Calcium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(G12V,Q63E), PDB code: 7c7j:

Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca202 b:24.5 occ:1.00 OD1 A:ASN155 2.3 40.8 1.0 OE2 A:GLU156 2.3 27.7 1.0 OE1 B:GLU156 2.5 43.8 1.0 O A:HOH316 2.6 22.1 1.0 OD1 B:ASN155 2.6 36.3 1.0 OE1 A:GLU156 2.7 24.5 1.0 O A:HOH318 2.8 20.3 1.0 CD A:GLU156 2.9 28.3 1.0 OE2 B:GLU156 2.9 44.9 1.0 CD B:GLU156 3.1 44.0 1.0 CG A:ASN155 3.4 37.8 1.0 CG B:ASN155 3.8 42.7 1.0 ND2 A:ASN155 4.2 27.5 1.0 CG A:GLU156 4.4 28.9 1.0 N A:ASN155 4.5 30.1 1.0 N B:ASN153 4.5 24.1 1.0 CB A:ASN155 4.5 23.9 1.0 O B:LYS151 4.5 34.3 1.0 ND2 B:ASN155 4.6 48.2 1.0 N A:ASN153 4.6 26.5 1.0 N A:VAL154 4.6 27.5 1.0 N B:VAL154 4.6 25.3 1.0 CG B:GLU156 4.7 36.0 1.0 N B:ASN155 4.7 33.5 1.0 N A:GLU156 4.7 20.0 1.0 CA B:ASN153 4.7 29.1 1.0 O A:LYS151 4.7 29.7 1.0 CB B:ASN155 4.8 27.8 1.0 CA A:ASN153 4.8 25.3 1.0 N B:GLU156 5.0 25.6 1.0 CA A:ASN155 5.0 33.7 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