Magnesium in PDB 3qlz: Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B)

The structure of Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B), PDB code: 3qlz was solved by J.L.Paulsen, S.D.Bendel, A.C.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.78 / 1.94
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	42.607, 42.607, 230.236, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.5

The binding sites of Magnesium atom in the Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B) (pdb code 3qlz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B), PDB code: 3qlz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg230 b:15.7 occ:1.00 OG A:SER97 3.2 19.5 1.0 NH1 B:ARG79 3.2 24.4 1.0 N6A A:NDP228 3.3 18.9 1.0 NH2 B:ARG79 3.3 23.0 1.0 N A:ARG99 3.4 17.2 1.0 O A:HOH302 3.4 26.6 1.0 N A:LEU98 3.6 18.0 1.0 CZ B:ARG79 3.6 25.1 1.0 CG A:ARG99 3.7 20.5 1.0 CB A:ARG99 3.7 17.9 1.0 CA A:SER97 4.0 20.1 1.0 CB A:SER97 4.0 19.6 1.0 C A:SER97 4.0 19.0 1.0 CD A:ARG99 4.1 22.9 1.0 CA A:ARG99 4.2 19.6 1.0 C6A A:NDP228 4.2 18.6 1.0 N1A A:NDP228 4.2 20.6 1.0 CA A:LEU98 4.3 18.2 1.0 CB A:LEU98 4.3 18.1 1.0 C A:LEU98 4.3 18.5 1.0 O B:HOH304 4.4 26.8 1.0 NE2 B:GLN129 4.4 19.1 1.0 NE2 A:GLN129 4.7 19.1 1.0 NH1 A:ARG79 4.7 24.6 1.0 O B:HOH231 4.7 6.3 1.0 NE B:ARG79 4.8 27.6 1.0 N6A B:NDP228 4.8 20.6 1.0 O A:SER97 4.9 17.0 1.0 N A:ASN100 4.9 20.5 1.0 O A:HOH273 5.0 26.2 1.0

Magnesium binding site 2 out of 3 in the Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg231 b:35.2 occ:1.00 O A:HOH306 3.1 32.4 1.0 N A:ASP82 3.2 33.5 1.0 NH1 A:ARG86 3.5 46.9 1.0 CB A:ASP82 3.6 37.0 1.0 CB A:PHE81 3.8 28.6 1.0 CB A:HIS94 3.8 22.9 1.0 CG A:ASP82 3.9 41.8 1.0 OD2 A:ASP82 3.9 46.2 1.0 CA A:ASP82 4.0 35.8 1.0 CD A:ARG86 4.0 36.8 1.0 CA A:PHE81 4.0 29.8 1.0 ND1 A:HIS94 4.1 24.0 1.0 C A:PHE81 4.1 31.5 1.0 CG A:PHE81 4.2 26.1 1.0 CD1 A:PHE81 4.3 25.8 1.0 CG1 A:VAL88 4.4 25.6 1.0 CG A:HIS94 4.5 22.3 1.0 CZ A:ARG86 4.5 46.2 1.0 CG A:ARG86 4.6 31.2 1.0 OD1 A:ASP82 4.7 44.4 1.0 NE A:ARG86 4.7 42.2 1.0 CB A:ARG86 4.7 28.1 1.0 N A:GLY83 4.8 35.0 1.0 C A:ASP82 4.9 35.5 1.0 CD2 A:PHE81 5.0 24.1 1.0

Magnesium binding site 3 out of 3 in the Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Candida Glabrata Dihydrofolate Reductase Complexed with Nadph and 5- [3-(2,5-Dimethoxyphenyl)Prop-1-Yn-1-Yl]-6-Propylpyrimidine-2,4- Diamine (UCP130B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg230 b:32.3 occ:1.00 N B:ASP82 3.2 33.5 1.0 CB B:ASP82 3.6 37.0 1.0 NE B:ARG86 3.7 42.2 1.0 NH1 B:ARG86 3.8 47.2 1.0 CB B:PHE81 3.8 28.6 1.0 CB B:HIS94 3.8 23.0 1.0 OD2 B:ASP82 3.9 46.1 1.0 CG B:ASP82 3.9 41.8 1.0 CA B:ASP82 4.0 35.8 1.0 CA B:PHE81 4.0 29.8 1.0 ND1 B:HIS94 4.1 24.1 1.0 C B:PHE81 4.1 31.5 1.0 CG B:PHE81 4.2 26.0 1.0 CZ B:ARG86 4.2 46.3 1.0 CD1 B:PHE81 4.3 25.7 1.0 CG1 B:VAL88 4.4 25.8 1.0 CG B:HIS94 4.4 22.6 1.0 OD1 B:ASP82 4.7 44.2 1.0 CB B:ARG86 4.8 28.4 1.0 CG B:ARG86 4.8 31.1 1.0 CD B:ARG86 4.8 37.2 1.0 N B:GLY83 4.8 35.0 1.0 CD2 B:PHE81 5.0 24.2 1.0 C B:ASP82 5.0 35.6 1.0

J.L.Paulsen, S.D.Bendel, A.C.Anderson. Crystal Structures of Candida Albicans Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal the Flexibility of Active Site Loop Residues Critical For Ligand Potency and Selectivity. Chem.Biol.Drug Des. V. 78 505 2011.
ISSN: ISSN 1747-0277
PubMed: 21726415
DOI: 10.1111/J.1747-0285.2011.01169.X