Magnesium in PDB 1oe0: Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp

All present enzymatic activity of Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp:
2.7.1.145;

The structure of Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp, PDB code: 1oe0 was solved by N.E.Mikkelsen, K.Johansson, A.Karlsson, W.Knecht, G.Andersen, J.Piskur, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.73 / 2.4
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.078, 119.680, 69.512, 90.00, 92.85, 90.00
R / Rfree (%)	22 / 24.2

The binding sites of Magnesium atom in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp (pdb code 1oe0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp, PDB code: 1oe0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp


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 Drosophila Deoxyribonucleoside Kinase in Complex with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:45.6 occ:1.00 OG1 A:THR34 2.0 51.2 1.0 O A:HOH2033 2.1 41.9 1.0 O1B A:TTP300 2.1 46.5 1.0 OE2 A:GLU104 2.1 47.2 1.0 O3G A:TTP300 2.1 41.6 1.0 OE2 A:GLU52 2.3 57.1 1.0 CD A:GLU104 3.1 46.0 1.0 PB A:TTP300 3.2 44.6 1.0 CB A:THR34 3.2 52.4 1.0 CD A:GLU52 3.3 57.5 1.0 O3B A:TTP300 3.3 43.7 1.0 PG A:TTP300 3.3 46.0 1.0 OE1 A:GLU104 3.5 46.9 1.0 OE1 A:GLU52 3.6 57.5 1.0 O3A A:TTP300 3.8 44.5 1.0 N A:THR34 3.9 51.2 1.0 O1G A:TTP300 4.0 44.3 1.0 NH2 A:ARG169 4.1 45.4 1.0 CA A:THR34 4.1 52.2 1.0 CG2 A:THR34 4.3 52.0 1.0 O2G A:TTP300 4.4 40.6 1.0 CG A:GLU104 4.5 45.0 1.0 O2B A:TTP300 4.5 44.4 1.0 CG A:GLU52 4.6 55.0 1.0 CA A:GLU52 4.6 50.8 1.0 O A:HOH2003 4.7 56.5 1.0 NH1 A:ARG167 4.8 56.8 1.0 CB A:GLU52 4.9 52.0 1.0 CG2 A:VAL54 4.9 48.7 1.0 CB A:LYS33 5.0 49.1 1.0 C A:LYS33 5.0 50.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp


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 Drosophila Deoxyribonucleoside Kinase in Complex with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:46.0 occ:1.00 OG1 B:THR34 2.1 49.4 1.0 O1B B:TTP300 2.1 41.8 1.0 OE2 B:GLU104 2.2 41.0 1.0 O3G B:TTP300 2.2 42.2 1.0 OE2 B:GLU52 2.2 47.6 1.0 O B:HOH2008 2.3 43.3 1.0 CD B:GLU104 3.2 43.3 1.0 PB B:TTP300 3.2 41.7 1.0 CD B:GLU52 3.2 50.0 1.0 CB B:THR34 3.2 49.4 1.0 O3B B:TTP300 3.3 43.3 1.0 PG B:TTP300 3.3 44.1 1.0 OE1 B:GLU104 3.5 45.5 1.0 OE1 B:GLU52 3.6 52.1 1.0 O B:HOH2025 3.6 60.0 1.0 O3A B:TTP300 3.8 41.2 1.0 N B:THR34 4.0 49.3 1.0 O1G B:TTP300 4.1 41.6 1.0 NH2 B:ARG169 4.1 41.6 1.0 CA B:THR34 4.2 49.7 1.0 CG2 B:THR34 4.3 47.9 1.0 O2G B:TTP300 4.5 42.5 1.0 CG B:GLU104 4.5 43.0 1.0 O2B B:TTP300 4.5 39.3 1.0 CG B:GLU52 4.6 49.3 1.0 CA B:GLU52 4.6 46.5 1.0 NH1 B:ARG167 4.8 52.9 1.0 O B:HOH2004 4.9 54.6 1.0 CB B:GLU52 4.9 46.0 1.0 CG2 B:VAL54 4.9 48.8 1.0 CB B:LYS33 5.0 46.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:43.9 occ:1.00 O1B C:TTP300 2.1 45.3 1.0 O3G C:TTP300 2.1 39.9 1.0 OG1 C:THR34 2.1 53.9 1.0 OE2 C:GLU104 2.1 46.9 1.0 OE2 C:GLU52 2.3 55.0 1.0 O C:HOH2007 2.4 49.4 1.0 PB C:TTP300 3.1 41.5 1.0 CD C:GLU104 3.2 46.8 1.0 O3B C:TTP300 3.2 42.2 1.0 PG C:TTP300 3.3 43.1 1.0 CB C:THR34 3.3 54.2 1.0 CD C:GLU52 3.3 54.2 1.0 OE1 C:GLU104 3.5 50.3 1.0 OE1 C:GLU52 3.7 54.6 1.0 O3A C:TTP300 3.8 41.5 1.0 N C:THR34 3.9 52.4 1.0 O1G C:TTP300 4.0 41.4 1.0 NH2 C:ARG169 4.1 37.7 1.0 CA C:THR34 4.2 53.4 1.0 CG2 C:THR34 4.4 52.2 1.0 O2G C:TTP300 4.4 40.1 1.0 O2B C:TTP300 4.4 42.8 1.0 O C:HOH2003 4.5 55.5 1.0 CG C:GLU104 4.5 45.2 1.0 CG C:GLU52 4.6 53.1 1.0 CA C:GLU52 4.7 50.3 1.0 NH1 C:ARG167 4.8 53.9 1.0 CG2 C:VAL54 4.9 49.2 1.0 CB C:GLU52 4.9 52.2 1.0 CB C:LYS33 4.9 50.0 1.0 C C:LYS33 5.0 52.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Drosophila Deoxyribonucleoside Kinase in Complex with Dttp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:46.8 occ:1.00 OG1 D:THR34 2.1 48.6 1.0 OE2 D:GLU104 2.1 41.2 1.0 O3G D:TTP300 2.1 37.9 1.0 O1B D:TTP300 2.2 40.5 1.0 OE2 D:GLU52 2.3 51.2 1.0 CD D:GLU104 3.1 42.4 1.0 PB D:TTP300 3.2 39.5 1.0 CB D:THR34 3.2 50.3 1.0 CD D:GLU52 3.3 52.5 1.0 O3B D:TTP300 3.3 40.0 1.0 PG D:TTP300 3.3 41.0 1.0 OE1 D:GLU104 3.5 43.7 1.0 OE1 D:GLU52 3.6 54.8 1.0 O3A D:TTP300 3.8 41.2 1.0 N D:THR34 3.9 49.6 1.0 O1G D:TTP300 4.0 40.3 1.0 NH2 D:ARG169 4.1 39.8 1.0 CA D:THR34 4.1 50.2 1.0 O D:HOH2036 4.3 45.4 1.0 CG2 D:THR34 4.3 47.4 1.0 O2G D:TTP300 4.4 39.3 1.0 CG D:GLU104 4.5 42.6 1.0 O2B D:TTP300 4.5 40.4 1.0 CG D:GLU52 4.6 51.1 1.0 CA D:GLU52 4.6 47.2 1.0 NH1 D:ARG167 4.8 53.6 1.0 CB D:GLU52 4.9 48.1 1.0 CG2 D:VAL54 4.9 47.1 1.0 CB D:LYS33 5.0 48.1 1.0 C D:LYS33 5.0 49.4 1.0

N.E.Mikkelsen, K.Johansson, A.Karlsson, W.Knecht, G.Andersen, J.Piskur, B.Munch-Petersen, H.Eklund. Structural Basis For Feedback Inhibition of the Deoxyribonucleoside Salvage Pathway:Studies of the Drosophila Deoxyribonucleoside Kinase Biochemistry V. 42 5706 2003.
ISSN: ISSN 0006-2960
PubMed: 12741827
DOI: 10.1021/BI0340043