Magnesium in PDB 6vc8: Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion

The structure of Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion, PDB code: 6vc8 was solved by T.H.Tran, D.R.Davies, T.E.Edwards, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.91 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.21, 82.33, 88.14, 90, 112.92, 90
R / Rfree (%)	21.2 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion (pdb code 6vc8). 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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion, PDB code: 6vc8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion


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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:58.0 occ:1.00 O2B A:GNP1001 2.1 47.9 1.0 O A:HOH1103 2.1 63.4 1.0 O1G A:GNP1001 2.1 53.2 1.0 OG A:SER17 2.1 51.7 1.0 O A:HOH1101 2.1 55.2 1.0 OG1 A:THR35 2.1 82.6 1.0 PG A:GNP1001 3.0 59.0 1.0 N3B A:GNP1001 3.0 58.2 1.0 CB A:THR35 3.1 86.4 1.0 PB A:GNP1001 3.1 55.8 1.0 CB A:SER17 3.4 49.7 1.0 N A:THR35 3.7 90.1 1.0 O2A A:GNP1001 4.0 55.2 1.0 O2G A:GNP1001 4.0 60.5 1.0 N A:SER17 4.0 48.1 1.0 OD2 A:ASP57 4.0 62.2 1.0 O3G A:GNP1001 4.0 59.7 1.0 CA A:THR35 4.0 88.8 1.0 CG2 A:THR35 4.1 85.5 1.0 O3A A:GNP1001 4.1 52.0 1.0 OD1 A:ASP57 4.3 60.0 1.0 O1B A:GNP1001 4.3 51.5 1.0 CA A:SER17 4.3 48.8 1.0 PA A:GNP1001 4.5 54.2 1.0 CG A:ASP57 4.5 59.2 1.0 O A:THR58 4.5 63.3 1.0 C A:PRO34 4.7 92.3 1.0 CB A:LYS16 4.8 44.3 1.0 O1A A:GNP1001 4.8 45.7 1.0 O A:ASP33 4.8 84.4 1.0 NZ A:LYS16 4.8 44.9 1.0 CE A:LYS16 4.8 44.6 1.0 CA A:PRO34 4.9 93.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion


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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:54.5 occ:1.00 O B:HOH1101 2.0 54.5 1.0 O2B B:GNP1001 2.0 48.1 1.0 O B:HOH1104 2.0 56.3 1.0 O1G B:GNP1001 2.0 60.3 1.0 OG B:SER17 2.0 53.0 1.0 OG1 B:THR35 2.0 65.0 1.0 CB B:SER17 3.0 51.2 1.0 PG B:GNP1001 3.1 63.3 1.0 CB B:THR35 3.2 63.7 1.0 PB B:GNP1001 3.2 47.0 1.0 N3B B:GNP1001 3.4 50.6 1.0 O2G B:GNP1001 3.7 48.0 1.0 N B:SER17 3.7 51.3 1.0 CA B:SER17 3.8 53.1 1.0 N B:THR35 3.9 70.3 1.0 O2A B:GNP1001 4.1 35.0 1.0 CG2 B:THR35 4.1 63.0 1.0 OD2 B:ASP57 4.1 64.6 1.0 O1B B:GNP1001 4.2 50.2 1.0 CA B:THR35 4.2 68.8 1.0 O B:ASP33 4.2 70.1 1.0 O3A B:GNP1001 4.3 51.7 1.0 OD1 B:ASP57 4.3 61.6 1.0 O3G B:GNP1001 4.4 61.0 1.0 O B:THR58 4.4 56.9 1.0 PA B:GNP1001 4.5 47.0 1.0 C B:LYS16 4.6 53.2 1.0 CG B:ASP57 4.6 62.7 1.0 CB B:LYS16 4.6 47.1 1.0 O1A B:GNP1001 4.6 50.1 1.0 CE B:LYS16 4.8 41.6 1.0 NZ B:LYS16 4.8 37.5 1.0 C B:PRO34 5.0 67.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion


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 Wild-Type KRAS4B(1-169) in Complex with Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:69.2 occ:1.00 O2B C:GNP1001 2.0 62.6 1.0 O C:HOH1101 2.0 67.7 1.0 O C:HOH1103 2.0 71.8 1.0 O C:HOH1106 2.0 76.2 1.0 O1G C:GNP1001 2.0 84.8 1.0 OG C:SER17 2.1 79.5 1.0 CB C:SER17 3.1 74.7 1.0 PG C:GNP1001 3.3 80.7 1.0 PB C:GNP1001 3.3 67.1 1.0 N3B C:GNP1001 3.6 72.2 1.0 N C:SER17 3.6 64.8 1.0 OD2 C:ASP57 3.9 79.0 1.0 O2G C:GNP1001 3.9 77.4 1.0 O2A C:GNP1001 3.9 65.1 1.0 CA C:SER17 4.0 68.2 1.0 O1B C:GNP1001 4.2 65.0 1.0 OD1 C:ASP57 4.2 76.3 1.0 O3A C:GNP1001 4.4 70.5 1.0 O3G C:GNP1001 4.4 77.5 1.0 PA C:GNP1001 4.4 67.3 1.0 CG C:ASP57 4.5 77.2 1.0 O1A C:GNP1001 4.6 66.7 1.0 CB C:LYS16 4.6 61.5 1.0 C C:LYS16 4.7 66.4 1.0 NZ C:LYS16 4.9 60.5 1.0 CE C:LYS16 4.9 61.8 1.0

T.H.Tran, D.K.Simanshu. Lipid Dependent Dynamics of the Ras Signaling Protein To Be Published.