Sodium in PDB 6mbq: Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation

The structure of Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation, PDB code: 6mbq was solved by S.Dharmaiah, D.R.Davies, J.Abendroth, W.G.Gillette, A.G.Stephen, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.45 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.020, 37.910, 99.990, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 17.9

The binding sites of Sodium atom in the Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation (pdb code 6mbq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation, PDB code: 6mbq:

Sodium binding site 1 out of 1 in the Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mg-Free Wild-Type Kras (2-166) Bound to Gmppnp in the State 1 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:8.0 occ:1.00 OD1 A:ASN26 2.3 7.8 1.0 O A:HOH434 2.3 20.8 1.0 O A:GLN22 2.4 4.8 1.0 O A:LEU23 2.5 5.7 1.0 O2 A:EDO202 2.5 11.3 1.0 O1 A:EDO202 2.5 16.2 1.0 HA A:LEU23 2.7 6.1 0.5 HA A:LEU23 2.7 6.1 0.5 HO2 A:EDO202 3.0 13.6 1.0 C A:LEU23 3.1 5.1 1.0 HA A:ASN26 3.1 6.8 1.0 C2 A:EDO202 3.2 13.8 1.0 HO1 A:EDO202 3.2 19.5 1.0 H22 A:EDO202 3.3 16.5 1.0 CA A:LEU23 3.3 5.0 0.5 CA A:LEU23 3.3 5.0 0.5 HZ2 A:LYS42 3.3 7.7 1.0 CG A:ASN26 3.4 7.3 1.0 C1 A:EDO202 3.4 15.1 1.0 C A:GLN22 3.4 4.8 1.0 H A:ASN26 3.5 6.2 1.0 HD22 A:LEU23 3.7 6.5 0.5 N A:LEU23 3.8 4.5 1.0 CA A:ASN26 3.8 5.7 1.0 HZ3 A:LYS42 3.9 7.7 1.0 N A:ASN26 4.0 5.2 1.0 H12 A:EDO202 4.0 18.1 1.0 NZ A:LYS42 4.0 6.4 1.0 HG3 A:GLN22 4.1 7.7 1.0 HD12 A:LEU23 4.1 7.5 0.5 CB A:ASN26 4.1 6.0 1.0 N A:ILE24 4.2 5.8 1.0 OD1 A:ASP153 4.2 12.5 1.0 H21 A:EDO202 4.2 16.5 1.0 H11 A:EDO202 4.3 18.1 1.0 HZ1 A:LYS42 4.3 7.7 1.0 HB3 A:ASN26 4.3 7.3 1.0 ND2 A:ASN26 4.4 7.5 1.0 OE1 A:GLN22 4.4 7.0 1.0 HD21 A:ASN26 4.5 9.0 1.0 HD13 A:LEU23 4.5 8.2 0.5 O A:HOH374 4.5 28.7 1.0 CD2 A:LEU23 4.6 5.5 0.5 CB A:LEU23 4.6 5.4 0.5 H A:LEU23 4.6 5.4 0.5 H A:LEU23 4.6 5.4 0.5 CB A:LEU23 4.7 5.5 0.5 CA A:GLN22 4.8 4.6 1.0 C A:ILE24 4.8 5.0 1.0 HD23 A:LEU23 4.8 6.5 0.5 HG A:LEU23 4.8 7.9 0.5 H A:ILE24 4.8 6.9 1.0 HA A:GLN22 4.8 5.5 1.0 CG A:GLN22 4.9 6.4 1.0 CA A:ILE24 4.9 5.3 1.0 CD1 A:LEU23 5.0 6.2 0.5 HB2 A:ASN26 5.0 7.3 1.0 HA A:ILE24 5.0 6.3 1.0 O A:ILE24 5.0 5.5 1.0 N A:GLN25 5.0 4.8 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