Calcium in PDB 7pc4: The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1

The structure of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1, PDB code: 7pc4 was solved by A.Cousido-Siah, G.Trave, G.Gogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.04 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.27, 61.73, 145.25, 90, 90, 90
R / Rfree (%)	20.5 / 26

The binding sites of Calcium atom in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 (pdb code 7pc4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1, PDB code: 7pc4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:125.2 occ:1.00 O A:GLY226 2.4 108.7 1.0 OE2 A:GLU229 2.6 102.8 1.0 OE1 A:GLU229 3.0 101.6 1.0 CD A:GLU229 3.2 97.0 1.0 O A:VAL227 3.2 86.8 1.0 C A:GLY226 3.5 107.2 1.0 C A:VAL227 4.3 88.7 1.0 CA A:GLY226 4.3 112.7 1.0 O A:HOH716 4.4 67.7 1.0 N A:VAL227 4.5 100.1 1.0 CB A:VAL227 4.6 92.3 1.0 CG A:GLU229 4.7 84.7 1.0 CA A:VAL227 4.7 93.7 1.0

Calcium binding site 2 out of 5 in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:111.7 occ:1.00 O A:LEU267 2.4 72.3 1.0 O A:HOH769 2.5 75.3 1.0 O A:LYS264 2.5 77.3 1.0 OE1 A:GLU272 3.0 85.9 1.0 C A:LEU267 3.6 73.8 1.0 CD A:GLU272 3.7 83.5 1.0 C A:LYS264 3.8 76.0 1.0 OE2 A:GLU272 3.9 87.9 1.0 CA A:SER268 4.2 73.5 1.0 CB A:SER268 4.2 74.2 1.0 O A:SER265 4.3 82.4 1.0 N A:SER268 4.4 73.5 1.0 CA A:SER265 4.4 82.0 1.0 C A:SER265 4.4 81.3 1.0 N A:SER265 4.5 77.6 1.0 N A:LEU267 4.6 75.5 1.0 CA A:LEU267 4.8 73.9 1.0 CA A:LYS264 4.8 70.5 1.0 CG A:LYS264 4.8 75.1 1.0 CG A:GLU272 4.9 76.8 1.0

Calcium binding site 3 out of 5 in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:88.2 occ:1.00 OD1 A:ASP338 2.2 94.9 1.0 O A:GLY296 2.3 93.5 1.0 O A:MET294 2.4 86.1 1.0 O A:GLY298 2.5 90.9 1.0 CG A:ASP338 3.2 91.5 1.0 OD2 A:ASP338 3.4 94.1 1.0 C A:GLY296 3.5 90.2 1.0 N A:GLY298 3.5 94.8 1.0 C A:GLY298 3.6 89.9 1.0 C A:MET294 3.6 83.6 1.0 N A:GLY296 4.0 86.3 1.0 CA A:GLY298 4.1 91.8 1.0 C A:LYS295 4.2 85.8 1.0 OG1 A:THR299 4.4 91.4 1.0 CA A:GLY296 4.4 87.0 1.0 CA A:MET294 4.4 77.3 1.0 N A:LYS295 4.5 83.3 1.0 CA A:LYS295 4.5 85.9 1.0 N A:LEU297 4.5 90.3 1.0 CB A:ASP338 4.5 84.3 1.0 C A:LEU297 4.6 96.3 1.0 O A:LYS295 4.6 86.2 1.0 CA A:LEU297 4.7 91.7 1.0 N A:THR299 4.7 87.2 1.0

Calcium binding site 4 out of 5 in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:76.2 occ:1.00 O A:GLY383 2.4 75.3 1.0 O A:GLY378 2.5 67.4 1.0 O A:ARG381 2.5 77.8 1.0 OE2 A:GLU423 2.5 72.6 1.0 O A:HOH745 2.6 66.5 1.0 OE1 A:GLU423 2.7 69.0 1.0 CD A:GLU423 3.0 70.1 1.0 C A:GLY383 3.4 76.5 1.0 N A:GLY383 3.5 79.8 1.0 C A:GLY378 3.5 68.6 1.0 C A:ARG381 3.6 77.5 1.0 C A:LYS382 3.9 78.4 1.0 CA A:LYS382 3.9 79.2 1.0 CA A:GLY383 4.0 79.2 1.0 N A:LYS382 4.2 79.9 1.0 CA A:VAL379 4.2 73.4 1.0 OG1 A:THR384 4.3 70.3 1.0 N A:VAL379 4.3 66.9 1.0 CA A:GLY378 4.5 66.5 1.0 CG A:GLU423 4.5 70.0 1.0 CG A:ARG381 4.5 72.9 1.0 N A:THR384 4.6 74.4 1.0 CA A:ARG381 4.7 76.1 1.0 C A:VAL379 4.7 73.8 1.0 O A:LYS382 4.7 76.7 1.0 N A:ARG381 4.7 77.9 1.0 CA A:THR384 4.9 73.5 1.0

Calcium binding site 5 out of 5 in the The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Pdz Domain of SNTB1 Complexed with the Pdz-Binding Motif of HTLV1- TAX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:48.3 occ:1.00 O A:MET454 2.4 55.5 1.0 O A:GLY458 2.4 52.8 1.0 O A:GLY456 2.4 60.9 1.0 OD2 A:ASP498 2.5 55.2 1.0 OD1 A:ASP498 2.5 54.0 1.0 CG A:ASP498 2.9 54.4 1.0 C A:MET454 3.4 52.0 1.0 C A:GLY458 3.5 56.5 1.0 C A:GLY456 3.7 58.3 1.0 CA A:MET454 3.9 50.3 1.0 N A:GLY458 4.0 57.8 1.0 N A:GLY456 4.2 57.5 1.0 CA A:GLY458 4.3 56.9 1.0 C A:LYS455 4.3 54.5 1.0 C A:LYS457 4.3 58.6 1.0 OG1 A:THR459 4.3 56.5 1.0 CB A:ASP498 4.4 53.8 1.0 O A:LYS455 4.4 56.6 1.0 O A:HOH744 4.4 52.9 1.0 O A:HOH710 4.5 44.5 1.0 N A:LYS455 4.5 48.6 1.0 CA A:GLY456 4.5 55.8 1.0 CB A:MET454 4.6 49.8 1.0 N A:THR459 4.6 56.2 1.0 N A:LYS457 4.6 59.1 1.0 CA A:LYS457 4.7 58.1 1.0 O A:LYS457 4.7 60.8 1.0 O A:HOH753 4.7 51.5 1.0 CA A:THR459 4.8 56.2 1.0 O A:HOH706 4.8 57.7 1.0 CA A:LYS455 4.8 49.8 1.0

A.Cousido-Siah, L.Carneiro, C.Kostmann, P.Ecsedi, L.Nyitray, G.Trave, G.Gogl. A Scalable Strategy to Solve Structures of Pdz Domains and Their Complexes. Acta Crystallogr D Struct V. 78 509 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35362473
DOI: 10.1107/S2059798322001784