Magnesium in PDB 2jaw: Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate

The structure of Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate, PDB code: 2jaw was solved by K.Wallden, B.Ruzzenente, V.Bianchi, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.86 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.604, 73.604, 106.374, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.6

The structure of Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate (pdb code 2jaw). 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 D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate, PDB code: 2jaw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate


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 D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1229 b:29.2 occ:1.00 O A:HOH2075 2.3 32.9 1.0 O A:THR124 2.3 21.3 1.0 O A:ALA119 2.4 22.9 1.0 O A:LEU121 2.4 25.1 1.0 O A:HOH2078 2.5 38.2 1.0 O A:HOH2079 2.9 40.5 1.0 C A:ALA119 3.4 22.6 1.0 C A:THR124 3.5 21.1 1.0 C A:LEU121 3.6 26.0 1.0 N A:LEU121 3.8 24.9 1.0 N A:THR124 3.9 23.8 1.0 C A:SER120 3.9 25.6 1.0 CA A:THR124 4.0 22.4 1.0 CB A:THR124 4.2 22.7 1.0 N A:SER120 4.2 23.9 1.0 CA A:SER120 4.3 25.1 1.0 CA A:LEU121 4.3 25.2 1.0 O A:HOH2083 4.4 32.1 1.0 O A:SER120 4.4 25.6 1.0 CA A:ALA119 4.4 22.1 1.0 O A:MET118 4.6 19.6 1.0 N A:GLN122 4.6 26.9 1.0 N A:ASP125 4.6 20.2 1.0 O A:HOH2080 4.7 35.0 1.0 C A:GLN122 4.7 27.6 1.0 N A:ASN123 4.8 26.9 1.0 CA A:GLN122 4.8 28.4 1.0 OD1 A:ASP125 4.9 24.5 1.0 CA A:ASP125 5.0 19.9 1.0 O A:HOH2077 5.0 36.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate


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 D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 5-Bromovinyldeoxyuridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1230 b:14.2 occ:1.00 O2P A:BVP1228 1.9 19.3 0.5 OD1 A:ASN41 2.0 16.8 1.0 O A:ASP43 2.0 14.2 1.0 O A:HOH2167 2.1 15.1 1.0 O1P A:BVP1228 2.1 14.4 0.5 OD1 A:ASP176 2.1 15.7 1.0 O A:HOH2168 2.1 18.2 1.0 CG A:ASN41 3.1 17.2 1.0 C A:ASP43 3.2 14.7 1.0 CG A:ASP176 3.2 17.8 1.0 P A:BVP1228 3.4 20.3 0.5 OD2 A:ASP176 3.6 19.0 1.0 P A:BVP1228 3.7 16.8 0.5 ND2 A:ASN41 3.7 13.5 1.0 O3P A:BVP1228 3.7 20.8 0.5 O A:HOH2172 4.0 16.6 0.5 CA A:ASP43 4.0 14.9 1.0 OD1 A:ASP175 4.0 17.4 1.0 CB A:ASP43 4.1 14.5 1.0 O2P A:BVP1228 4.1 17.1 0.5 N A:ASP43 4.2 14.7 1.0 N A:GLY44 4.2 15.2 1.0 O1P A:BVP1228 4.2 21.1 0.5 O A:HOH2171 4.3 17.5 0.5 CA A:GLY44 4.3 15.4 1.0 O5' A:BVP1228 4.4 23.1 0.5 O3P A:BVP1228 4.4 16.7 0.5 CB A:ASN41 4.4 15.7 1.0 N A:ASP176 4.4 15.8 1.0 CB A:ASP176 4.5 16.9 1.0 O A:HOH2170 4.5 28.8 1.0 CE1 A:PHE75 4.5 24.6 1.0 O5' A:BVP1228 4.7 19.1 0.5 CG A:ASP175 4.7 17.5 1.0 C A:GLY44 4.8 15.5 1.0 C5' A:BVP1228 4.8 27.6 1.0 CG2 A:VAL45 4.8 14.1 1.0 C A:MET42 4.8 14.8 1.0 N A:ARG177 4.9 18.3 1.0 CZ A:PHE75 4.9 23.7 1.0 CA A:ASP176 4.9 17.1 1.0 N A:VAL45 5.0 14.9 1.0 OD2 A:ASP175 5.0 19.4 1.0

K.Wallden, A.Rinaldo-Matthis, B.Ruzzenente, C.Rampazzo, V.Bianchi, P.Nordlund. Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues. Biochemistry V. 46 13809 2007.
ISSN: ISSN 0006-2960
PubMed: 17985935
DOI: 10.1021/BI7014794