Manganese in PDB 8i8t: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+, PDB code: 8i8t was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.37 / 1.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.476, 47.512, 124.061, 90, 90, 90
R / Rfree (%)	15 / 18

The binding sites of Manganese atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+ (pdb code 8i8t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+, PDB code: 8i8t:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:15.1 occ:0.70 OP3 A:IGU201 2.0 24.7 1.0 OE2 A:GLU56 2.1 18.7 1.0 O A:HOH423 2.2 14.0 0.5 O A:HOH383 2.2 18.0 1.0 O A:GLY36 2.3 16.5 1.0 OE2 A:GLU100 2.3 30.9 1.0 MN A:MN204 2.6 22.4 0.2 CD A:GLU56 3.1 16.9 1.0 P A:IGU201 3.3 19.2 1.0 CD A:GLU100 3.4 32.9 1.0 C A:GLY36 3.5 14.3 1.0 OE1 A:GLU56 3.5 17.3 1.0 OP2 A:IGU201 3.8 27.4 1.0 CG A:GLU100 3.9 30.5 1.0 O A:HOH461 3.9 38.3 1.0 O A:HOH398 4.0 34.6 1.0 CA A:GLY37 4.0 13.6 1.0 OE1 A:GLU52 4.0 27.4 1.0 O A:HOH329 4.2 33.3 1.0 N A:GLY37 4.2 13.5 1.0 O5' A:IGU201 4.3 19.8 1.0 OP1 A:IGU201 4.3 26.6 1.0 NZ A:LYS23 4.3 25.9 1.0 CE A:LYS23 4.4 24.8 1.0 O A:HOH391 4.4 16.6 1.0 CG A:GLU56 4.4 17.9 1.0 OE1 A:GLU100 4.4 34.4 1.0 N A:GLY36 4.5 12.8 1.0 CA A:GLY36 4.6 14.6 1.0 O A:HOH337 4.7 21.8 1.0 C4' A:IGU201 4.8 16.0 1.0 CD A:GLU52 4.9 23.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:17.8 occ:0.10 OE2 A:GLU52 2.3 26.3 1.0 O A:HOH343 2.4 31.1 1.0 O A:HOH337 2.9 21.8 1.0 O A:HOH423 3.3 14.0 0.5 CD A:GLU52 3.3 23.5 1.0 OE1 A:GLU52 3.6 27.4 1.0 MN A:MN204 3.7 22.4 0.2 O A:HOH461 3.9 38.3 1.0 NH1 A:ARG51 4.0 25.1 1.0 N A:LYS38 4.2 13.8 1.0 O A:LYS38 4.3 17.6 1.0 O A:HOH479 4.4 51.7 1.0 O A:HOH499 4.5 25.6 0.3 NE2 A:GLN40 4.5 27.8 1.0 CA A:GLY37 4.6 13.6 1.0 OE1 A:GLU55 4.6 41.1 1.0 CG A:GLU52 4.7 20.4 1.0 C A:GLY37 4.8 14.1 1.0 O A:HOH329 4.8 33.3 1.0 NH2 A:ARG51 4.9 23.0 1.0 O A:HOH398 4.9 34.6 1.0 CZ A:ARG51 4.9 23.5 1.0 CB A:LYS38 5.0 15.1 1.0 CA A:LYS38 5.0 14.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:22.4 occ:0.20 O A:HOH423 1.4 14.0 0.5 OE2 A:GLU56 2.2 18.7 1.0 O A:HOH398 2.2 34.6 1.0 OE1 A:GLU52 2.3 27.4 1.0 MN A:MN202 2.6 15.1 0.7 O A:HOH461 2.7 38.3 1.0 CD A:GLU56 3.2 16.9 1.0 CD A:GLU52 3.3 23.5 1.0 OE2 A:GLU100 3.3 30.9 1.0 O A:GLY36 3.4 16.5 1.0 MN A:MN203 3.7 17.8 0.1 CG A:GLU56 3.7 17.9 1.0 OE2 A:GLU52 3.7 26.3 1.0 CD A:GLU100 4.0 32.9 1.0 OE1 A:GLU56 4.2 17.3 1.0 OP3 A:IGU201 4.2 24.7 1.0 C A:GLY36 4.3 14.3 1.0 O A:HOH329 4.3 33.3 1.0 O A:HOH337 4.4 21.8 1.0 CA A:GLY37 4.4 13.6 1.0 O A:HOH383 4.5 18.0 1.0 OE1 A:GLU55 4.6 41.1 1.0 CG A:GLU52 4.6 20.4 1.0 CG A:GLU100 4.6 30.5 1.0 OE1 A:GLU100 4.7 34.4 1.0 N A:GLY37 4.7 13.5 1.0 OP2 A:IGU201 4.8 27.4 1.0 CB A:GLU52 4.8 17.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Damp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:13.5 occ:0.25 OE2 B:GLU56 2.1 31.9 1.0 OP2 B:IGU201 2.2 66.9 1.0 O B:HOH396 2.2 27.9 1.0 O B:HOH417 2.3 35.5 1.0 O B:HOH350 2.3 38.7 1.0 O B:GLY36 2.4 18.2 1.0 CD B:GLU56 3.2 30.7 1.0 P B:IGU201 3.4 33.3 1.0 C B:GLY36 3.6 16.4 1.0 OE1 B:GLU56 3.6 29.1 1.0 O B:HOH471 3.8 47.4 1.0 OP1 B:IGU201 3.9 57.0 1.0 O5' B:IGU201 4.1 32.9 1.0 OE1 B:GLU52 4.1 30.1 1.0 CA B:GLY37 4.1 15.7 1.0 CE B:LYS23 4.1 31.5 0.5 O B:HOH358 4.2 23.4 1.0 N B:GLY37 4.3 15.3 1.0 NZ B:LYS23 4.3 31.9 0.5 O B:HOH443 4.4 52.8 1.0 CG B:GLU56 4.4 30.1 1.0 C4' B:IGU201 4.6 19.4 1.0 N B:GLY36 4.6 15.9 1.0 OE2 B:GLU100 4.6 42.4 0.5 O B:HOH314 4.7 25.0 1.0 OP3 B:IGU201 4.7 49.8 1.0 CA B:GLY36 4.7 16.1 1.0 O B:HOH309 4.8 64.9 1.0 C5' B:IGU201 4.9 20.3 1.0 O B:HOH312 4.9 48.6 1.0 OE1 B:GLU100 5.0 46.9 0.5

T.Nakamura, Y.Koga-Ogawa, K.Fujimiya, M.Chirifu, M.Goto, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Protonation States of Asp Residues in the Human Nudix Hydrolase MTH1 Contribute to Its Broad Substrate Recognition. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 36914375
DOI: 10.1002/1873-3468.14611