Magnesium in PDB 6kyk: Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1

The structure of Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1, PDB code: 6kyk was solved by Q.Cai, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 2.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.032, 54.107, 203.110, 90.00, 109.51, 90.00
R / Rfree (%)	24 / 30

The binding sites of Magnesium atom in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1 (pdb code 6kyk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1, PDB code: 6kyk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1


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 Ntd-Ank Mutant in Complex with RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:52.9 occ:1.00 OG C:SER17 1.5 61.3 1.0 OG1 C:THR35 1.7 51.6 1.0 O C:HOH303 1.9 67.7 1.0 O3G C:GNP201 2.2 54.7 1.0 O2B C:GNP201 2.3 58.8 1.0 O C:HOH301 2.6 41.0 1.0 CB C:SER17 2.9 64.1 1.0 CB C:THR35 2.9 57.2 1.0 OD2 C:ASP57 3.3 52.6 1.0 CG2 C:THR35 3.5 60.5 1.0 PB C:GNP201 3.6 54.1 1.0 PG C:GNP201 3.6 58.4 1.0 N C:SER17 3.7 55.9 1.0 OD1 C:ASP57 3.7 74.2 1.0 CA C:SER17 3.7 61.6 1.0 CG C:ASP57 3.8 59.1 1.0 O C:THR58 4.0 52.5 1.0 N3B C:GNP201 4.0 59.7 1.0 CA C:THR35 4.2 61.2 1.0 O1A C:GNP201 4.2 51.5 1.0 N C:THR35 4.2 67.8 1.0 O1B C:GNP201 4.4 62.6 1.0 O2G C:GNP201 4.5 56.1 1.0 O1G C:GNP201 4.6 66.0 1.0 CB C:LYS16 4.6 47.3 1.0 O C:ASP33 4.6 59.4 1.0 O3A C:GNP201 4.6 52.9 1.0 C C:LYS16 4.7 55.5 1.0 PA C:GNP201 4.8 54.7 1.0 O2A C:GNP201 4.8 55.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1


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 Ntd-Ank Mutant in Complex with RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:91.8 occ:1.00 OG1 D:THR35 1.6 65.4 1.0 OG D:SER17 1.7 54.8 1.0 O2B D:GNP201 2.0 51.0 1.0 O3G D:GNP201 2.1 72.9 1.0 O D:HOH303 2.2 39.7 1.0 O D:HOH305 2.2 36.0 1.0 CB D:SER17 2.9 52.8 1.0 CB D:THR35 3.0 63.7 1.0 PB D:GNP201 3.3 50.7 1.0 PG D:GNP201 3.5 71.3 1.0 N3B D:GNP201 3.6 60.5 1.0 CG2 D:THR35 3.7 65.2 1.0 OD2 D:ASP57 3.8 52.5 1.0 O1A D:GNP201 3.8 52.1 1.0 N D:THR35 3.9 56.9 1.0 CA D:SER17 4.0 58.8 1.0 N D:SER17 4.0 62.0 1.0 CA D:THR35 4.0 59.9 1.0 O D:ASP33 4.1 84.3 1.0 O1G D:GNP201 4.2 62.8 1.0 O1B D:GNP201 4.3 47.3 1.0 O3A D:GNP201 4.3 44.2 1.0 O2A D:GNP201 4.3 57.0 1.0 PA D:GNP201 4.4 52.4 1.0 O2G D:GNP201 4.5 58.4 1.0 OD1 D:ASP57 4.5 46.4 1.0 CG D:ASP57 4.5 50.7 1.0 C D:PRO34 4.7 63.3 1.0 O D:THR58 4.7 44.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:64.9 occ:1.00 OG E:SER17 1.6 75.9 1.0 O E:HOH303 2.0 47.1 1.0 O3G E:GNP201 2.1 62.8 1.0 O2B E:GNP201 2.2 79.0 1.0 O E:HOH302 2.3 60.4 1.0 OG1 E:THR35 2.4 60.8 1.0 CB E:SER17 2.9 78.2 1.0 CG2 E:THR35 3.3 61.7 1.0 CB E:THR35 3.4 65.9 1.0 PG E:GNP201 3.5 70.7 1.0 OD2 E:ASP57 3.5 55.8 1.0 PB E:GNP201 3.6 65.7 1.0 N E:SER17 3.8 72.2 1.0 CA E:SER17 3.8 77.1 1.0 OD1 E:ASP57 3.9 60.7 1.0 N3B E:GNP201 4.0 69.5 1.0 O1A E:GNP201 4.0 59.6 1.0 CG E:ASP57 4.1 55.8 1.0 N E:THR35 4.2 66.8 1.0 O E:THR58 4.2 60.1 1.0 O2G E:GNP201 4.2 76.7 1.0 CA E:THR35 4.4 64.8 1.0 O1B E:GNP201 4.4 81.7 1.0 O1G E:GNP201 4.5 79.6 1.0 O E:ASP33 4.5 54.2 1.0 O3A E:GNP201 4.6 61.2 1.0 PA E:GNP201 4.6 67.5 1.0 O2A E:GNP201 4.7 71.4 1.0 CB E:LYS16 4.8 57.0 1.0 C E:LYS16 4.8 68.0 1.0 O E:HOH305 4.9 39.2 1.0 C E:PRO34 5.0 61.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of SHANK3 Ntd-Ank Mutant in Complex with RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:85.7 occ:1.00 OG F:SER17 1.5 58.3 1.0 O F:HOH303 1.7 44.2 1.0 OG1 F:THR35 1.8 69.5 1.0 O2B F:GNP201 2.0 64.9 1.0 O3G F:GNP201 2.3 57.7 1.0 O F:HOH301 2.4 47.3 1.0 CB F:SER17 2.7 55.4 1.0 CB F:THR35 3.2 58.7 1.0 PB F:GNP201 3.5 60.2 1.0 PG F:GNP201 3.7 61.5 1.0 O1A F:GNP201 3.7 51.6 1.0 OD2 F:ASP57 3.8 59.4 1.0 CA F:SER17 3.9 59.5 1.0 N F:THR35 3.9 49.8 1.0 O F:ASP33 3.9 66.5 1.0 CG2 F:THR35 3.9 57.2 1.0 N F:SER17 4.0 64.7 1.0 CA F:THR35 4.1 54.4 1.0 N3B F:GNP201 4.1 61.3 1.0 O3A F:GNP201 4.2 55.0 1.0 PA F:GNP201 4.3 55.0 1.0 O2A F:GNP201 4.3 61.1 1.0 O1G F:GNP201 4.5 57.2 1.0 C F:PRO34 4.5 54.1 1.0 O1B F:GNP201 4.5 49.1 1.0 CG F:ASP57 4.6 58.8 1.0 OD1 F:ASP57 4.6 50.9 1.0 O2G F:GNP201 4.7 61.0 1.0 CA F:PRO34 4.9 62.9 1.0 O F:THR58 5.0 49.9 1.0

Q.Cai, T.Hosokawa, Y.Hayashi, M.Zhang. SHANK3 Binds to and Stabilizes the Active Form of RAP1 and Hras Gtpases Via Its Ntd-Ank Tandem with Distinct Mechanisms To Be Published.