Magnesium in PDB 2jat: Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound

All present enzymatic activity of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound:
2.7.1.113;

The structure of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound, PDB code: 2jat was solved by M.Welin, L.Wang, S.Eriksson, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	83.931, 83.931, 53.310, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 26.6

The binding sites of Magnesium atom in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound (pdb code 2jat). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound, PDB code: 2jat:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:65.1 occ:1.00 O1P A:DCM1205 2.0 50.0 1.0 O2 A:POP1204 2.2 58.0 1.0 OG A:SER14 3.3 36.7 1.0 P A:DCM1205 3.4 51.9 1.0 OD2 A:ASP77 3.5 35.9 1.0 O2P A:DCM1205 3.5 51.5 1.0 P1 A:POP1204 3.5 56.2 1.0 O3 A:POP1204 3.8 57.5 1.0 CB A:SER14 3.9 34.4 1.0 OD1 A:ASP77 4.1 36.5 1.0 O A:POP1204 4.2 58.6 1.0 CG A:ASP77 4.2 36.2 1.0 N A:SER14 4.2 33.9 1.0 O3P A:DCM1205 4.2 50.3 1.0 CE A:LYS13 4.4 32.5 1.0 O5' A:DCM1205 4.5 52.8 1.0 O4 A:POP1204 4.5 58.9 1.0 CA A:SER14 4.6 34.5 1.0 O1 A:POP1204 4.6 57.1 1.0 CB A:LYS13 4.8 34.4 1.0 C5' A:DCM1205 5.0 53.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1202 b:69.0 occ:1.00 O1P B:DCM1204 2.0 49.8 1.0 O5 B:POP1203 2.2 60.5 1.0 OG B:SER14 3.3 36.7 1.0 P2 B:POP1203 3.4 58.8 1.0 P B:DCM1204 3.5 51.8 1.0 OD2 B:ASP77 3.6 35.8 1.0 O4 B:POP1203 3.6 59.9 1.0 O2P B:DCM1204 3.7 52.2 1.0 CB B:SER14 3.9 34.4 1.0 O B:POP1203 3.9 60.7 1.0 OD1 B:ASP77 4.2 36.4 1.0 O3P B:DCM1204 4.2 49.6 1.0 N B:SER14 4.2 33.9 1.0 CG B:ASP77 4.3 36.2 1.0 O1 B:POP1203 4.4 61.1 1.0 CE B:LYS13 4.4 32.6 1.0 O5' B:DCM1204 4.6 52.9 1.0 CA B:SER14 4.6 34.5 1.0 O6 B:POP1203 4.6 59.9 1.0 CB B:LYS13 4.8 34.5 1.0 P1 B:POP1203 4.9 62.1 1.0

M.Welin, L.Wang, S.Eriksson, H.Eklund. Structure-Function Analysis of A Bacterial Deoxyadenosine Kinase Reveals the Basis For Substrate Specificity. J.Mol.Biol. V. 366 1615 2007.
ISSN: ISSN 0022-2836
PubMed: 17229440
DOI: 10.1016/J.JMB.2006.12.010