Magnesium in PDB 1nmx: Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp

All present enzymatic activity of Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp:
2.7.4.9;

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp, PDB code: 1nmx was solved by N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.10 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.515, 101.515, 50.012, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.8

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp (pdb code 1nmx). 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 Human Thymidylate Kinase with Fltmp and Adp, PDB code: 1nmx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp


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 Human Thymidylate Kinase with Fltmp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:15.1 occ:1.00 O2B A:ADP302 2.1 14.3 1.0 O A:HOH505 2.1 16.0 1.0 O A:HOH506 2.1 14.4 1.0 OG A:SER20 2.1 11.7 1.0 O A:HOH507 2.1 18.0 1.0 O A:HOH504 2.2 14.6 1.0 CB A:SER20 3.2 14.0 1.0 PB A:ADP302 3.3 16.2 1.0 O3B A:ADP302 3.7 16.8 1.0 N A:SER20 4.0 12.8 1.0 OP1 A:FDM301 4.0 18.9 1.0 O A:HOH626 4.1 30.2 1.0 O1A A:ADP302 4.1 14.9 1.0 OD2 A:ASP96 4.1 16.0 1.0 CA A:SER20 4.2 12.6 1.0 O A:HOH523 4.2 16.8 1.0 OD1 A:ASP96 4.3 13.4 1.0 O3A A:ADP302 4.4 15.1 1.0 P1 A:FDM301 4.4 23.5 1.0 OP2 A:FDM301 4.4 24.2 1.0 O1B A:ADP302 4.4 17.8 1.0 OP3 A:FDM301 4.4 23.0 1.0 PA A:ADP302 4.7 16.2 1.0 O A:HOH753 4.7 45.0 1.0 CG A:ASP96 4.7 10.8 1.0 CE A:LYS19 4.8 18.7 1.0 CB A:LYS19 4.8 15.1 1.0 O2A A:ADP302 5.0 16.1 1.0 O A:HOH681 5.0 28.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Adp


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 Human Thymidylate Kinase with Fltmp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:24.2 occ:0.50 O A:HOH503 2.1 23.9 1.0 O A:HOH501 2.1 30.0 1.0 O A:HOH502 2.2 29.6 1.0 OE1 A:GLN119 4.2 17.8 1.0 O A:HOH806 4.2 44.5 1.0 OD1 A:ASP115 4.4 24.1 1.0 CD A:GLN119 4.4 16.6 1.0 OD2 A:ASP115 4.5 25.2 1.0 NE2 A:GLN119 4.7 19.9 1.0 CG A:ASP115 4.9 21.0 1.0

N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie. Structures of Human Thymidylate Kinase in Complex with Prodrugs: Implications For the Structure-Based Design of Novel Compounds Biochemistry V. 42 2568 2003.
ISSN: ISSN 0006-2960
PubMed: 12614151
DOI: 10.1021/BI027302T