Magnesium in PDB 7c7j: Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E)

The structure of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E), PDB code: 7c7j was solved by L.X.Xiao, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.215, 191.926, 48.876, 90, 90, 90
R / Rfree (%)	18.5 / 25.5

The structure of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E) (pdb code 7c7j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E), PDB code: 7c7j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:33.5 occ:1.00 OG A:SER17 2.1 49.8 1.0 OG1 A:THR35 2.2 34.7 1.0 O1G A:GTP201 2.2 66.3 1.0 O2B A:GTP201 2.5 22.7 1.0 PG A:GTP201 2.9 73.4 1.0 O3G A:GTP201 3.0 73.4 1.0 O A:ASP33 3.2 53.4 1.0 CB A:SER17 3.2 22.9 1.0 O2A A:GTP201 3.2 34.6 1.0 O3B A:GTP201 3.4 49.0 1.0 CB A:THR35 3.4 32.9 1.0 PB A:GTP201 3.5 27.2 1.0 N A:THR35 3.8 43.2 1.0 O A:HOH315 3.9 25.9 1.0 PA A:GTP201 4.0 34.3 1.0 O3A A:GTP201 4.1 28.3 1.0 CA A:THR35 4.1 41.6 1.0 CE1 A:TYR32 4.2 39.2 1.0 O2G A:GTP201 4.3 72.2 1.0 O1A A:GTP201 4.4 29.7 1.0 C A:ASP33 4.4 49.7 1.0 CA A:SER17 4.4 33.8 1.0 N A:SER17 4.4 32.4 1.0 OD2 A:ASP57 4.4 73.1 1.0 C A:PRO34 4.4 47.9 1.0 CG2 A:THR35 4.5 25.3 1.0 CD1 A:TYR32 4.7 37.9 1.0 CA A:PRO34 4.7 45.4 1.0 OD1 A:ASP57 4.7 71.7 1.0 O1B A:GTP201 4.9 31.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:39.3 occ:1.00 O1G B:GTP201 2.0 62.2 1.0 OG B:SER17 2.1 49.2 1.0 OG1 B:THR35 2.4 47.0 1.0 O2B B:GTP201 2.5 24.9 1.0 PG B:GTP201 2.8 87.6 1.0 O2A B:GTP201 3.0 28.3 1.0 CB B:SER17 3.1 24.0 1.0 O3G B:GTP201 3.2 97.8 1.0 O B:ASP33 3.2 68.4 1.0 O3B B:GTP201 3.2 52.2 1.0 PB B:GTP201 3.4 25.2 1.0 CB B:THR35 3.7 44.7 1.0 O B:HOH316 3.9 37.7 1.0 PA B:GTP201 3.9 24.9 1.0 N B:THR35 4.1 43.4 1.0 O3A B:GTP201 4.1 32.6 1.0 N B:SER17 4.2 22.4 1.0 O2G B:GTP201 4.2 89.8 1.0 CA B:SER17 4.3 34.2 1.0 O1A B:GTP201 4.3 29.6 1.0 C B:ASP33 4.4 61.0 1.0 OD2 B:ASP57 4.4 68.0 1.0 CE1 B:TYR32 4.5 39.9 1.0 CA B:THR35 4.5 40.9 1.0 CA B:PRO34 4.6 55.8 1.0 C B:PRO34 4.7 59.8 1.0 O1B B:GTP201 4.7 30.6 1.0 OD1 B:ASP57 4.8 76.1 1.0 CG2 B:THR35 4.8 43.1 1.0 CD1 B:TYR32 4.9 41.0 1.0 N B:PRO34 5.0 59.9 1.0

X.L.Xu, J.P.Liu, Y.L.Wang, Y.Wang, X.Gong, L.F.Pan. Mechanistic Insights Into the Interactions of Ras Subfamily Gtpases with the Spn Domain of Autism-Associated SHANK3. Chin.J.Chem. V. 38 1635 2020.
ISSN: ISSN 1001-604X
DOI: 10.1002/CJOC.202000278