Magnesium in PDB 6kyh: Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras

The structure of Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras, PDB code: 6kyh 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)	46.75 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.569, 154.464, 116.949, 90.00, 108.35, 90.00
R / Rfree (%)	22.7 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras (pdb code 6kyh). 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 A42K Mutant in Complex with Hras, PDB code: 6kyh:
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 A42K Mutant in Complex with Hras


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 A42K Mutant in Complex with Hras within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:63.3 occ:1.00 OG1 F:THR35 1.4 53.8 1.0 OG F:SER17 1.5 48.6 1.0 O3G F:GNP201 1.7 68.4 1.0 O2B F:GNP201 2.5 72.6 1.0 CB F:THR35 2.8 52.1 1.0 CB F:SER17 2.9 48.1 1.0 PG F:GNP201 3.2 68.3 1.0 OD2 F:ASP57 3.3 43.2 1.0 CG2 F:THR35 3.6 52.5 1.0 OD1 F:ASP57 3.7 40.2 1.0 N F:THR35 3.7 52.0 1.0 PB F:GNP201 3.7 68.3 1.0 CA F:THR35 3.8 51.0 1.0 CA F:SER17 3.8 47.8 1.0 CG F:ASP57 3.9 42.4 1.0 N3B F:GNP201 3.9 69.9 1.0 O2G F:GNP201 3.9 67.3 1.0 N F:SER17 3.9 48.7 1.0 O1G F:GNP201 4.1 59.7 1.0 O F:ASP33 4.3 66.8 1.0 O F:THR58 4.4 44.2 1.0 O1B F:GNP201 4.5 73.9 1.0 C F:PRO34 4.7 54.7 1.0 O2A F:GNP201 4.7 57.8 1.0 NZ F:LYS16 4.7 47.6 1.0 O1A F:GNP201 4.9 65.4 1.0 CE F:LYS16 4.9 47.6 1.0 O3A F:GNP201 4.9 63.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras


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 A42K Mutant in Complex with Hras within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg202 b:42.1 occ:1.00 O2B G:GNP201 1.6 67.4 1.0 OG G:SER17 1.6 53.6 1.0 OG1 G:THR35 1.9 40.3 1.0 O3G G:GNP201 2.3 74.0 1.0 PB G:GNP201 2.8 65.5 1.0 CB G:SER17 3.0 53.9 1.0 CB G:THR35 3.1 43.0 1.0 OD2 G:ASP57 3.1 52.1 1.0 O1B G:GNP201 3.3 66.2 1.0 O1A G:GNP201 3.3 51.1 1.0 OD1 G:ASP57 3.4 63.3 1.0 N G:SER17 3.5 56.7 1.0 PG G:GNP201 3.6 67.6 1.0 CG G:ASP57 3.6 55.9 1.0 CA G:SER17 3.7 52.2 1.0 N3B G:GNP201 3.7 65.2 1.0 CG2 G:THR35 3.9 43.2 1.0 O3A G:GNP201 4.0 56.8 1.0 O G:THR58 4.1 43.5 1.0 N G:THR35 4.1 47.4 1.0 CA G:THR35 4.2 44.2 1.0 PA G:GNP201 4.2 51.7 1.0 CB G:LYS16 4.3 61.4 1.0 O2G G:GNP201 4.5 64.4 1.0 C G:LYS16 4.5 57.5 1.0 CE G:LYS16 4.6 64.2 1.0 O1G G:GNP201 4.6 69.2 1.0 NZ G:LYS16 4.7 63.2 1.0 O G:ASP33 4.8 59.0 1.0 O2A G:GNP201 4.8 50.5 1.0 CA G:LYS16 4.9 59.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras


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 A42K Mutant in Complex with Hras within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg202 b:50.3 occ:1.00 OG H:SER17 1.5 64.5 1.0 O2B H:GNP201 1.7 68.1 1.0 OG1 H:THR35 1.8 61.1 1.0 O3G H:GNP201 2.2 67.3 1.0 CB H:SER17 2.9 62.5 1.0 NZ H:LYS16 2.9 64.8 1.0 PB H:GNP201 3.0 67.4 1.0 CB H:THR35 3.2 61.9 1.0 O1A H:GNP201 3.4 58.3 1.0 OD2 H:ASP57 3.4 46.2 1.0 O1B H:GNP201 3.5 74.5 1.0 PG H:GNP201 3.5 69.3 1.0 OD1 H:ASP57 3.6 48.5 1.0 N3B H:GNP201 3.7 68.2 1.0 N H:SER17 3.7 59.9 1.0 CA H:SER17 3.7 59.7 1.0 CG H:ASP57 3.8 47.5 1.0 CG2 H:THR35 3.9 64.3 1.0 N H:THR35 3.9 58.4 1.0 O3A H:GNP201 4.2 64.4 1.0 CA H:THR35 4.2 59.5 1.0 O H:ASP33 4.2 61.7 1.0 O H:THR58 4.3 43.6 1.0 PA H:GNP201 4.3 61.3 1.0 CE H:LYS16 4.3 61.3 1.0 O2G H:GNP201 4.4 71.4 1.0 O1G H:GNP201 4.5 76.7 1.0 C H:PRO34 4.8 61.5 1.0 C H:LYS16 4.8 56.9 1.0 CB H:LYS16 4.9 56.8 1.0 O2A H:GNP201 4.9 63.9 1.0 O H:THR35 4.9 68.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of SHANK3 Ntd-Ank A42K Mutant in Complex with Hras


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 A42K Mutant in Complex with Hras within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:60.2 occ:1.00 OG E:SER17 1.2 59.0 1.0 OG1 E:THR35 1.9 64.8 1.0 O3G E:GNP201 2.0 81.4 1.0 O2B E:GNP201 2.1 90.8 1.0 CB E:SER17 2.6 58.3 1.0 CB E:THR35 3.1 59.4 1.0 OD2 E:ASP57 3.3 47.4 1.0 PB E:GNP201 3.4 79.0 1.0 CA E:SER17 3.4 57.5 1.0 PG E:GNP201 3.4 76.8 1.0 N E:SER17 3.4 60.3 1.0 OD1 E:ASP57 3.6 49.1 1.0 N3B E:GNP201 3.8 77.0 1.0 CG E:ASP57 3.8 47.2 1.0 CG2 E:THR35 3.9 59.0 1.0 O1B E:GNP201 4.1 76.8 1.0 O E:ASP33 4.1 63.2 1.0 N E:THR35 4.1 56.4 1.0 CA E:THR35 4.2 56.6 1.0 O2G E:GNP201 4.3 71.9 1.0 O1G E:GNP201 4.3 71.3 1.0 O2A E:GNP201 4.4 60.4 1.0 O3A E:GNP201 4.5 71.4 1.0 C E:LYS16 4.6 59.8 1.0 O E:THR58 4.6 52.8 1.0 O1A E:GNP201 4.8 64.6 1.0 PA E:GNP201 4.8 65.0 1.0 CB E:LYS16 4.8 56.4 1.0 C E:SER17 4.8 54.4 1.0 C E:PRO34 4.9 56.8 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.