Calcium in PDB 7pcb: The Pdz Domain of SNX27 Fused with ANXA2

The structure of The Pdz Domain of SNX27 Fused with ANXA2, PDB code: 7pcb 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)	46.17 / 2.00
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.68, 59.21, 180.96, 90, 90, 90
R / Rfree (%)	19 / 20.5

The binding sites of Calcium atom in the The Pdz Domain of SNX27 Fused with ANXA2 (pdb code 7pcb). 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 SNX27 Fused with ANXA2, PDB code: 7pcb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the The Pdz Domain of SNX27 Fused with ANXA2


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 SNX27 Fused with ANXA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:71.6 occ:1.00 O A:GLY165 2.4 59.7 1.0 O A:HOH812 2.5 68.8 1.0 O A:HOH802 2.5 69.7 1.0 O A:HOH781 2.5 63.7 1.0 OE1 A:GLU168 2.5 68.9 1.0 O A:VAL166 2.5 63.9 1.0 OE2 A:GLU168 2.6 68.5 1.0 CD A:GLU168 2.9 65.1 1.0 C A:GLY165 3.4 64.0 1.0 C A:VAL166 3.7 60.6 1.0 N A:VAL166 4.2 63.0 1.0 CA A:GLY165 4.3 67.8 1.0 CA A:VAL166 4.3 59.6 1.0 CG A:GLU168 4.4 53.7 1.0 CB A:VAL166 4.5 54.3 1.0 N A:GLU168 4.8 52.0 1.0 N A:ASP167 4.8 56.8 1.0

Calcium binding site 2 out of 5 in the The Pdz Domain of SNX27 Fused with ANXA2


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 SNX27 Fused with ANXA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:63.7 occ:1.00 O A:LYS203 2.5 58.8 1.0 O A:HOH813 2.5 68.0 1.0 O A:LEU206 2.6 48.0 1.0 O A:HOH678 2.7 73.2 1.0 OE1 A:GLU211 2.9 54.3 1.0 CD A:GLU211 3.6 50.9 1.0 OE2 A:GLU211 3.6 56.4 1.0 C A:LYS203 3.7 53.3 1.0 C A:LEU206 3.7 44.5 1.0 CA A:SER207 4.2 46.4 1.0 CA A:SER204 4.3 56.8 1.0 CB A:SER207 4.4 49.9 1.0 N A:SER207 4.4 45.8 1.0 N A:SER204 4.5 52.7 1.0 C A:SER204 4.5 58.6 1.0 O A:SER204 4.5 66.2 1.0 CA A:LYS203 4.8 49.1 1.0 CG A:LYS203 4.8 56.0 1.0 N A:LEU206 4.8 44.5 1.0 CG A:GLU211 4.8 42.0 1.0 CA A:LEU206 4.9 42.4 1.0

Calcium binding site 3 out of 5 in the The Pdz Domain of SNX27 Fused with ANXA2


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 SNX27 Fused with ANXA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:47.0 occ:1.00 O A:HOH780 2.5 56.8 1.0 O A:GLY235 2.6 48.1 1.0 O A:HOH602 2.7 55.2 1.0 OD1 A:ASP277 2.7 59.2 1.0 O A:GLY237 2.8 58.8 1.0 O A:MET233 2.8 47.4 1.0 OD2 A:ASP277 3.0 59.3 1.0 CG A:ASP277 3.2 56.6 1.0 O A:LEU236 3.5 74.0 1.0 C A:MET233 3.7 47.6 1.0 C A:GLY235 3.7 52.3 1.0 C A:GLY237 3.8 62.2 1.0 C A:LEU236 3.9 67.7 1.0 OG1 A:THR238 4.2 55.6 1.0 C A:LYS234 4.2 56.8 1.0 O A:LYS234 4.3 59.9 1.0 CA A:MET233 4.3 41.4 1.0 N A:GLY235 4.4 55.1 1.0 N A:GLY237 4.5 66.5 1.0 N A:LYS234 4.5 51.1 1.0 N A:LEU236 4.5 52.3 1.0 CA A:LEU236 4.5 59.4 1.0 CA A:GLY235 4.7 53.1 1.0 N A:THR238 4.7 55.0 1.0 CA A:GLY237 4.7 67.5 1.0 CA A:LYS234 4.7 57.6 1.0 CB A:ASP277 4.7 45.8 1.0 CB A:MET233 4.9 38.3 1.0 CA A:THR238 4.9 49.0 1.0

Calcium binding site 4 out of 5 in the The Pdz Domain of SNX27 Fused with ANXA2


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 SNX27 Fused with ANXA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:46.0 occ:1.00 O A:GLY317 2.4 41.4 1.0 O A:ARG320 2.4 52.1 1.0 O A:HOH768 2.4 55.4 1.0 O A:GLY322 2.4 45.8 1.0 O A:HOH721 2.4 53.6 1.0 OE2 A:GLU362 2.5 45.0 1.0 OE1 A:GLU362 2.5 43.5 1.0 CD A:GLU362 2.8 42.7 1.0 C A:GLY317 3.3 40.5 1.0 C A:GLY322 3.4 48.1 1.0 C A:ARG320 3.6 52.7 1.0 N A:GLY322 3.6 51.4 1.0 O A:HOH828 4.0 76.7 1.0 C A:LYS321 4.0 52.9 1.0 CA A:GLY322 4.0 48.1 1.0 CA A:GLY317 4.1 38.7 1.0 N A:VAL318 4.2 39.7 1.0 OG1 A:THR323 4.2 45.9 1.0 CA A:VAL318 4.2 43.3 1.0 CA A:LYS321 4.3 56.5 1.0 CG A:GLU362 4.3 39.3 1.0 O A:HOH623 4.3 49.0 1.0 N A:LYS321 4.4 54.0 1.0 C A:VAL318 4.4 46.9 1.0 N A:ARG320 4.4 55.0 1.0 O A:VAL318 4.5 49.5 1.0 O A:HOH705 4.5 51.9 1.0 N A:THR323 4.5 46.7 1.0 CA A:ARG320 4.6 53.0 1.0 CG A:ARG320 4.6 49.5 1.0 O A:LYS321 4.7 52.4 1.0 O A:HOH775 4.8 63.9 1.0 CA A:THR323 4.8 44.4 1.0

Calcium binding site 5 out of 5 in the The Pdz Domain of SNX27 Fused with ANXA2


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 SNX27 Fused with ANXA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:34.0 occ:1.00 O A:GLY397 2.4 35.0 1.0 O A:GLY395 2.4 37.1 1.0 O A:MET393 2.4 33.2 1.0 OD2 A:ASP437 2.5 31.2 1.0 OD1 A:ASP437 2.5 34.2 1.0 CG A:ASP437 2.8 35.2 1.0 C A:MET393 3.4 30.8 1.0 C A:GLY397 3.5 36.3 1.0 C A:GLY395 3.6 38.7 1.0 N A:GLY397 3.9 39.0 1.0 CA A:MET393 4.0 31.1 1.0 N A:GLY395 4.1 32.0 1.0 CA A:GLY397 4.2 36.8 1.0 CB A:ASP437 4.3 35.0 1.0 C A:LYS396 4.3 37.4 1.0 C A:LYS394 4.3 33.0 1.0 OG1 A:THR398 4.4 35.8 1.0 O A:HOH649 4.4 48.4 1.0 N A:LYS394 4.5 28.7 1.0 CA A:GLY395 4.5 30.5 1.0 N A:THR398 4.6 30.9 1.0 CB A:MET393 4.6 33.6 1.0 N A:LYS396 4.6 37.2 1.0 O A:LYS394 4.7 36.2 1.0 CA A:LYS396 4.7 36.3 1.0 O A:LYS396 4.8 37.2 1.0 CA A:THR398 4.8 32.6 1.0 O A:HOH761 4.9 42.7 1.0 CA A:LYS394 4.9 31.2 1.0 O A:HOH693 4.9 34.7 1.0 CA A:ASP437 5.0 38.1 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