Magnesium in PDB 8t72: Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion

All present enzymatic activity of Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion:
3.6.5.2;

The structure of Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion, PDB code: 8t72 was solved by T.H.Tran, M.J.Whitley, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.901, 102.066, 54.031, 90, 113.77, 90
R / Rfree (%)	19.2 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion (pdb code 8t72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion, PDB code: 8t72:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Wt KRAS4A with Bound 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 Wt KRAS4A with Bound Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:35.8 occ:1.00 O1B A:GNP201 2.0 29.7 1.0 O A:HOH307 2.0 29.5 1.0 OG1 A:THR35 2.1 41.0 1.0 O1G A:GNP201 2.1 37.6 1.0 O A:HOH316 2.1 32.5 1.0 OG A:SER17 2.1 35.2 1.0 HB A:THR35 2.8 49.8 1.0 CB A:THR35 3.0 41.5 1.0 HB2 A:SER17 3.0 40.0 1.0 CB A:SER17 3.1 33.4 1.0 PG A:GNP201 3.2 34.4 1.0 PB A:GNP201 3.2 28.6 1.0 H A:THR35 3.3 52.7 1.0 H A:SER17 3.3 33.7 1.0 N3B A:GNP201 3.4 32.6 1.0 HB2 A:LYS16 3.8 27.7 1.0 N A:THR35 3.8 43.9 1.0 HB3 A:SER17 3.8 40.0 1.0 N A:SER17 3.8 28.1 1.0 HG21 A:THR35 3.9 50.6 1.0 O1A A:GNP201 3.9 35.5 1.0 HE2 A:LYS16 4.0 40.4 1.0 HOG3 A:GNP201 4.0 37.8 0.0 CA A:THR35 4.0 44.1 1.0 OD2 A:ASP57 4.0 38.0 1.0 CG2 A:THR35 4.0 42.2 1.0 CA A:SER17 4.0 29.2 1.0 O3G A:GNP201 4.1 31.5 1.0 OD1 A:ASP57 4.1 42.8 1.0 O2B A:GNP201 4.2 26.6 1.0 O3A A:GNP201 4.2 28.4 1.0 HNB3 A:GNP201 4.3 39.1 0.0 HA A:PRO34 4.3 56.9 1.0 O A:THR58 4.3 41.1 1.0 HA A:SER17 4.3 35.1 1.0 HZ2 A:LYS16 4.4 40.2 1.0 O2G A:GNP201 4.4 34.5 1.0 O A:ASP33 4.4 47.4 1.0 CG A:ASP57 4.4 46.0 1.0 HA A:THR35 4.5 52.9 1.0 PA A:GNP201 4.6 30.3 1.0 HG22 A:THR35 4.6 50.6 1.0 O2A A:GNP201 4.6 28.3 1.0 HG23 A:THR35 4.7 50.6 1.0 HE1 A:TYR32 4.7 63.9 1.0 CB A:LYS16 4.7 23.1 1.0 C A:PRO34 4.8 48.9 1.0 HA A:ALA59 4.8 42.5 1.0 CE A:LYS16 4.9 33.7 1.0 C A:LYS16 4.9 30.3 1.0 HOG2 A:GNP201 5.0 41.4 0.0 HB3 A:LYS16 5.0 27.7 1.0 H A:LYS16 5.0 28.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Wt KRAS4A with Bound 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 Wt KRAS4A with Bound Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:34.4 occ:1.00 O C:HOH326 2.1 38.8 1.0 O A:HOH328 2.1 32.9 1.0 O A:HOH325 2.2 46.8 1.0 O C:HOH312 2.2 32.9 1.0 O C:HOH325 3.9 68.7 1.0 O C:THR124 4.0 29.6 1.0 O C:HOH330 4.0 42.2 1.0 O A:THR124 4.2 28.3 1.0 O A:HOH356 4.2 35.1 1.0 HE22 C:GLN129 4.3 54.7 1.0 OE1 C:GLN129 4.4 36.4 1.0 OE1 A:GLN129 4.6 33.1 1.0 OD2 A:ASP126 4.7 80.5 1.0 HE22 A:GLN129 4.7 48.1 1.0 OD2 C:ASP126 4.8 81.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Wt KRAS4A with Bound 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 Wt KRAS4A with Bound Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:35.5 occ:1.00 HOG3 B:GNP201 1.7 64.5 0.0 O3G B:GNP201 1.8 53.8 1.0 O1B B:GNP201 1.9 46.4 1.0 O B:HOH306 2.2 43.5 1.0 OG1 B:THR35 2.3 76.7 1.0 OG B:SER17 2.7 52.2 1.0 HB2 B:SER17 2.8 66.0 1.0 HB B:THR35 2.9 95.4 1.0 HG1 B:THR35 3.0 92.0 1.0 PG B:GNP201 3.1 48.3 1.0 CB B:THR35 3.1 79.5 1.0 CB B:SER17 3.2 55.0 1.0 PB B:GNP201 3.2 36.7 1.0 H B:SER17 3.3 55.2 1.0 N3B B:GNP201 3.4 34.1 1.0 H B:THR35 3.7 93.0 1.0 OD2 B:ASP57 3.7 59.2 1.0 HB2 B:LYS16 3.8 56.2 1.0 HG22 B:THR35 3.8 95.8 1.0 N B:SER17 3.8 46.0 1.0 O1A B:GNP201 3.9 54.1 1.0 O2G B:GNP201 3.9 52.3 1.0 HB3 B:SER17 4.0 66.0 1.0 OD1 B:ASP57 4.0 58.5 1.0 CA B:SER17 4.0 51.5 1.0 CG2 B:THR35 4.1 79.8 1.0 N B:THR35 4.1 77.5 1.0 HE2 B:LYS16 4.1 60.9 1.0 O1G B:GNP201 4.1 61.1 1.0 O2B B:GNP201 4.2 33.9 1.0 HZ2 B:LYS16 4.2 52.2 1.0 O B:THR58 4.2 56.8 1.0 CA B:THR35 4.2 80.8 1.0 HNB3 B:GNP201 4.3 41.0 0.0 HA B:SER17 4.3 61.8 1.0 CG B:ASP57 4.3 58.3 1.0 O3A B:GNP201 4.4 32.9 1.0 O B:ASP33 4.4 78.9 1.0 HG21 B:THR35 4.7 95.8 1.0 HG23 B:THR35 4.7 95.8 1.0 CB B:LYS16 4.7 46.8 1.0 HOG2 B:GNP201 4.7 62.8 0.0 O B:HOH319 4.7 63.4 1.0 HA B:PRO34 4.7 98.9 1.0 PA B:GNP201 4.7 43.6 1.0 HA B:THR35 4.7 97.0 1.0 HB3 B:LYS16 4.9 56.2 1.0 NZ B:LYS16 4.9 43.5 1.0 C B:LYS16 4.9 49.4 1.0 CE B:LYS16 4.9 50.8 1.0 HOB2 B:GNP201 5.0 40.7 0.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Wt KRAS4A with Bound Gmppnp and Mg Ion


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 Wt KRAS4A with Bound Gmppnp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:45.6 occ:1.00 HG C:SER17 1.7 44.5 1.0 O C:HOH306 1.8 45.4 1.0 O C:HOH303 1.9 39.3 1.0 O2B C:GNP201 2.0 35.5 1.0 O1G C:GNP201 2.0 46.0 1.0 OG C:SER17 2.1 37.1 1.0 O C:HOH335 2.1 50.9 1.0 HB2 C:SER17 3.1 49.8 1.0 CB C:SER17 3.1 41.5 1.0 PG C:GNP201 3.2 44.9 1.0 PB C:GNP201 3.3 34.2 1.0 H C:SER17 3.3 44.8 1.0 N3B C:GNP201 3.4 42.4 1.0 HB3 C:SER17 3.8 49.8 1.0 N C:SER17 3.9 37.3 1.0 HB2 C:LYS16 3.9 39.3 1.0 O3G C:GNP201 4.0 38.8 1.0 HE2 C:LYS16 4.0 43.9 1.0 OD1 C:ASP57 4.0 47.3 1.0 CA C:SER17 4.1 34.9 1.0 O C:THR58 4.1 49.4 1.0 O1B C:GNP201 4.1 39.2 1.0 OD2 C:ASP57 4.1 50.6 1.0 O2A C:GNP201 4.2 44.7 1.0 O3A C:GNP201 4.3 29.0 1.0 HA C:SER17 4.3 41.9 1.0 O2G C:GNP201 4.4 53.6 1.0 CG C:ASP57 4.5 47.0 1.0 HA C:ALA59 4.6 75.2 1.0 HZ2 C:LYS16 4.6 48.2 1.0 PA C:GNP201 4.7 40.6 1.0 CB C:LYS16 4.8 32.8 1.0 O1A C:GNP201 4.9 38.0 1.0 C C:LYS16 4.9 35.3 1.0 CE C:LYS16 4.9 36.5 1.0 HZ3 C:LYS16 4.9 48.2 1.0 H C:LYS16 5.0 40.8 1.0

M.J.Whitley, T.H.Tran, M.Yi, S.Dharmaiah, G.Cornilescu, D.K.Simanshu. Comparative Analysis of KRAS4A and KRAS4B Splice Variants Reveals Distinctive Structural and Functional Properties Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADJ4137