Magnesium in PDB 6jwp: Crystal Structure of Egoc

The structure of Crystal Structure of Egoc, PDB code: 6jwp was solved by T.Zhang, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.24 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.675, 120.547, 323.274, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28.5

The binding sites of Magnesium atom in the Crystal Structure of Egoc (pdb code 6jwp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Egoc, PDB code: 6jwp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Egoc


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 Egoc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:88.5 occ:1.00 O2A A:GNP401 2.4 79.1 1.0 OG1 A:THR41 2.7 96.8 1.0 OG A:SER20 2.7 87.5 1.0 N A:THR41 2.7 97.2 1.0 O2B A:GNP401 2.8 86.0 1.0 O A:GLY39 3.0 97.9 1.0 O1G A:GNP401 3.0 94.5 1.0 CB A:SER20 3.2 88.0 1.0 C A:ALA40 3.4 94.7 1.0 CA A:ALA40 3.5 91.6 1.0 CB A:THR41 3.6 0.3 1.0 CA A:THR41 3.6 0.3 1.0 PA A:GNP401 3.7 75.4 1.0 C A:GLY39 3.9 94.8 1.0 PB A:GNP401 3.9 88.3 1.0 CG2 A:THR41 4.0 0.2 1.0 PG A:GNP401 4.1 95.0 1.0 N A:ALA40 4.1 91.7 1.0 N3B A:GNP401 4.2 91.6 1.0 O1A A:GNP401 4.2 74.7 1.0 O3A A:GNP401 4.2 82.1 1.0 O3G A:GNP401 4.4 95.2 1.0 O A:ALA40 4.5 94.7 1.0 CA A:SER20 4.6 86.0 1.0 CB A:ALA40 4.7 89.1 1.0 N A:SER20 4.8 86.0 1.0 O5' A:GNP401 4.9 73.7 1.0 C A:THR41 5.0 0.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Egoc


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 Egoc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:70.7 occ:1.00 O1G B:GNP401 2.0 95.0 1.0 O2B B:GNP401 2.3 82.5 1.0 OG B:SER23 2.4 76.6 1.0 OG1 B:THR44 2.7 91.0 1.0 PG B:GNP401 2.9 93.9 1.0 N3B B:GNP401 3.0 88.6 1.0 PB B:GNP401 3.2 84.9 1.0 NH1 B:ARG19 3.2 0.1 1.0 O2G B:GNP401 3.4 93.8 1.0 N B:THR44 3.5 97.7 1.0 CB B:SER23 3.5 77.9 1.0 OE1 B:GLU62 3.6 73.0 1.0 OE2 B:GLU62 3.9 73.3 1.0 CB B:THR44 3.9 91.7 1.0 CD B:GLU62 4.1 73.2 1.0 CA B:THR44 4.2 95.2 1.0 O3G B:GNP401 4.2 93.8 1.0 O3A B:GNP401 4.2 86.2 1.0 O2A B:GNP401 4.2 84.7 1.0 CA B:SER43 4.3 97.1 1.0 O B:THR44 4.3 92.6 1.0 O1B B:GNP401 4.4 80.2 1.0 C B:SER43 4.4 98.3 1.0 N B:SER23 4.4 77.8 1.0 O B:GLU42 4.5 94.3 1.0 CG2 B:THR44 4.5 85.7 1.0 CZ B:ARG19 4.5 0.5 1.0 CA B:SER23 4.6 78.2 1.0 PA B:GNP401 4.7 87.6 1.0 C B:THR44 4.8 95.8 1.0 O1A B:GNP401 4.8 88.6 1.0 C B:GLU42 5.0 95.7 1.0 N B:SER43 5.0 96.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Egoc


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 Egoc within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:44.0 occ:1.00 OG F:SER20 2.3 44.1 1.0 O3G F:GNP401 2.4 56.6 1.0 O2B F:GNP401 2.4 52.5 1.0 O2A F:GNP401 2.4 51.1 1.0 OG1 F:THR41 2.6 46.9 1.0 PG F:GNP401 2.9 56.5 1.0 O1G F:GNP401 3.0 55.2 1.0 N3B F:GNP401 3.0 54.6 1.0 PB F:GNP401 3.1 53.2 1.0 CB F:SER20 3.2 45.5 1.0 N F:THR41 3.2 51.0 1.0 PA F:GNP401 3.4 50.4 1.0 CB F:THR41 3.4 47.9 1.0 O3A F:GNP401 3.6 51.7 1.0 O F:GLY39 3.8 60.5 1.0 CA F:THR41 3.9 49.5 1.0 O1A F:GNP401 3.9 49.9 1.0 CA F:ALA40 4.0 53.4 1.0 C F:ALA40 4.1 52.4 1.0 O2G F:GNP401 4.3 55.8 1.0 N F:SER20 4.4 46.6 1.0 CA F:SER20 4.4 45.9 1.0 O1B F:GNP401 4.6 53.6 1.0 C F:GLY39 4.7 58.0 1.0 CG2 F:THR41 4.7 47.6 1.0 O5' F:GNP401 4.8 48.7 1.0 N F:ALA40 4.8 56.2 1.0 OD2 F:ASP61 5.0 50.9 1.0

T.Zhang, M.P.Peli-Gulli, Z.Zhang, X.Tang, J.Ye, C.De Virgilio, J.Ding. Structural Insights Into the Ego-Tc-Mediated Membrane Tethering of the TORC1-Regulatory Rag Gtpases. Sci Adv V. 5 X8164 2019.
ISSN: ESSN 2375-2548
PubMed: 31579828
DOI: 10.1126/SCIADV.AAX8164