Magnesium in PDB 9hgg: SETD2 Peptide Bound to Spop Math Domain

All present enzymatic activity of SETD2 Peptide Bound to Spop Math Domain:
2.1.1.359;

The structure of SETD2 Peptide Bound to Spop Math Domain, PDB code: 9hgg was solved by L.Makhlouf, E.Zeqiraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.56 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.565, 51.043, 54.901, 90, 90, 90
R / Rfree (%)	19.4 / 25.6

The binding sites of Magnesium atom in the SETD2 Peptide Bound to Spop Math Domain (pdb code 9hgg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the SETD2 Peptide Bound to Spop Math Domain, PDB code: 9hgg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the SETD2 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SETD2 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:17.1 occ:0.50 H A:ASN39 2.4 28.1 1.0 HD22 A:ASN39 2.4 38.1 1.0 MG A:MG203 2.8 38.2 0.5 HA A:ILE38 3.0 26.3 1.0 N A:ASN39 3.2 23.2 1.0 ND2 A:ASN39 3.2 31.5 1.0 HB2 A:ASN39 3.4 32.1 1.0 HG22 A:ILE38 3.4 27.6 1.0 HD21 A:ASN39 3.7 38.1 1.0 CA A:ILE38 3.8 21.7 1.0 O A:THR37 4.0 27.9 1.0 CB A:ASN39 4.0 26.5 1.0 C A:ILE38 4.0 17.5 1.0 CG A:ASN39 4.1 25.9 1.0 CA A:ASN39 4.1 27.0 1.0 O A:HOH329 4.3 33.4 1.0 CG2 A:ILE38 4.3 22.7 1.0 HG12 A:ILE38 4.4 30.9 1.0 O A:ASN39 4.5 24.6 1.0 CB A:ILE38 4.6 18.7 1.0 HG21 A:ILE38 4.7 27.6 1.0 HE1 A:TRP36 4.7 33.9 1.0 N A:ILE38 4.8 20.5 1.0 C A:THR37 4.8 20.2 1.0 C A:ASN39 4.8 26.2 1.0 HB3 A:ASN39 4.9 32.1 1.0 HA A:ASN39 4.9 32.7 1.0 CG1 A:ILE38 5.0 25.4 1.0 HG23 A:ILE38 5.0 27.6 1.0

Magnesium binding site 2 out of 5 in the SETD2 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SETD2 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.3 occ:1.00 HZ3 A:LYS115 2.3 41.9 1.0 H A:LYS115 2.3 25.9 1.0 HG22 A:THR114 2.9 39.2 1.0 NZ A:LYS115 3.1 34.7 1.0 N A:LYS115 3.2 21.3 1.0 HA A:LYS115 3.2 25.2 1.0 HZ2 A:LYS115 3.3 41.9 1.0 HZ1 A:LYS115 3.5 41.9 1.0 HG2 A:LYS115 3.5 30.7 1.0 HA A:THR114 3.6 25.8 1.0 CA A:LYS115 3.7 20.7 1.0 CG2 A:THR114 3.8 32.4 1.0 HG21 A:THR114 4.0 39.2 1.0 HD3 A:LYS115 4.0 28.3 1.0 C A:THR114 4.2 24.6 1.0 CE A:LYS115 4.2 27.8 1.0 CG A:LYS115 4.3 25.3 1.0 CA A:THR114 4.3 21.2 1.0 HG23 A:THR114 4.3 39.2 1.0 HE2 A:LYS115 4.3 33.7 1.0 H A:ALA116 4.3 29.3 1.0 CD A:LYS115 4.4 23.3 1.0 CB A:LYS115 4.6 22.3 1.0 CB A:THR114 4.7 25.4 1.0 C A:LYS115 4.8 27.5 1.0 N A:ALA116 4.9 24.1 1.0

Magnesium binding site 3 out of 5 in the SETD2 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SETD2 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:38.2 occ:0.50 O A:HOH329 2.3 33.4 1.0 HE1 A:TRP36 2.6 33.9 1.0 MG A:MG201 2.8 17.1 0.5 O A:HOH372 3.0 34.7 0.5 O A:THR37 3.3 27.9 1.0 NE1 A:TRP36 3.4 28.0 1.0 HA A:ILE38 3.8 26.3 1.0 HD22 A:ASN39 3.9 38.1 1.0 HD1 A:TRP36 3.9 29.9 1.0 CD1 A:TRP36 4.1 24.6 1.0 HD21 A:ASN39 4.3 38.1 1.0 ND2 A:ASN39 4.4 31.5 1.0 C A:THR37 4.4 20.2 1.0 CE2 A:TRP36 4.5 22.6 1.0 H A:ASN39 4.5 28.1 1.0 HZ2 A:TRP36 4.5 34.6 1.0 HG12 A:ILE38 4.5 30.9 1.0 O A:HOH339 4.6 22.1 1.0 CA A:ILE38 4.7 21.7 1.0 CZ2 A:TRP36 4.9 28.6 1.0 N A:ILE38 5.0 20.5 1.0

Magnesium binding site 4 out of 5 in the SETD2 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SETD2 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:29.1 occ:1.00 HH22 A:ARG121 2.6 40.0 1.0 HH12 A:ARG121 3.1 41.6 1.0 NH2 A:ARG121 3.5 33.0 1.0 HH2 A:TRP131 3.6 30.7 1.0 NH1 A:ARG121 3.8 34.4 1.0 HE2 A:TYR123 3.9 27.4 1.0 HD2 A:TYR123 4.0 31.3 1.0 CH2 A:TRP131 4.1 25.3 1.0 HH21 A:ARG121 4.1 40.0 1.0 CZ A:ARG121 4.1 34.9 1.0 HZ2 A:TRP131 4.2 33.1 1.0 CE2 A:TYR123 4.4 22.6 1.0 CZ2 A:TRP131 4.4 27.4 1.0 CD2 A:TYR123 4.4 25.8 1.0 HH11 A:ARG121 4.6 41.6 1.0 CZ3 A:TRP131 4.9 22.6 1.0

Magnesium binding site 5 out of 5 in the SETD2 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of SETD2 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:54.8 occ:1.00 O A:HOH373 2.1 43.1 1.0 O A:HOH313 3.0 31.3 1.0 HG3 A:GLU46 4.1 33.9 1.0 O A:HOH366 4.3 34.9 1.0 HB3 A:GLU50 4.5 32.5 1.0 OE2 A:GLU46 4.5 28.0 1.0 OE2 A:GLU50 4.6 51.7 1.0 O A:VAL51 4.9 25.0 1.0 CG A:GLU46 4.9 28.0 1.0 O A:HOH399 5.0 47.4 1.0 HG2 A:GLU46 5.0 33.9 1.0

L.Makhlouf, M.Mishra, H.Makhlouf, I.Manfield, L.Busino, E.Zeqiraj. Sequence Rules For A Long Spop-Binding Degron Required For Protein Ubiquitylation. Biochem.J. 2025.
ISSN: ESSN 1470-8728
PubMed: 40178506
DOI: 10.1042/BCJ20253041