Atomistry » Magnesium » PDB 8ely-8ezi » 8ezg
Atomistry »
  Magnesium »
    PDB 8ely-8ezi »
      8ezg »

Magnesium in PDB 8ezg: Monobody 12D1 Bound to Kras(G12D)

Enzymatic activity of Monobody 12D1 Bound to Kras(G12D)

All present enzymatic activity of Monobody 12D1 Bound to Kras(G12D):
3.6.5.2;

Protein crystallography data

The structure of Monobody 12D1 Bound to Kras(G12D), PDB code: 8ezg was solved by T.Hattori, E.Glasser, P.Akkapeddi, G.Ketavarapu, K.W.Teng, A.Koide, S.Koide, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.17 / 2.52
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 156.477, 156.477, 64.624, 90, 90, 120
R / Rfree (%) 17.1 / 21.3

Other elements in 8ezg:

The structure of Monobody 12D1 Bound to Kras(G12D) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Monobody 12D1 Bound to Kras(G12D) (pdb code 8ezg). 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 Monobody 12D1 Bound to Kras(G12D), PDB code: 8ezg:

Magnesium binding site 1 out of 1 in 8ezg

Go back to Magnesium Binding Sites List in 8ezg
Magnesium binding site 1 out of 1 in the Monobody 12D1 Bound to Kras(G12D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Monobody 12D1 Bound to Kras(G12D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:43.4
occ:1.00
O A:HOH315 2.0 43.3 1.0
O A:HOH348 2.1 48.4 1.0
O A:HOH309 2.1 40.5 1.0
O1B A:GDP201 2.3 33.1 1.0
OG A:SER17 2.3 38.4 1.0
O A:HOH302 2.5 42.7 1.0
O3B A:GDP201 3.3 33.5 1.0
PB A:GDP201 3.3 36.1 1.0
CB A:SER17 3.6 29.6 1.0
N A:SER17 4.0 33.2 1.0
O A:THR58 4.1 45.1 1.0
O A:HOH313 4.1 33.5 1.0
OD2 A:ASP57 4.2 48.7 1.0
O2B A:GDP201 4.3 33.3 1.0
O2A A:GDP201 4.3 28.1 1.0
CA A:SER17 4.4 37.0 1.0
OD1 A:ASP57 4.4 46.2 1.0
O B:HOH344 4.5 45.3 1.0
O3A A:GDP201 4.6 48.3 1.0
O A:HOH306 4.6 51.4 1.0
CG A:ASP57 4.6 52.0 1.0
NZ A:LYS16 4.7 26.4 1.0
PA A:GDP201 4.9 37.1 1.0
CB A:LYS16 4.9 36.5 1.0
CE A:LYS16 4.9 31.9 1.0
O1A A:GDP201 4.9 29.0 1.0

Reference:

P.Akkapeddi, T.Hattori, I.Khan, E.Glasser, A.Koide, G.Ketavarapu, M.Whaby, M.Zuberi, K.W.Teng, J.Lefler, L.Maso, I.Bang, M.C.Ostrowski, J.P.O'bryan, S.Koide. Exploring Switch II Pocket Conformation of Kras(G12D) with Mutant-Selective Monobody Inhibitors. Proc.Natl.Acad.Sci.Usa V. 120 85120 2023.
ISSN: ESSN 1091-6490
PubMed: 37399416
DOI: 10.1073/PNAS.2302485120
Page generated: Fri Oct 4 01:24:55 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy