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Magnesium in PDB 6xgv: Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

Enzymatic activity of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

All present enzymatic activity of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf:
2.7.11.1; 3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgv was solved by T.H.Tran, A.H.Chan, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.36 / 2.11
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.75, 132.75, 89.48, 90, 90, 120
R / Rfree (%) 18.4 / 20.4

Other elements in 6xgv:

The structure of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Chlorine (Cl) 1 atom
Arsenic (As) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (pdb code 6xgv). 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-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgv:

Magnesium binding site 1 out of 1 in 6xgv

Go back to Magnesium Binding Sites List in 6xgv
Magnesium binding site 1 out of 1 in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf


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-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:51.5
occ:1.00
 O1B A:GNP201 2.0 44.2 1.0
O2G A:GNP201 2.0 48.1 1.0
OG1 A:THR35 2.1 47.2 1.0
OG A:SER17 2.2 43.5 1.0
O A:HOH310 2.2 44.8 1.0
O A:HOH305 2.2 55.8 1.0
CB A:THR35 3.1 48.3 1.0
PG A:GNP201 3.2 48.4 0.2
PB A:GNP201 3.2 46.2 1.0
CB A:SER17 3.3 42.4 1.0
N3B A:GNP201 3.5 50.1 1.0
N A:SER17 3.9 42.4 1.0
N A:THR35 3.9 58.2 1.0
O1A A:GNP201 4.0 49.8 1.0
O1G A:GNP201 4.0 50.2 1.0
OD2 A:ASP57 4.0 50.0 1.0
CA A:THR35 4.1 56.9 1.0
CG2 A:THR35 4.1 48.0 1.0
CA A:SER17 4.2 41.2 1.0
O2B A:GNP201 4.2 47.0 1.0
O A:ASP33 4.3 64.4 1.0
OD1 A:ASP57 4.3 49.3 1.0
O3A A:GNP201 4.3 47.4 1.0
O3G A:GNP201 4.3 56.7 0.3
PA A:GNP201 4.5 48.2 1.0
CG A:ASP57 4.6 52.0 1.0
O A:THR58 4.6 46.5 1.0
O2A A:GNP201 4.6 49.7 1.0
C A:PRO34 4.9 65.5 1.0
CE A:LYS16 4.9 49.3 1.0
CB A:LYS16 4.9 40.2 1.0
C A:LYS16 5.0 41.4 1.0

Reference:

T.H.Tran, A.H.Chan, S.Dharmaiah, D.K.Simanshu. Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) Nat Commun 2020.
ISSN: ESSN 2041-1723
Page generated: Wed Aug 13 20:08:58 2025

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