Calcium in PDB 7qqn: The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3

The structure of The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3, PDB code: 7qqn 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)	45.47 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.83, 132.44, 63.66, 90, 100.77, 90
R / Rfree (%)	22 / 26.3

The binding sites of Calcium atom in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 (pdb code 7qqn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3, PDB code: 7qqn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


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 SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:80.7 occ:1.00 O A:HOH666 2.5 55.2 1.0 O A:VAL174 2.7 50.2 1.0 O A:GLY173 2.8 70.1 1.0 OE2 A:GLU176 3.0 61.8 1.0 OE1 A:GLU176 3.3 61.7 1.0 CD A:GLU176 3.5 61.6 1.0 C A:GLY173 3.6 71.7 1.0 C A:VAL174 3.8 55.1 1.0 CA A:GLY173 4.3 75.8 1.0 N A:VAL174 4.4 67.8 1.0 CA A:VAL174 4.6 60.2 1.0 N A:ASP175 4.8 56.2 1.0 CG A:GLU176 4.9 60.3 1.0 CA A:ASP175 4.9 56.3 1.0 N A:GLU176 5.0 54.5 1.0

Calcium binding site 2 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


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 SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:58.1 occ:1.00 O A:GLY325 2.5 61.4 1.0 O A:GLY330 2.5 61.3 1.0 OE1 A:GLU370 2.5 55.2 1.0 O A:ARG328 2.5 66.8 1.0 O A:HOH670 2.6 59.9 1.0 OE2 A:GLU370 2.8 53.6 1.0 CD A:GLU370 3.0 53.0 1.0 N A:GLY330 3.4 68.4 1.0 C A:GLY330 3.4 63.3 1.0 C A:GLY325 3.6 57.9 1.0 C A:ARG328 3.7 68.4 1.0 CA A:GLY330 3.9 66.3 1.0 C A:LYS329 4.0 69.5 1.0 CA A:LYS329 4.2 71.7 1.0 O A:VAL326 4.4 68.4 1.0 CA A:GLY325 4.4 56.4 1.0 N A:LYS329 4.4 71.3 1.0 OG1 A:THR331 4.4 64.2 1.0 N A:VAL326 4.4 56.8 1.0 CA A:VAL326 4.4 56.8 1.0 CG A:GLU370 4.5 50.7 1.0 C A:VAL326 4.5 62.5 1.0 N A:THR331 4.6 63.7 1.0 N A:ARG328 4.8 66.8 1.0 CA A:ARG328 4.8 68.4 1.0 O A:LYS329 4.8 70.0 1.0 CG A:ARG328 4.9 63.6 1.0

Calcium binding site 3 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


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 SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:69.4 occ:1.00 OD2 A:ASP445 2.4 42.5 1.0 O A:GLY403 2.4 46.9 1.0 O A:GLY405 2.5 37.0 1.0 O A:MET401 2.6 43.6 1.0 CG A:ASP445 3.1 42.3 1.0 OD1 A:ASP445 3.1 46.0 1.0 C A:MET401 3.5 41.0 1.0 C A:GLY405 3.6 43.8 1.0 C A:GLY403 3.6 47.2 1.0 N A:GLY405 3.9 47.3 1.0 CA A:MET401 4.0 37.7 1.0 N A:GLY403 4.1 42.4 1.0 OG1 A:THR406 4.2 40.3 1.0 CA A:GLY405 4.3 44.1 1.0 C A:LYS404 4.3 48.0 1.0 C A:LYS402 4.4 42.7 1.0 CA A:GLY403 4.5 46.1 1.0 N A:LYS402 4.5 41.6 1.0 CB A:ASP445 4.5 37.7 1.0 N A:LYS404 4.6 52.9 1.0 O A:HOH624 4.6 35.4 1.0 CB A:MET401 4.6 32.1 1.0 CA A:LYS404 4.6 53.3 1.0 N A:THR406 4.7 44.0 1.0 O A:LYS402 4.7 42.1 1.0 O A:LYS404 4.9 46.9 1.0 CA A:LYS402 4.9 43.4 1.0 CA A:THR406 4.9 44.5 1.0

Calcium binding site 4 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


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 SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:147.8 occ:1.00 OD1 A:ASP285 2.4 73.1 1.0 O A:GLY243 2.4 112.4 1.0 O A:GLY245 2.7 76.7 1.0 O A:MET241 2.9 67.9 1.0 CG A:ASP285 3.2 72.7 1.0 C A:GLY243 3.4 111.7 1.0 OD2 A:ASP285 3.5 75.0 1.0 N A:GLY245 3.6 102.9 1.0 C A:GLY245 3.6 78.9 1.0 C A:LEU244 3.7 117.3 1.0 CA A:LEU244 3.9 119.3 1.0 C A:MET241 4.0 66.4 1.0 N A:LEU244 4.0 117.6 1.0 CA A:GLY245 4.1 91.2 1.0 OG1 A:THR246 4.1 65.4 1.0 O A:LEU244 4.2 118.1 1.0 N A:GLY243 4.5 96.7 1.0 CA A:GLY243 4.5 104.6 1.0 CA A:MET241 4.5 60.6 1.0 CB A:ASP285 4.6 69.5 1.0 C A:LYS242 4.7 86.8 1.0 N A:THR246 4.7 70.0 1.0 O A:LYS242 5.0 83.0 1.0 N A:LYS242 5.0 73.4 1.0

Calcium binding site 5 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


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 SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:87.1 occ:1.00 O C:GLY173 2.6 60.0 1.0 O C:VAL174 2.7 51.6 1.0 OE1 C:GLU176 3.0 54.9 1.0 OE2 C:GLU176 3.2 54.6 1.0 C C:GLY173 3.4 61.1 1.0 CD C:GLU176 3.5 55.2 1.0 C C:VAL174 3.8 54.1 1.0 CA C:GLY173 4.1 62.4 1.0 N C:VAL174 4.2 59.5 1.0 O C:HOH676 4.4 47.8 1.0 CA C:VAL174 4.5 55.0 1.0 CB C:VAL174 4.9 53.8 1.0 N C:ASP175 4.9 54.8 1.0 CG C:GLU176 5.0 55.3 1.0

Calcium binding site 6 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:104.6 occ:1.00 CB C:SER215 3.3 56.5 1.0 O C:LEU214 3.6 45.7 1.0 CA C:SER215 3.7 54.2 1.0 OE1 C:GLU219 3.9 58.1 1.0 O C:LYS211 4.1 46.5 1.0 OE2 C:GLU219 4.3 60.4 1.0 C C:LEU214 4.4 47.9 1.0 CD C:GLU219 4.4 56.7 1.0 N C:SER215 4.4 49.9 1.0 OG C:SER215 4.6 56.9 1.0 NZ C:LYS211 4.7 56.1 1.0 C C:SER215 4.9 54.6 1.0 N C:GLY216 5.0 55.4 1.0

Calcium binding site 7 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:78.1 occ:1.00 O C:HOH639 2.5 48.5 1.0 OD2 C:ASP285 2.6 54.2 1.0 O C:GLY245 3.0 68.6 1.0 O C:MET241 3.2 62.8 1.0 O C:GLY243 3.2 68.3 1.0 CG C:ASP285 3.5 55.0 1.0 OD1 C:ASP285 3.8 57.5 1.0 C C:MET241 3.9 60.8 1.0 C C:GLY245 4.0 66.6 1.0 O C:LEU244 4.0 72.4 1.0 OG1 C:THR246 4.0 73.4 1.0 C C:GLY243 4.2 68.3 1.0 C C:LEU244 4.4 71.5 1.0 C C:LYS242 4.5 70.3 1.0 CA C:MET241 4.5 54.3 1.0 N C:GLY243 4.6 69.3 1.0 CE A:LYS299 4.6 66.8 1.0 N C:LYS242 4.6 68.1 1.0 CA C:GLY245 4.7 69.7 1.0 N C:GLY245 4.7 71.3 1.0 O C:LYS242 4.7 74.9 1.0 CA C:LYS242 4.7 72.0 1.0 CB C:ASP285 4.8 53.7 1.0 N C:THR246 4.8 63.4 1.0 CA C:THR246 5.0 60.9 1.0 CA C:GLY243 5.0 69.2 1.0

Calcium binding site 8 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:49.0 occ:1.00 O C:GLY330 2.2 58.0 1.0 O C:HOH620 2.3 27.2 1.0 O C:ARG328 2.4 59.7 1.0 O C:GLY325 2.4 57.1 1.0 O C:HOH702 2.5 34.9 1.0 OE1 C:GLU370 2.6 45.2 1.0 OE2 C:GLU370 2.8 44.0 1.0 CD C:GLU370 3.1 46.8 1.0 C C:GLY330 3.4 58.9 1.0 C C:GLY325 3.4 47.9 1.0 C C:ARG328 3.5 60.7 1.0 N C:GLY330 3.6 49.2 1.0 C C:LYS329 3.9 57.6 1.0 OG1 C:THR331 4.0 61.7 1.0 CA C:GLY330 4.0 57.4 1.0 CA C:LYS329 4.1 63.8 1.0 O C:HOH709 4.1 52.9 1.0 CA C:GLY325 4.2 44.2 1.0 N C:LYS329 4.2 62.9 1.0 N C:VAL326 4.4 46.9 1.0 CG C:ARG328 4.4 50.8 1.0 N C:THR331 4.5 61.5 1.0 CA C:VAL326 4.5 48.7 1.0 N C:ARG328 4.5 58.1 1.0 CA C:ARG328 4.5 58.5 1.0 CG C:GLU370 4.6 49.0 1.0 C C:VAL326 4.6 51.8 1.0 O C:LYS329 4.6 55.6 1.0 O C:VAL326 4.6 56.5 1.0 CA C:THR331 4.7 59.7 1.0 CB C:THR331 5.0 59.2 1.0

Calcium binding site 9 out of 9 in the The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Pdz Domain of SNTG1 Complexed with the Acetylated Pdz-Binding Motif of TRPV3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:51.9 occ:1.00 O C:GLY403 2.4 55.9 1.0 OD2 C:ASP445 2.4 40.9 1.0 O C:GLY405 2.5 47.5 1.0 O C:MET401 2.5 42.6 1.0 OD1 C:ASP445 2.6 40.5 1.0 CG C:ASP445 2.9 41.7 1.0 C C:MET401 3.4 45.7 1.0 C C:GLY403 3.6 54.9 1.0 C C:GLY405 3.6 44.9 1.0 CA C:MET401 3.8 47.5 1.0 N C:GLY405 4.0 47.1 1.0 N C:GLY403 4.1 51.3 1.0 C C:LYS404 4.3 48.2 1.0 C C:LYS402 4.3 50.0 1.0 CA C:GLY405 4.3 40.3 1.0 N C:LYS402 4.3 47.6 1.0 CB C:ASP445 4.4 40.8 1.0 CA C:GLY403 4.4 53.3 1.0 N C:LYS404 4.6 55.6 1.0 CB C:MET401 4.6 47.0 1.0 O C:HOH628 4.6 47.6 1.0 O C:LYS402 4.6 49.8 1.0 OG1 C:THR406 4.6 45.1 1.0 CA C:LYS404 4.7 52.4 1.0 O C:LYS404 4.7 47.0 1.0 N C:THR406 4.7 43.9 1.0 CA C:LYS402 4.8 48.5 1.0 O C:SER400 5.0 53.4 1.0 CA C:THR406 5.0 46.9 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