Magnesium in PDB 6mbu: Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)

The structure of Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3), PDB code: 6mbu 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)	42.09 / 1.45
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.185, 84.185, 41.916, 90.00, 90.00, 120.00
R / Rfree (%)	13.4 / 18.2

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3) (pdb code 6mbu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3), PDB code: 6mbu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)


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 (1-169) Bound to Gdp and Mg (Space Group P3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:10.3 occ:1.00 O3B A:GDP204 2.1 10.1 1.0 O A:HOH332 2.1 11.1 1.0 O A:HOH325 2.1 10.7 1.0 O A:HOH311 2.1 10.5 1.0 OG A:SER17 2.1 10.8 1.0 O A:HOH344 2.1 10.9 1.0 HB2 A:SER17 3.2 12.5 1.0 CB A:SER17 3.2 10.4 1.0 H A:SER17 3.3 11.2 1.0 PB A:GDP204 3.3 9.9 1.0 HD1 A:TYR32 3.4 14.8 1.0 HA A:PRO34 3.4 15.5 1.0 O1B A:GDP204 3.5 10.8 1.0 HB3 A:SER17 3.9 12.5 1.0 N A:SER17 3.9 9.3 1.0 HB2 A:LYS16 3.9 10.8 1.0 HE1 A:TYR32 4.0 14.3 1.0 HE2 A:LYS16 4.0 16.1 1.0 OD2 A:ASP57 4.1 11.7 1.0 O1A A:GDP204 4.1 10.7 1.0 CA A:SER17 4.1 10.1 1.0 CD1 A:TYR32 4.1 12.3 1.0 OD1 A:ASP57 4.2 12.9 1.0 O2B A:GDP204 4.3 9.8 1.0 CA A:PRO34 4.3 12.9 1.0 O A:PRO34 4.3 13.8 1.0 O A:ASP33 4.3 12.3 1.0 O3A A:GDP204 4.4 8.9 1.0 HA A:SER17 4.4 12.2 1.0 CE1 A:TYR32 4.5 11.9 1.0 O A:ILE36 4.5 12.6 1.0 HB2 A:ALA59 4.5 17.8 1.0 PA A:GDP204 4.5 10.5 1.0 O2A A:GDP204 4.6 11.6 1.0 CG A:ASP57 4.6 12.0 1.0 O A:THR58 4.6 13.0 1.0 C A:PRO34 4.6 13.2 1.0 O A:TYR32 4.7 13.5 1.0 HZ1 A:LYS16 4.7 15.0 1.0 HA A:ALA59 4.8 16.2 1.0 CB A:LYS16 4.9 9.0 1.0 HZ3 A:LYS16 4.9 15.0 1.0 HB3 A:TYR32 4.9 15.1 1.0 CE A:LYS16 4.9 13.4 1.0 C A:LYS16 5.0 10.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)


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 (1-169) Bound to Gdp and Mg (Space Group P3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:85.7 occ:1.00 O A:HOH380 2.0 27.3 1.0 O A:HOH396 2.0 38.1 1.0 OD1 A:ASN26 2.2 30.6 1.0 O A:HOH413 2.4 22.0 1.0 O A:HOH411 2.4 30.5 1.0 CG A:ASN26 3.4 27.4 1.0 HD3 A:ARG149 4.1 32.4 1.0 OD1 A:ASP153 4.1 26.6 1.0 HD21 A:ASN26 4.2 39.4 1.0 OD2 A:ASP153 4.2 28.4 1.0 HA A:ASN26 4.3 17.3 1.0 ND2 A:ASN26 4.3 32.8 1.0 HB3 A:ASN26 4.3 27.1 1.0 O A:LEU23 4.3 16.2 1.0 O A:GLN22 4.4 12.3 1.0 CB A:ASN26 4.4 22.6 1.0 HA A:LEU23 4.5 15.1 1.0 CG A:ASP153 4.6 23.4 1.0 HZ3 A:LYS42 4.6 41.5 1.0 HZ1 A:LYS42 4.8 41.5 1.0 CA A:ASN26 4.9 14.4 1.0 CD A:ARG149 4.9 27.0 1.0 NE A:ARG149 5.0 28.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)


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 Kras (1-169) Bound to Gdp and Mg (Space Group P3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:13.5 occ:0.33 O A:HOH328 2.1 14.4 1.0 O A:HOH366 2.1 17.6 1.0 HE22 A:GLN129 3.7 38.5 1.0 O A:THR124 4.0 12.9 1.0 O A:HOH367 4.1 18.2 1.0 NE2 A:GLN129 4.4 32.0 1.0 OE1 A:GLN129 4.5 21.3 1.0 CD A:GLN129 4.8 26.2 1.0 HE21 A:GLN129 4.9 38.5 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:12.2 occ:1.00 O2B B:GDP203 2.0 11.4 1.0 O B:HOH342 2.0 15.1 1.0 O B:HOH326 2.1 10.8 1.0 OG B:SER17 2.1 11.6 1.0 O B:HOH315 2.1 12.4 1.0 O B:HOH366 2.1 13.7 1.0 HB2 B:SER17 3.1 13.7 1.0 CB B:SER17 3.2 11.4 1.0 H B:SER17 3.3 13.3 1.0 PB B:GDP203 3.3 11.2 1.0 HA B:PRO34 3.4 28.1 1.0 O1B B:GDP203 3.6 11.7 1.0 HD2 B:TYR32 3.6 19.3 1.0 HB3 B:SER17 3.8 13.7 1.0 N B:SER17 3.9 11.1 1.0 HB2 B:LYS16 3.9 12.2 1.0 HE2 B:LYS16 4.0 15.5 1.0 O1A B:GDP203 4.0 13.3 1.0 OD2 B:ASP57 4.0 12.8 1.0 CA B:SER17 4.1 8.9 1.0 OD1 B:ASP57 4.2 13.5 1.0 O3B B:GDP203 4.3 11.6 1.0 CA B:PRO34 4.3 23.4 1.0 O3A B:GDP203 4.4 9.9 1.0 O B:ASP33 4.4 17.0 1.0 HA B:SER17 4.4 10.6 1.0 HB3 B:TYR32 4.4 18.6 1.0 O B:PRO34 4.5 26.5 1.0 O B:THR58 4.5 15.0 1.0 PA B:GDP203 4.5 11.8 1.0 CG B:ASP57 4.5 12.2 1.0 CD2 B:TYR32 4.6 16.1 1.0 O2A B:GDP203 4.6 12.7 1.0 HA B:ALA59 4.6 31.4 1.0 O B:TYR32 4.6 17.0 1.0 O B:ILE36 4.6 16.9 1.0 C B:PRO34 4.7 24.4 1.0 HZ1 B:LYS16 4.7 13.2 1.0 HB2 B:ALA59 4.7 37.0 1.0 CB B:LYS16 4.9 10.2 1.0 CE B:LYS16 4.9 12.9 1.0 HZ3 B:LYS16 4.9 13.2 1.0 C B:LYS16 5.0 10.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Wild-Type Kras (1-169) Bound to Gdp and Mg (Space Group P3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:56.7 occ:1.00 O B:HOH369 2.0 70.2 1.0 O A:HOH382 2.1 48.4 1.0 O A:HOH341 2.2 27.3 1.0 O B:HOH386 2.2 27.3 1.0 O B:HOH324 2.4 40.3 1.0 OD1 B:ASN26 3.3 36.8 1.0 O B:HOH321 3.3 59.0 1.0 CG B:ASN26 4.1 33.0 1.0 HD3 B:ARG149 4.1 20.9 1.0 OE2 A:GLU31 4.1 20.1 1.0 OD2 B:ASP153 4.2 21.3 1.0 OD1 B:ASP153 4.2 19.7 1.0 HA B:ASN26 4.2 22.1 1.0 HB2 B:ASN26 4.2 31.1 1.0 HZ1 B:LYS42 4.5 54.2 1.0 O B:GLN22 4.6 13.3 1.0 OE1 A:GLU31 4.6 20.1 1.0 CG B:ASP153 4.6 17.4 1.0 CB B:ASN26 4.6 25.9 1.0 HZ2 B:LYS42 4.7 54.2 1.0 HA B:LEU23 4.7 15.4 1.0 CD A:GLU31 4.8 18.1 1.0 O B:LEU23 4.9 17.1 1.0 CA B:ASN26 4.9 18.4 1.0 CD B:ARG149 4.9 17.5 1.0 HG2 B:ARG149 5.0 19.2 1.0 ND2 B:ASN26 5.0 34.8 1.0 NZ B:LYS42 5.0 45.2 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