Magnesium in PDB 6v65: Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex

Protein crystallography data

The structure of Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex, PDB code: 6v65 was solved by W.Yan, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.68 / 2.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.556, 70.553, 80.311, 90.00, 99.61, 90.00
R / Rfree (%) 22.1 / 24.1

Other elements in 6v65:

The structure of Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex (pdb code 6v65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex, PDB code: 6v65:

Magnesium binding site 1 out of 1 in 6v65

Go back to Magnesium Binding Sites List in 6v65
Magnesium binding site 1 out of 1 in the Crystal Structure of Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex


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 Kras(Gmppnp)-NF1(Grd)-SPRED1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:72.4
occ:1.00
OG C:SER17 1.8 87.5 1.0
O3G C:GNP501 2.0 72.7 1.0
O1B C:GNP501 2.3 84.7 1.0
OG1 C:THR35 2.4 72.4 1.0
CB C:SER17 3.0 48.3 1.0
CG2 C:THR35 3.2 0.3 1.0
PG C:GNP501 3.4 72.5 1.0
OD2 C:ASP57 3.4 80.7 1.0
CB C:THR35 3.4 81.2 1.0
PB C:GNP501 3.5 59.7 1.0
N C:SER17 3.6 59.2 1.0
OD1 C:ASP57 3.8 85.8 1.0
CA C:SER17 3.8 46.0 1.0
N3B C:GNP501 3.9 61.7 1.0
CG C:ASP57 3.9 84.0 1.0
O2G C:GNP501 4.0 60.1 1.0
N C:THR35 4.1 68.9 1.0
O2B C:GNP501 4.1 71.3 1.0
O C:THR58 4.2 46.6 1.0
CA C:THR35 4.3 73.0 1.0
O1G C:GNP501 4.4 45.3 1.0
CB C:LYS16 4.5 54.5 1.0
O1A C:GNP501 4.5 58.4 1.0
C C:LYS16 4.6 64.6 1.0
O C:ASP33 4.6 94.8 1.0
O3A C:GNP501 4.7 59.3 1.0
O2A C:GNP501 4.8 75.8 1.0
CE C:LYS16 4.8 46.1 1.0
PA C:GNP501 4.9 72.7 1.0
NZ B:LYS1436 4.9 63.8 1.0

Reference:

W.Yan, E.Markegard, S.Dharmaiah, A.Urisman, M.Drew, D.Esposito, K.Scheffzek, D.V.Nissley, F.Mccormick, D.K.Simanshu. Structural Insights Into the SPRED1-Neurofibromin-Kras Complex and Disruption of SPRED1-Neurofibromin Interaction By Oncogenic Egfr. Cell Rep V. 32 07909 2020.
ISSN: ESSN 2211-1247
PubMed: 32697994
DOI: 10.1016/J.CELREP.2020.107909
Page generated: Tue Dec 15 01:07:55 2020

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