Calcium in PDB 5otn: Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp

The structure of Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp, PDB code: 5otn was solved by R.Gustafsson, L.Henriksson, A.-S.Jemth, L.Brautigam, J.Carreras Puigvert, E.Homan, U.Warpman Berglund, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.32 / 0.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.528, 55.379, 65.920, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 13.3

The structure of Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp (pdb code 5otn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp, PDB code: 5otn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca211 b:5.5 occ:1.00 OE2 A:GLU100 2.3 8.0 1.0 O A:GLY36 2.3 5.6 1.0 OP1 A:6OG201 2.4 6.1 1.0 OE2 A:GLU56 2.4 7.2 1.0 O A:HOH426 2.4 7.2 1.0 OE1 A:GLU56 2.9 8.1 1.0 CD A:GLU56 2.9 6.3 1.0 CD A:GLU100 3.5 6.5 1.0 C A:GLY36 3.5 4.8 1.0 P A:6OG201 3.6 5.5 1.0 OP2 A:6OG201 3.7 5.8 1.0 O2 A:GOL205 3.8 6.8 1.0 O5' A:6OG201 4.2 6.3 1.0 CA A:CA213 4.2 5.8 1.0 O A:HOH331 4.2 7.0 1.0 OE1 A:GLU100 4.2 8.1 1.0 NZ A:LYS23 4.2 6.1 1.0 CG A:GLU56 4.2 6.2 1.0 N A:GLY36 4.2 5.0 1.0 CE A:LYS23 4.4 6.5 1.0 CA A:GLY37 4.4 5.0 1.0 N A:GLY37 4.4 4.9 1.0 OE2 A:GLU52 4.5 7.0 1.0 CA A:GLY36 4.5 5.1 1.0 CG A:GLU100 4.6 6.8 1.0 O A:HOH344 4.6 6.3 1.0 OP3 A:6OG201 4.8 6.2 1.0 SD A:MET101 5.0 6.4 0.7

Calcium binding site 2 out of 3 in the Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca212 b:6.6 occ:1.00 OE1 A:GLU55 2.4 8.6 1.0 O A:HOH397 2.4 10.4 1.0 O A:HOH331 2.5 7.0 1.0 OE1 A:GLU52 2.5 10.3 1.0 OE2 A:GLU52 2.6 7.0 1.0 CD A:GLU52 2.9 7.5 1.0 CD A:GLU55 3.4 7.6 1.0 CA A:CA213 3.8 5.8 1.0 NH2 A:ARG51 4.0 10.6 0.3 OE2 A:GLU55 4.1 9.6 1.0 O A:HOH436 4.3 30.4 1.0 O A:HOH421 4.4 18.9 1.0 O A:HOH435 4.4 14.0 1.0 CG A:GLU52 4.4 7.0 1.0 CB A:GLU55 4.4 6.7 1.0 O A:HOH362 4.5 7.5 1.0 CG A:GLU55 4.5 6.9 1.0 OE2 A:GLU56 4.5 7.2 1.0 O A:HOH308 4.6 12.4 1.0 O A:HOH335 4.6 17.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Zebrafish MTH1 in Complex with O6-Methyl-Dgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca213 b:5.8 occ:1.00 OE1 A:GLU100 2.4 8.1 1.0 O2 A:GOL205 2.5 6.8 1.0 O3 A:GOL205 2.5 6.9 1.0 O A:HOH331 2.6 7.0 1.0 CD A:GLU100 3.2 6.5 1.0 C3 A:GOL205 3.3 7.2 1.0 OE2 A:GLU100 3.3 8.0 1.0 C2 A:GOL205 3.4 6.9 1.0 CA A:CA212 3.8 6.6 1.0 OE2 A:GLU52 4.1 7.0 1.0 OE2 A:GLU56 4.2 7.2 1.0 CA A:CA211 4.2 5.5 1.0 O A:HOH435 4.4 14.0 1.0 NH2 A:ARG25 4.4 8.9 1.0 OP2 A:6OG201 4.5 5.8 1.0 CG A:GLU100 4.6 6.8 1.0 OP1 A:6OG201 4.7 6.1 1.0 C1 A:GOL205 4.7 7.2 1.0 NE A:ARG25 5.0 9.7 1.0

A.S.Jemth, R.Gustafsson, L.Brautigam, L.Henriksson, K.S.A.Vallin, A.Sarno, I.Almlof, E.Homan, A.Rasti, U.Warpman Berglund, P.Stenmark, T.Helleday. Mutt Homologue 1 (MTH1) Catalyzes the Hydrolysis of Mutagenic O6-Methyl-Dgtp. Nucleic Acids Res. V. 46 10888 2018.
ISSN: ESSN 1362-4962
PubMed: 30304478
DOI: 10.1093/NAR/GKY896