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Magnesium in PDB 6zj0: Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18

Protein crystallography data

The structure of Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18, PDB code: 6zj0 was solved by D.Kessler, G.Fischer, J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.61 / 1.76
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.075, 93.075, 55.256, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18 (pdb code 6zj0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18, PDB code: 6zj0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6zj0

Go back to Magnesium Binding Sites List in 6zj0
Magnesium binding site 1 out of 2 in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18


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 Hras-G12D in Complex with Gcp and Compound 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:45.9
occ:1.00
O A:HOH323 2.0 33.7 1.0
O2B A:GCP203 2.0 39.2 1.0
OG A:SER17 2.0 38.5 1.0
OG1 A:THR35 2.0 65.2 1.0
O3G A:GCP203 2.1 43.2 1.0
O A:HOH326 2.2 37.2 1.0
HB A:THR35 2.8 86.5 0.0
CB A:THR35 2.9 65.4 1.0
HB2 A:SER17 3.0 48.6 0.0
CB A:SER17 3.1 37.1 1.0
H A:SER17 3.1 42.7 0.0
PB A:GCP203 3.2 39.4 1.0
H A:THR35 3.2 89.8 0.0
H3B2 A:GCP203 3.3 54.6 0.0
PG A:GCP203 3.3 44.3 1.0
C3B A:GCP203 3.4 41.9 1.0
HG21 A:THR35 3.6 87.4 0.0
HB2 A:LYS16 3.7 39.9 0.0
N A:SER17 3.8 35.1 1.0
HB3 A:SER17 3.8 50.4 0.0
CG2 A:THR35 3.9 65.7 1.0
N A:THR35 3.9 67.1 1.0
CA A:SER17 3.9 36.2 1.0
HE2 A:LYS16 4.0 46.1 0.0
CA A:THR35 4.0 65.9 1.0
OD2 A:ASP57 4.1 46.6 1.0
O2A A:GCP203 4.1 40.4 1.0
OD1 A:ASP57 4.2 44.5 1.0
O1B A:GCP203 4.2 38.0 1.0
O3A A:GCP203 4.2 39.5 1.0
O1G A:GCP203 4.2 44.5 1.0
HA A:SER17 4.3 46.0 0.0
O2G A:GCP203 4.3 44.8 1.0
O A:THR58 4.3 45.5 1.0
H3B1 A:GCP203 4.3 53.0 0.0
O A:HOH375 4.4 64.7 1.0
CG A:ASP57 4.5 45.0 1.0
PA A:GCP203 4.5 40.4 1.0
HA A:THR35 4.5 92.8 0.0
HA A:PRO34 4.6 94.6 0.0
O A:ASP33 4.6 72.1 1.0
HG22 A:THR35 4.6 89.4 0.0
HG23 A:THR35 4.6 91.0 0.0
HZ3 A:LYS16 4.6 44.0 0.0
O1A A:GCP203 4.7 40.0 1.0
CB A:LYS16 4.7 33.8 1.0
HA A:ALA59 4.8 67.8 0.0
C A:LYS16 4.8 34.6 1.0
H A:LYS16 4.9 36.7 0.0
C A:PRO34 5.0 69.0 1.0
CE A:LYS16 5.0 37.8 1.0

Magnesium binding site 2 out of 2 in 6zj0

Go back to Magnesium Binding Sites List in 6zj0
Magnesium binding site 2 out of 2 in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18


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 Hras-G12D in Complex with Gcp and Compound 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:49.5
occ:0.53
HE21 A:GLN129 2.9 45.0 0.0
NE2 A:GLN129 3.4 37.5 1.0
HE22 A:GLN129 3.4 44.1 0.0
HH12 A:ARG128 3.8 85.4 0.0
CD A:GLN129 4.5 36.0 1.0
HG2 A:GLN129 4.5 40.6 0.0
HH22 A:ARG128 4.6 84.9 0.0
O A:HOH380 4.8 68.1 1.0
NH1 A:ARG128 4.8 68.4 1.0
O A:HOH463 4.9 92.8 0.3

Reference:

D.Kessler, A.Bergner, J.Bottcher, G.Fischer, S.Dobel, M.Hinkel, B.Mullauer, A.Weiss-Puxbaum, D.B.Mcconnell. Drugging All Ras Isoforms with One Pocket. Future Med Chem V. 12 1911 2020.
ISSN: ISSN 1756-8927
PubMed: 32779487
DOI: 10.4155/FMC-2020-0221
Page generated: Wed Oct 2 02:26:06 2024

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