Magnesium in PDB 6mbt: Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2)

The structure of Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2), PDB code: 6mbt was solved by S.Dharmaiah, T.H.Tran, W.Yan, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.47 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.287, 41.552, 115.380, 90.00, 105.05, 90.00
R / Rfree (%)	17.7 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2) (pdb code 6mbt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2), PDB code: 6mbt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2)


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 Kras Bound to Gdp and Mg (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:11.3 occ:1.00 O A:HOH320 2.0 8.3 1.0 O3B A:GDP201 2.1 9.7 1.0 O A:HOH324 2.1 9.4 1.0 O A:HOH357 2.1 10.2 1.0 OG A:SER17 2.1 9.4 1.0 O A:HOH338 2.2 10.6 1.0 HB2 A:SER17 3.1 11.3 1.0 CB A:SER17 3.2 9.4 1.0 PB A:GDP201 3.3 10.7 1.0 H A:SER17 3.3 11.5 1.0 HA A:PRO34 3.4 13.8 1.0 HD2 A:TYR32 3.5 25.9 1.0 O2B A:GDP201 3.5 11.0 1.0 HB3 A:SER17 3.9 11.3 1.0 N A:SER17 3.9 9.6 1.0 HB2 A:LYS16 4.0 10.9 1.0 OD2 A:ASP57 4.1 12.3 1.0 CA A:SER17 4.1 9.9 1.0 HE2 A:LYS16 4.1 13.1 1.0 HE2 A:TYR32 4.1 27.0 1.0 O2A A:GDP201 4.2 12.7 1.0 OD1 A:ASP57 4.2 12.1 1.0 CA A:PRO34 4.3 11.5 1.0 CD2 A:TYR32 4.3 21.6 1.0 O A:PRO34 4.3 10.7 1.0 O1B A:GDP201 4.3 10.8 1.0 O3A A:GDP201 4.4 11.4 1.0 O A:ASP33 4.4 10.6 1.0 HA A:SER17 4.4 11.9 1.0 O A:ILE36 4.5 10.9 1.0 CG A:ASP57 4.6 12.1 1.0 PA A:GDP201 4.6 12.6 1.0 HB2 A:ALA59 4.6 14.5 1.0 O A:THR58 4.6 10.2 1.0 C A:PRO34 4.6 10.8 1.0 CE2 A:TYR32 4.6 22.5 1.0 O1A A:GDP201 4.7 12.7 1.0 HZ2 A:LYS16 4.7 12.6 1.0 HZ1 A:LYS16 4.8 12.6 1.0 HA A:ALA59 4.9 14.0 1.0 CB A:LYS16 4.9 9.1 1.0 HB3 A:PRO34 4.9 14.2 1.0 O A:TYR32 5.0 16.7 1.0 CE A:LYS16 5.0 10.9 1.0 C A:LYS16 5.0 9.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Wild-Type Kras Bound to Gdp and Mg (Space Group C2)


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 Kras Bound to Gdp and Mg (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:9.9 occ:1.00 O B:HOH338 2.1 9.9 1.0 OG B:SER17 2.1 11.3 1.0 O2B B:GDP201 2.1 9.4 1.0 O B:HOH325 2.1 11.9 1.0 O B:HOH321 2.1 10.5 1.0 O B:HOH352 2.2 10.9 1.0 HB2 B:SER17 3.1 12.9 1.0 CB B:SER17 3.2 10.7 1.0 PB B:GDP201 3.3 10.5 1.0 HA B:PRO34 3.4 14.3 1.0 H B:SER17 3.4 11.1 1.0 HD2 B:TYR32 3.5 23.0 1.0 O1B B:GDP201 3.5 11.4 1.0 HB3 B:SER17 3.8 12.9 1.0 N B:SER17 4.0 9.2 1.0 HB2 B:LYS16 4.0 11.9 1.0 HE2 B:TYR32 4.0 24.1 1.0 HE2 B:LYS16 4.1 12.4 1.0 O1A B:GDP201 4.1 13.4 1.0 CA B:SER17 4.1 9.4 1.0 OD2 B:ASP57 4.2 11.8 1.0 CA B:PRO34 4.3 11.9 1.0 CD2 B:TYR32 4.3 19.2 1.0 OD1 B:ASP57 4.3 11.1 1.0 O B:PRO34 4.3 10.9 1.0 O3B B:GDP201 4.4 10.0 1.0 O3A B:GDP201 4.4 10.7 1.0 O B:ASP33 4.4 12.3 1.0 HA B:SER17 4.4 11.3 1.0 O B:ILE36 4.5 12.7 1.0 CE2 B:TYR32 4.5 20.0 1.0 PA B:GDP201 4.6 12.5 1.0 C B:PRO34 4.6 11.5 1.0 CG B:ASP57 4.6 10.9 1.0 O B:THR58 4.6 9.1 1.0 O2A B:GDP201 4.7 13.1 1.0 HB2 B:ALA59 4.7 13.4 1.0 HA B:ALA59 4.8 12.6 1.0 O B:TYR32 4.9 14.1 1.0 CB B:LYS16 4.9 9.9 1.0 HZ1 B:LYS16 4.9 13.1 1.0 HB3 B:PRO34 5.0 15.2 1.0

S.Dharmaiah, T.H.Tran, S.Messing, C.Agamasu, W.K.Gillette, W.Yan, T.Waybright, P.Alexander, D.Esposito, D.V.Nissley, F.Mccormick, A.G.Stephen, D.K.Simanshu. Structures of N-Terminally Processed Kras Provide Insight Into the Role of N-Acetylation. Sci Rep V. 9 10512 2019.
ISSN: ESSN 2045-2322
PubMed: 31324887
DOI: 10.1038/S41598-019-46846-W