4.5 49.0 1.0
CB A:ASP288 4.5 51.2 1.0
N A:ILE285 4.5 51.3 1.0
O A:GLN320 4.5 55.5 1.0
N A:ASN286 4.6 51.0 1.0
CA A:ASP284 4.6 52.3 1.0
CB A:ASP284 4.7 52.3 1.0
CD1 A:LEU319 4.8 53.0 1.0
N A:ASP288 4.8 51.2 1.0
N A:ALA291 4.8 54.2 1.0
CA A:ASP292 4.8 49.0 1.0
CB A:ASN286 4.9 51.0 1.0
C A:ALA291 4.9 54.2 1.0

Calcium binding site 3 out of 5 in 7y1t

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Calcium binding site 3 out of 5 in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:46.8
occ:1.00
 OD1 A:ASP353 2.4 55.6 1.0
OD2 A:ASP357 2.4 50.0 1.0
O A:PHE355 2.5 54.6 1.0
OD1 A:ASP351 2.6 53.5 1.0
OD1 A:ASP357 2.6 50.0 1.0
CG A:ASP357 2.8 50.0 1.0
OD2 A:ASP353 3.1 55.6 1.0
CG A:ASP353 3.1 55.6 1.0
CG A:ASP351 3.5 53.5 1.0
C A:PHE355 3.5 54.6 1.0
OD1 A:ASP349 3.7 53.5 1.0
OD2 A:ASP351 3.7 53.5 1.0
O A:ASN356 3.9 52.0 1.0
C A:ASN356 3.9 52.0 1.0
CB A:ASP357 4.2 50.0 1.0
N A:ASP357 4.3 50.0 1.0
CA A:ASN356 4.3 52.0 1.0
N A:ASN356 4.3 52.0 1.0
CA A:PHE355 4.5 54.6 1.0
CB A:PHE355 4.5 54.6 1.0
ND2 A:ASN377 4.5 49.3 1.0
CB A:ASP353 4.6 55.6 1.0
N A:GLY378 4.6 52.4 1.0
N A:ASP351 4.6 53.5 1.0
CA A:ASP357 4.7 50.0 1.0
N A:LEU350 4.7 51.4 1.0
N A:PHE355 4.7 54.6 1.0
N A:ASP353 4.8 55.6 1.0
CG A:ASP349 4.8 53.5 1.0
CB A:ASP351 4.9 53.5 1.0
CA A:ASP349 4.9 53.5 1.0

Calcium binding site 4 out of 5 in 7y1t

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Calcium binding site 4 out of 5 in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:50.2
occ:1.00
 OD1 A:ASP422 2.5 53.1 1.0
OD2 A:ASP422 2.5 53.1 1.0
O A:TYR420 2.5 54.4 1.0
OD1 A:ASP416 2.5 57.3 1.0
CG A:ASP422 2.6 53.1 1.0
OD1 A:ASN418 2.7 56.2 1.0
ND2 A:ASN418 3.1 56.2 1.0
OD1 A:ASP414 3.2 55.0 1.0
CG A:ASP416 3.2 57.3 1.0
OD2 A:ASP416 3.2 57.3 1.0
CG A:ASN418 3.2 56.2 1.0
C A:TYR420 3.6 54.4 1.0
CB A:ASP422 3.9 53.1 1.0
CB A:TYR420 4.0 54.4 1.0
N A:ASP422 4.0 53.1 1.0
CA A:TYR420 4.2 54.4 1.0
CA A:ASP422 4.4 53.1 1.0
CG A:ASP414 4.4 55.0 1.0
N A:TYR420 4.4 54.4 1.0
N A:ALA438 4.4 53.1 1.0
C A:PRO421 4.6 49.7 1.0
CB A:ASP416 4.6 57.3 1.0
CB A:ALA438 4.6 53.1 1.0
N A:ASP416 4.7 57.3 1.0
O A:ALA438 4.7 53.1 1.0
N A:PRO421 4.7 49.7 1.0
CB A:ASN418 4.7 56.2 1.0
N A:ILE415 4.8 58.7 1.0
CA A:PRO421 4.9 49.7 1.0
CG2 A:ILE415 4.9 58.7 1.0

Calcium binding site 5 out of 5 in 7y1t

Go back to Calcium Binding Sites List in 7y1t
Calcium binding site 5 out of 5 in the Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Integrin Alphav/BETA8 and L-Tgf-BETA1 at A Ratio of 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:64.7
occ:1.00
 OD1 B:ASN207 2.3 73.3 1.0
O B:PRO211 2.4 67.8 1.0
OE2 B:GLU212 2.4 69.2 1.0
OD2 B:ASP151 2.4 67.3 1.0
OD1 B:ASP209 2.5 71.7 1.0
CD B:GLU212 2.7 69.2 1.0
OE1 B:GLU212 3.0 69.2 1.0
CG B:ASN207 3.0 73.3 1.0
ND2 B:ASN207 3.0 73.3 1.0
O B:ASP209 3.1 71.7 1.0
C B:PRO211 3.4 67.8 1.0
CG B:ASP151 3.5 67.3 1.0
CG B:ASP209 3.6 71.7 1.0
CG B:GLU212 3.7 69.2 1.0
CA B:GLU212 3.8 69.2 1.0
CB B:ASP151 3.9 67.3 1.0
N B:GLU212 4.0 69.2 1.0
C B:ASP209 4.0 71.7 1.0
OD2 B:ASP209 4.2 71.7 1.0
O B:THR210 4.2 70.7 1.0
CB B:GLU212 4.2 69.2 1.0
C B:THR210 4.4 70.7 1.0
NE2 B:HIS247 4.5 64.8 1.0
CB B:ASN207 4.5 73.3 1.0
OD1 B:ASP151 4.5 67.3 1.0
N B:PRO211 4.6 67.8 1.0
CA B:PRO211 4.6 67.8 1.0
N B:ASP209 4.7 71.7 1.0
CA B:ASP209 4.7 71.7 1.0
CD2 B:HIS247 4.7 64.8 1.0
CB B:ASP209 4.8 71.7 1.0
O B:VAL150 4.9 61.8 1.0
N B:THR210 4.9 70.7 1.0
C B:GLU212 5.0 69.2 1.0

Reference:

Z.Duan, X.Lin, L.Wang, Q.Zhen, Y.Jiang, C.Chen, J.Yang, C.H.Lee, Y.Qin, Y.Li, B.Zhao, J.Wang, Z.Zhang. Specificity of Tgf-Beta 1 Signal Designated By LRRC33 and Integrin Alpha V Beta 8. Nat Commun V. 13 4988 2022.
ISSN: ESSN 2041-1723
PubMed: 36008481
DOI: 10.1038/S41467-022-32655-9
Page generated: Tue Apr 4 19:14:57 2023

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