Magnesium in PDB 3kko: Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp

The structure of Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp, PDB code: 3kko was solved by S.Muraoka, F.Shima, J.Liao, Y.Ijiri, K.Matsumoto, M.Ye, T.Inoue, T.Kataoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.196, 192.248, 43.235, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp (pdb code 3kko). 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 M-Ras P40D/D41E/L51R in Complex with Gppnhp, PDB code: 3kko:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp


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 M-Ras P40D/D41E/L51R in Complex with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg180 b:19.4 occ:1.00 O2G A:GNP179 2.0 20.9 1.0 O2B A:GNP179 2.0 16.8 1.0 OG1 A:THR45 2.1 17.1 1.0 OG A:SER27 2.1 14.3 1.0 O A:HOH1002 2.1 18.4 1.0 O A:HOH1001 2.2 15.6 1.0 CB A:SER27 3.1 14.5 1.0 CB A:THR45 3.1 17.6 1.0 PG A:GNP179 3.1 19.2 1.0 PB A:GNP179 3.2 16.5 1.0 N3B A:GNP179 3.3 17.5 1.0 N A:THR45 3.9 18.9 1.0 N A:SER27 3.9 14.5 1.0 CA A:SER27 4.0 14.6 1.0 O3G A:GNP179 4.0 20.2 1.0 OD2 A:ASP67 4.1 20.6 1.0 CA A:THR45 4.1 17.6 1.0 OD1 A:ASP67 4.1 19.6 1.0 O1A A:GNP179 4.2 18.1 1.0 CG2 A:THR45 4.2 15.2 1.0 O3A A:GNP179 4.3 16.4 1.0 O1B A:GNP179 4.3 15.4 1.0 O1G A:GNP179 4.3 20.1 1.0 O A:HOH1022 4.4 26.2 1.0 O A:ASP43 4.5 21.0 1.0 O A:THR68 4.5 17.5 1.0 CG A:ASP67 4.5 17.6 1.0 PA A:GNP179 4.5 18.0 1.0 O2A A:GNP179 4.7 17.4 1.0 C A:PRO44 4.8 20.1 1.0 CB A:LYS26 4.9 14.9 1.0 C A:LYS26 4.9 14.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp


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 M-Ras P40D/D41E/L51R in Complex with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg180 b:18.3 occ:1.00 O2G B:GNP179 2.0 18.3 1.0 OG B:SER27 2.1 15.8 1.0 O2B B:GNP179 2.1 17.0 1.0 O B:HOH1002 2.1 18.4 1.0 O B:HOH1001 2.1 18.0 1.0 OG1 B:THR45 2.1 19.5 1.0 CB B:THR45 3.1 20.3 1.0 CB B:SER27 3.1 15.6 1.0 PG B:GNP179 3.2 19.2 1.0 PB B:GNP179 3.3 17.4 1.0 N3B B:GNP179 3.3 18.1 1.0 N B:SER27 3.8 15.7 1.0 N B:THR45 3.8 21.6 1.0 OD2 B:ASP67 4.0 21.6 1.0 O3G B:GNP179 4.0 18.2 1.0 CA B:SER27 4.0 16.1 1.0 CA B:THR45 4.1 20.6 1.0 OD1 B:ASP67 4.1 21.4 1.0 CG2 B:THR45 4.2 20.5 1.0 O1A B:GNP179 4.2 17.6 1.0 O1B B:GNP179 4.3 15.9 1.0 O B:HOH1064 4.3 33.0 1.0 O3A B:GNP179 4.3 18.3 1.0 O1G B:GNP179 4.4 19.8 1.0 CG B:ASP67 4.4 21.7 1.0 O B:THR68 4.4 19.0 1.0 O B:ASP43 4.5 25.1 1.0 PA B:GNP179 4.6 18.1 1.0 O2A B:GNP179 4.7 17.1 1.0 CB B:LYS26 4.7 15.1 1.0 C B:PRO44 4.7 22.7 1.0 C B:LYS26 4.9 15.6 1.0 CE B:LYS26 4.9 15.7 1.0 CA B:PRO44 5.0 23.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of M-Ras P40D/D41E/L51R in Complex with Gppnhp


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 M-Ras P40D/D41E/L51R in Complex with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg180 b:15.9 occ:1.00 O2G P:GNP179 1.9 16.7 1.0 O2B P:GNP179 2.0 15.5 1.0 O P:HOH1002 2.1 15.5 1.0 O P:HOH1001 2.2 15.2 1.0 OG P:SER27 2.2 15.3 1.0 OG1 P:THR45 2.2 16.5 1.0 PG P:GNP179 3.1 16.5 1.0 CB P:THR45 3.2 16.8 1.0 CB P:SER27 3.2 15.3 1.0 PB P:GNP179 3.2 15.6 1.0 N3B P:GNP179 3.2 15.5 1.0 N P:THR45 3.8 17.8 1.0 O3G P:GNP179 3.9 16.3 1.0 N P:SER27 4.0 15.3 1.0 CA P:THR45 4.1 17.6 1.0 OD2 P:ASP67 4.1 18.7 1.0 CA P:SER27 4.1 15.5 1.0 O1A P:GNP179 4.1 14.3 1.0 O3A P:GNP179 4.2 14.8 1.0 OD1 P:ASP67 4.2 16.4 1.0 O1B P:GNP179 4.2 13.1 1.0 O1G P:GNP179 4.3 14.7 1.0 CG2 P:THR45 4.3 17.9 1.0 O P:HOH1061 4.4 31.7 1.0 O P:ASP43 4.4 21.5 1.0 O P:THR68 4.5 15.9 1.0 PA P:GNP179 4.5 14.7 1.0 CG P:ASP67 4.5 17.4 1.0 O2A P:GNP179 4.7 15.1 1.0 C P:PRO44 4.7 19.2 1.0 CA P:PRO44 5.0 19.9 1.0 CB P:LYS26 5.0 14.0 1.0

F.Shima, Y.Ijiri, S.Muraoka, J.Liao, M.Ye, M.Araki, K.Matsumoto, N.Yamamoto, T.Sugimoto, Y.Yoshikawa, T.Kumasaka, M.Yamamoto, A.Tamura, T.Kataoka. Structural Basis For Conformational Dynamics of Gtp-Bound Ras Protein J.Biol.Chem. V. 285 22696 2010.
ISSN: ISSN 0021-9258
PubMed: 20479006
DOI: 10.1074/JBC.M110.125161