Magnesium in PDB 3kkq: Crystal Structure of M-Ras P40D in Complex with Gdp

The structure of Crystal Structure of M-Ras P40D in Complex with Gdp, PDB code: 3kkq 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)	29.51 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.947, 70.754, 43.445, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of M-Ras P40D in Complex with Gdp (pdb code 3kkq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of M-Ras P40D in Complex with Gdp, PDB code: 3kkq:

Magnesium binding site 1 out of 1 in the Crystal Structure of M-Ras P40D in Complex with Gdp


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 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg180 b:5.1 occ:1.00 O A:HOH1001 2.0 6.0 1.0 O2B A:GDP179 2.0 4.8 1.0 O A:HOH1003 2.1 6.6 1.0 OG A:SER27 2.1 5.5 1.0 O A:HOH1004 2.1 5.9 1.0 O A:HOH1002 2.1 6.7 1.0 CB A:SER27 3.2 5.6 1.0 PB A:GDP179 3.3 4.7 1.0 O3B A:GDP179 3.5 5.4 1.0 N A:SER27 3.9 4.9 1.0 CA A:SER27 4.1 5.5 1.0 OD2 A:ASP67 4.1 6.5 1.0 O1A A:GDP179 4.1 8.1 1.0 OD1 A:ASP67 4.2 5.6 1.0 O A:ASP43 4.2 8.9 1.0 O A:PRO44 4.3 8.5 1.0 CD2 A:TYR42 4.3 12.3 1.0 O1B A:GDP179 4.3 5.0 1.0 O3A A:GDP179 4.3 5.7 1.0 CB A:ALA69 4.4 7.7 1.0 O A:ILE46 4.5 7.8 1.0 O A:THR68 4.6 5.7 1.0 CA A:PRO44 4.6 9.4 1.0 PA A:GDP179 4.6 6.2 1.0 CG A:ASP67 4.6 5.7 1.0 O A:HOH1051 4.6 14.7 1.0 C A:PRO44 4.7 8.8 1.0 O2A A:GDP179 4.8 8.9 1.0 CE2 A:TYR42 4.8 14.8 1.0 CB A:LYS26 4.9 5.4 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