Magnesium in PDB 8uuc: Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)

The structure of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G), PDB code: 8uuc was solved by C.H.Trasvina-Arenas, S.S.David, A.J.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.62 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	38.832, 84.137, 225.742, 90, 90, 90
R / Rfree (%)	17.6 / 19.7

The structure of Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) (pdb code 8uuc). 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 A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G), PDB code: 8uuc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)


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 A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:32.7 occ:1.00 O A:GLN108 2.5 32.8 1.0 O A:ILE113 2.7 26.4 1.0 O A:LEU110 2.7 28.4 1.0 OP2 C:DC10 2.8 35.6 1.0 OP1 C:DC10 3.4 31.6 1.0 P C:DC10 3.5 29.4 1.0 C A:GLN108 3.5 33.2 1.0 C A:ILE113 3.6 22.5 1.0 C A:LEU110 3.7 27.5 1.0 O C:HOH201 3.9 47.4 1.0 O A:HOH457 3.9 42.3 1.0 N A:ILE113 4.0 26.0 1.0 N A:LEU110 4.0 30.6 1.0 C A:ALA109 4.2 31.1 1.0 CA A:ILE113 4.3 24.6 1.0 CA A:GLN108 4.3 29.1 1.0 N A:GLY112 4.4 24.9 1.0 N A:ALA109 4.4 31.2 1.0 N A:PRO111 4.5 28.5 1.0 CA A:PRO111 4.5 26.4 1.0 CA A:LEU110 4.5 30.3 1.0 N A:GLY114 4.5 23.6 1.0 CA A:ALA109 4.5 35.6 1.0 O A:ALA109 4.5 35.9 1.0 O5' C:DC10 4.6 29.9 1.0 CB A:ILE113 4.7 23.7 1.0 O3' C:DT9 4.7 29.3 1.0 C A:PRO111 4.7 24.4 1.0 CA A:GLY114 4.8 24.0 1.0 O A:LEU107 4.8 30.4 1.0 C A:GLY112 4.9 24.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G)


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 A Bacterial Clusterless Mutyx Bound to An Abasic Site Analog (Thf) Opposite D(8-Oxo-G) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:59.6 occ:1.00 O A:HOH567 2.4 53.7 1.0 O A:HOH548 2.5 48.9 1.0 O C:HOH229 2.5 40.0 1.0 O B:HOH224 2.5 48.2 1.0 O C:HOH233 2.8 42.1 1.0 N4 C:DC5 3.6 29.5 1.0 O B:HOH214 3.9 42.5 1.0 O6 B:DG8 4.2 28.5 1.0 C7 B:DT7 4.3 26.0 1.0 O A:HOH525 4.3 44.4 1.0 O C:HOH232 4.4 45.4 1.0 CB A:PHE204 4.4 33.4 1.0 N4 C:DC4 4.7 30.7 1.0 N A:PHE204 4.8 36.4 1.0 C5 B:DT7 4.9 25.9 1.0 O4 B:DT7 4.9 25.9 1.0 O B:HOH229 4.9 42.6 1.0 C4 C:DC5 4.9 29.3 1.0

C.H.Trasvina-Arenas, M.Hashemian, M.Malek, S.Merrill, A.J.Fisher, S.S.David. Crystal Structure of Mutyx: A Novel Clusterless Adenine Dna Glycosylase with A Distinct C-Terminal Domain and 8-Oxoguanine Recognition Sphere. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 39803464
DOI: 10.1101/2025.01.03.631205