Magnesium in PDB 1nn5: Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp

All present enzymatic activity of Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp:
2.7.4.9;

The structure of Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp, PDB code: 1nn5 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)	35.50 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.100, 101.100, 49.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp (pdb code 1nn5). 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 D4TMP + Appnhp, PDB code: 1nn5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp


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 D4TMP + Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:12.6 occ:1.00 O2B A:ANP303 2.1 12.9 1.0 O2G A:ANP303 2.1 14.5 1.0 O A:HOH504 2.1 12.1 1.0 O A:HOH506 2.1 14.2 1.0 O A:HOH505 2.1 15.1 1.0 OG A:SER20 2.1 11.0 1.0 PB A:ANP303 3.2 13.0 1.0 CB A:SER20 3.3 10.6 1.0 PG A:ANP303 3.3 20.1 1.0 N3B A:ANP303 3.5 14.2 1.0 O A:HOH509 3.9 28.0 1.0 N A:SER20 3.9 10.7 1.0 O A:HOH763 3.9 41.2 1.0 O A:HOH639 4.0 32.8 1.0 O A:HOH518 4.0 47.5 1.0 OP2 A:2DT301 4.1 31.8 1.0 OD2 A:ASP96 4.1 12.2 1.0 O A:HOH754 4.1 50.7 1.0 O2A A:ANP303 4.1 13.4 1.0 CA A:SER20 4.2 9.3 1.0 O3G A:ANP303 4.3 22.4 1.0 O1B A:ANP303 4.3 12.7 1.0 O A:HOH524 4.3 17.9 1.0 OD1 A:ASP96 4.3 11.8 1.0 O1G A:ANP303 4.3 25.7 1.0 O3A A:ANP303 4.4 12.9 1.0 CG A:ASP96 4.6 10.8 1.0 PA A:ANP303 4.7 13.2 1.0 CB A:LYS19 4.8 9.7 1.0 O A:HOH715 4.8 35.1 1.0 CE A:LYS19 4.9 12.9 1.0 C A:LYS19 5.0 10.7 1.0 O A:HOH695 5.0 35.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Thymidylate Kinase with D4TMP + Appnhp


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 D4TMP + Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.0 occ:0.50 O A:HOH503 2.2 21.9 1.0 O A:HOH501 2.2 20.7 1.0 O A:HOH502 2.2 25.7 1.0 OE1 A:GLN119 4.1 13.9 1.0 O A:HOH728 4.3 34.6 1.0 OD1 A:ASP115 4.4 21.8 1.0 OD2 A:ASP115 4.4 20.4 1.0 CD A:GLN119 4.4 11.7 1.0 O A:HOH789 4.5 38.3 1.0 NE2 A:GLN119 4.7 14.4 1.0 CG A:ASP115 4.9 19.5 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