Magnesium in PDB 8vm2: Crystal Structure of Nras Q61K Bound to Gtp

All present enzymatic activity of Crystal Structure of Nras Q61K Bound to Gtp:
3.6.5.2;

The structure of Crystal Structure of Nras Q61K Bound to Gtp, PDB code: 8vm2 was solved by T.Gebregiworgis, J.Y.L.Chan, D.A.Kuntz, G.G.Prive, C.B.Marshall, M.Ikura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 1.74
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.789, 55.699, 149.291, 90, 98.15, 90
R / Rfree (%)	17.2 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Nras Q61K Bound to Gtp (pdb code 8vm2). 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 Nras Q61K Bound to Gtp, PDB code: 8vm2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Nras Q61K Bound to Gtp


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 Nras Q61K Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:15.6 occ:1.00 OG A:SER17 2.0 17.6 1.0 O3G A:GTP201 2.0 17.1 1.0 O A:HOH310 2.1 15.2 1.0 OG1 A:THR35 2.1 19.9 1.0 O1B A:GTP201 2.1 17.6 1.0 O A:HOH323 2.2 21.1 1.0 CB A:THR35 3.0 17.3 1.0 CB A:SER17 3.1 17.9 1.0 PG A:GTP201 3.2 16.8 1.0 PB A:GTP201 3.3 15.6 1.0 O3B A:GTP201 3.4 14.8 1.0 N A:THR35 3.8 20.2 1.0 N A:SER17 3.9 14.2 1.0 O1G A:GTP201 4.0 17.6 1.0 CA A:THR35 4.0 19.3 1.0 CA A:SER17 4.0 17.3 1.0 OD2 A:ASP57 4.0 17.4 1.0 CG2 A:THR35 4.1 17.5 1.0 OD1 A:ASP57 4.1 16.4 1.0 O A:HOH355 4.2 30.4 1.0 O3A A:GTP201 4.2 17.5 1.0 O2A A:GTP201 4.3 17.8 1.0 O2B A:GTP201 4.4 14.8 1.0 O2G A:GTP201 4.4 21.8 1.0 O A:ASP33 4.4 24.7 1.0 CG A:ASP57 4.4 15.0 1.0 O A:THR58 4.5 14.8 1.0 O1A A:GTP201 4.6 17.8 1.0 PA A:GTP201 4.6 17.7 1.0 C A:PRO34 4.7 22.6 1.0 CB A:LYS16 4.9 12.2 1.0 CE A:LYS16 4.9 11.6 1.0 C A:LYS16 5.0 13.6 1.0 O A:HOH427 5.0 26.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Nras Q61K Bound to Gtp


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 Nras Q61K Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:13.8 occ:1.00 OG B:SER17 1.9 16.0 1.0 O2G B:GTP201 2.0 13.2 1.0 O2B B:GTP201 2.1 15.1 1.0 O B:HOH328 2.1 12.2 1.0 OG1 B:THR35 2.1 17.0 1.0 O B:HOH343 2.1 16.4 1.0 CB B:THR35 3.1 15.1 1.0 CB B:SER17 3.1 14.0 1.0 PB B:GTP201 3.3 14.9 1.0 PG B:GTP201 3.3 14.9 1.0 O3B B:GTP201 3.4 12.5 1.0 N B:THR35 3.8 16.2 1.0 N B:SER17 3.8 14.4 1.0 CA B:SER17 4.0 16.2 1.0 CA B:THR35 4.0 15.9 1.0 OD2 B:ASP57 4.0 19.2 1.0 O3G B:GTP201 4.1 12.4 1.0 CG2 B:THR35 4.1 15.1 1.0 OD1 B:ASP57 4.1 17.4 1.0 O3A B:GTP201 4.2 14.3 1.0 O B:HOH320 4.3 31.2 1.0 O2A B:GTP201 4.3 16.3 1.0 O1G B:GTP201 4.4 17.1 1.0 O1B B:GTP201 4.4 16.8 1.0 O B:ASP33 4.4 21.8 1.0 CG B:ASP57 4.5 16.4 1.0 O B:THR58 4.5 16.0 1.0 PA B:GTP201 4.5 16.5 1.0 O1A B:GTP201 4.5 15.5 1.0 C B:PRO34 4.7 18.2 1.0 CE B:LYS16 4.9 12.3 1.0 C B:LYS16 4.9 13.0 1.0 CB B:LYS16 5.0 11.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Nras Q61K Bound to Gtp


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 Nras Q61K Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:15.0 occ:1.00 O2G C:GTP201 2.0 15.3 1.0 OG C:SER17 2.0 12.7 1.0 O2B C:GTP201 2.0 13.2 1.0 OG1 C:THR35 2.1 15.7 1.0 O C:HOH306 2.1 13.2 1.0 O C:HOH339 2.2 16.5 1.0 CB C:THR35 3.0 17.1 1.0 CB C:SER17 3.1 12.3 1.0 PG C:GTP201 3.2 15.2 1.0 PB C:GTP201 3.2 13.9 1.0 O3B C:GTP201 3.4 13.6 1.0 N C:SER17 3.8 10.6 1.0 N C:THR35 3.9 16.6 1.0 O3G C:GTP201 4.0 14.0 1.0 CA C:SER17 4.0 10.9 1.0 CG2 C:THR35 4.0 19.0 1.0 OD2 C:ASP57 4.1 14.3 1.0 CA C:THR35 4.1 16.5 1.0 OD1 C:ASP57 4.1 16.1 1.0 O3A C:GTP201 4.1 10.5 1.0 O C:HOH309 4.2 23.6 1.0 O2A C:GTP201 4.2 16.7 1.0 O1B C:GTP201 4.4 12.9 1.0 O1G C:GTP201 4.4 18.9 1.0 O C:ASP33 4.4 17.6 1.0 CG C:ASP57 4.5 17.9 1.0 O C:THR58 4.5 17.1 1.0 PA C:GTP201 4.5 12.9 1.0 O1A C:GTP201 4.5 13.1 1.0 C C:PRO34 4.7 17.4 1.0 CB C:LYS16 4.9 9.8 1.0 C C:LYS16 4.9 12.3 1.0 CE C:LYS16 5.0 11.5 1.0

T.Gebregiworgis, J.Y.Chan, D.A.Kuntz, G.G.Prive, C.B.Marshall, M.Ikura. Crystal Structure of Nras Q61K with A Ligand-Induced Pocket Near Switch II. Eur J Cell Biol V. 103 51414 2024.
ISSN: ISSN 1618-1298
PubMed: 38640594
DOI: 10.1016/J.EJCB.2024.151414