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Magnesium in PDB 8ood: Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15

Enzymatic activity of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15

All present enzymatic activity of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15, PDB code: 8ood was solved by M.Schroeder, M.Renatus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.26 / 1.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.496, 81.496, 232.723, 90, 90, 120
R / Rfree (%) 17 / 18.6

Other elements in 8ood:

The structure of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 (pdb code 8ood). 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 Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15, PDB code: 8ood:

Magnesium binding site 1 out of 1 in 8ood

Go back to Magnesium Binding Sites List in 8ood
Magnesium binding site 1 out of 1 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15


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 Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:43.7
occ:1.00
 O A:HIS1134 1.9 12.2 1.0
O A:THR1114 1.9 13.4 1.0
OD1 A:ASN1132 2.0 12.7 1.0
O A:HOH1637 2.0 12.5 1.0
HA A:ASN1135 2.8 12.0 1.0
HA3 A:GLY1115 2.8 11.8 1.0
CG A:ASN1132 3.0 13.5 1.0
C A:HIS1134 3.0 12.2 1.0
C A:THR1114 3.1 13.1 1.0
HD21 A:ASN1132 3.1 12.9 1.0
CA A:GLY1115 3.4 11.6 1.0
ND2 A:ASN1132 3.4 12.7 1.0
OD1 A:ASN1135 3.5 12.4 1.0
C A:GLY1115 3.5 11.6 1.0
H A:HIS1134 3.5 11.2 1.0
CA A:ASN1135 3.6 11.9 1.0
N A:GLY1115 3.7 12.0 1.0
O A:GLY1115 3.7 11.8 1.0
N A:ASN1135 3.7 11.8 1.0
HG3 A:GLN1116 3.9 18.3 1.0
OXT A:ACT1503 4.0 21.3 1.0
HB A:THR1114 4.0 16.1 1.0
N A:HIS1134 4.2 11.3 1.0
O A:ACT1503 4.2 32.1 1.0
N A:GLN1116 4.2 11.7 1.0
CA A:HIS1134 4.2 11.1 1.0
CA A:THR1114 4.3 13.2 1.0
HA A:ASN1132 4.3 12.3 1.0
HA2 A:GLY1115 4.3 11.4 1.0
HD22 A:ASN1132 4.3 13.3 1.0
CB A:ASN1132 4.3 12.6 1.0
HG2 A:GLN1116 4.4 18.5 1.0
H A:SER1136 4.4 11.7 1.0
HA A:THR1114 4.4 13.8 1.0
CG A:ASN1135 4.4 12.1 1.0
C A:ASN1135 4.4 12.3 1.0
C A:ACT1503 4.4 23.0 1.0
H A:GLN1116 4.5 12.0 1.0
CB A:THR1114 4.6 16.0 1.0
H A:GLY1115 4.6 12.0 1.0
N A:SER1136 4.6 11.8 1.0
HB2 A:ASN1132 4.6 13.1 1.0
CB A:ASN1135 4.6 11.8 1.0
CG A:GLN1116 4.6 17.9 1.0
H A:ASN1135 4.6 11.9 1.0
HA A:GLN1116 4.7 13.1 1.0
CA A:ASN1132 4.7 12.4 1.0
HB2 A:HIS1134 4.8 11.4 1.0
O A:SER1136 4.8 12.1 1.0
H A:CYS1133 4.8 11.5 1.0
HA A:HIS1134 4.8 11.7 1.0
OG1 A:THR1114 4.9 17.1 1.0
H1 A:ACT1502 4.9 12.6 0.5
HB3 A:ASN1135 5.0 12.3 1.0
C A:ASN1132 5.0 13.1 1.0

Reference:

M.Schroder, M.Renatus, C.R.Thoma. Reinstating Targeted Protein Degradation with DCAF1 Protacs in Crbn Protac Resistant Settings Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.04.09.536153
Page generated: Fri Aug 15 11:37:35 2025

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