Magnesium in PDB 6p0z: Crystal Structure of N-Acetylated Kras (2-169) Bound to Gdp and Mg

The structure of Crystal Structure of N-Acetylated Kras (2-169) Bound to Gdp and Mg, PDB code: 6p0z 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)	37.23 / 1.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.194, 41.571, 115.410, 90.00, 104.59, 90.00
R / Rfree (%)	14.5 / 16.6

The binding sites of Magnesium atom in the Crystal Structure of N-Acetylated Kras (2-169) Bound to Gdp and Mg (pdb code 6p0z). 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 N-Acetylated Kras (2-169) Bound to Gdp and Mg, PDB code: 6p0z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of N-Acetylated Kras (2-169) Bound to Gdp and Mg


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 N-Acetylated Kras (2-169) Bound to Gdp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:9.0 occ:1.00 O2B A:GDP202 2.0 8.6 1.0 O A:HOH331 2.0 9.4 1.0 O A:HOH393 2.1 9.8 1.0 O A:HOH321 2.1 10.2 1.0 O A:HOH317 2.1 10.1 1.0 OG A:SER17 2.1 8.9 1.0 HB2 A:SER17 3.2 10.3 1.0 CB A:SER17 3.2 8.6 1.0 PB A:GDP202 3.3 8.8 1.0 H A:SER17 3.3 9.9 1.0 HD2 A:TYR32 3.4 32.4 1.0 HA A:PRO34 3.4 19.8 1.0 O1B A:GDP202 3.5 9.8 1.0 HB3 A:SER17 3.9 10.3 1.0 N A:SER17 3.9 8.2 1.0 HB2 A:LYS16 4.0 10.2 1.0 HE2 A:TYR32 4.0 33.3 1.0 HE2 A:LYS16 4.1 12.7 1.0 O1A A:GDP202 4.1 11.2 1.0 OD2 A:ASP57 4.1 10.3 1.0 CA A:SER17 4.1 8.6 1.0 CD2 A:TYR32 4.2 27.0 1.0 OD1 A:ASP57 4.2 9.9 1.0 O A:PRO34 4.2 14.2 1.0 CA A:PRO34 4.3 16.5 1.0 O A:ASP33 4.3 16.4 1.0 O3B A:GDP202 4.3 8.8 1.0 O3A A:GDP202 4.3 9.6 1.0 HA A:SER17 4.4 10.3 1.0 O A:ILE36 4.5 10.8 1.0 CE2 A:TYR32 4.5 27.8 1.0 PA A:GDP202 4.6 9.7 1.0 O A:THR58 4.6 8.4 1.0 CG A:ASP57 4.6 9.7 1.0 C A:PRO34 4.6 14.0 1.0 HB2 A:ALA59 4.6 12.1 1.0 HZ3 A:LYS16 4.7 11.6 1.0 HZ1 A:LYS16 4.7 11.6 1.0 O2A A:GDP202 4.7 10.5 1.0 O A:TYR32 4.8 21.3 1.0 CB A:LYS16 4.9 8.5 1.0 HB3 A:TYR32 4.9 30.8 1.0 CE A:LYS16 5.0 10.6 1.0 HA A:ALA59 5.0 10.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of N-Acetylated Kras (2-169) Bound to Gdp and Mg


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 N-Acetylated Kras (2-169) Bound to Gdp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:10.0 occ:1.00 O3B B:GDP202 2.0 9.9 1.0 O B:HOH331 2.1 10.2 1.0 O B:HOH366 2.1 10.6 1.0 O B:HOH328 2.1 10.9 1.0 O B:HOH324 2.1 10.8 1.0 OG B:SER17 2.1 9.6 1.0 HB2 B:SER17 3.2 11.4 1.0 CB B:SER17 3.2 9.5 1.0 PB B:GDP202 3.3 10.1 1.0 H B:SER17 3.3 10.5 1.0 HD2 B:TYR32 3.4 19.3 0.5 HA B:PRO34 3.4 14.6 1.0 O2B B:GDP202 3.5 11.1 1.0 HD2 B:TYR32 3.7 21.1 0.6 HB3 B:SER17 3.9 11.4 1.0 N B:SER17 3.9 8.7 1.0 HB2 B:LYS16 4.0 11.3 1.0 CA B:SER17 4.1 9.0 1.0 OD2 B:ASP57 4.1 10.3 1.0 O2A B:GDP202 4.1 14.8 1.0 HE2 B:TYR32 4.2 20.7 0.5 OD1 B:ASP57 4.2 10.7 1.0 CD2 B:TYR32 4.2 16.1 0.5 HE2 B:LYS16 4.2 14.7 1.0 O B:PRO34 4.2 11.5 1.0 O B:ASP33 4.3 11.9 1.0 CA B:PRO34 4.3 12.2 1.0 O1B B:GDP202 4.3 10.2 1.0 O3A B:GDP202 4.4 11.1 1.0 HA B:SER17 4.4 10.8 1.0 O B:ILE36 4.4 10.4 1.0 HB2 B:ALA59 4.6 14.7 1.0 C B:PRO34 4.6 10.9 1.0 PA B:GDP202 4.6 12.3 1.0 O B:THR58 4.6 10.5 1.0 CG B:ASP57 4.6 9.9 1.0 CD2 B:TYR32 4.6 17.6 0.6 CE2 B:TYR32 4.6 17.2 0.5 O1A B:GDP202 4.7 11.9 1.0 HB3 B:TYR32 4.7 21.8 0.6 HA B:ALA59 4.8 13.3 1.0 HZ2 B:LYS16 4.8 13.6 1.0 HZ3 B:LYS16 4.8 13.6 1.0 HB3 B:TYR32 4.9 20.8 0.5 O B:TYR32 4.9 16.2 1.0 HE2 B:TYR32 4.9 22.7 0.6 CB B:LYS16 4.9 9.4 1.0 HB1 B:ALA59 5.0 14.7 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