Magnesium in PDB 1nn3: Crystal Structure of Human Thymidylate Kinase with D4TMP + Adp

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

The structure of Crystal Structure of Human Thymidylate Kinase with D4TMP + Adp, PDB code: 1nn3 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)	35.70 / 1.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.004, 101.004, 49.840, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Human Thymidylate Kinase with D4TMP + Adp (pdb code 1nn3). 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 + Adp, PDB code: 1nn3:
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 + 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 D4TMP + Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:12.8 occ:1.00 O2B A:ADP302 2.0 10.3 1.0 O A:HOH507 2.0 14.6 1.0 O A:HOH506 2.1 14.6 1.0 O A:HOH504 2.1 11.7 1.0 OG A:SER20 2.1 10.5 1.0 O A:HOH505 2.1 14.3 1.0 CB A:SER20 3.2 9.3 1.0 PB A:ADP302 3.3 12.1 1.0 O3B A:ADP302 3.5 16.3 1.0 N A:SER20 3.9 9.2 1.0 OP2 A:2DT301 4.0 29.1 1.0 O1A A:ADP302 4.1 12.5 1.0 OP3 A:2DT301 4.1 17.2 1.0 OD2 A:ASP96 4.1 11.8 1.0 O A:HOH684 4.1 33.9 1.0 CA A:SER20 4.2 8.4 1.0 O A:HOH754 4.2 15.7 1.0 O3A A:ADP302 4.3 13.6 1.0 OD1 A:ASP96 4.3 11.0 1.0 O1B A:ADP302 4.3 11.9 1.0 P A:2DT301 4.4 24.2 1.0 PA A:ADP302 4.6 12.6 1.0 CG A:ASP96 4.7 9.1 1.0 O A:HOH670 4.8 32.6 1.0 O A:HOH520 4.8 27.0 1.0 CE A:LYS19 4.8 15.5 1.0 CB A:LYS19 4.9 8.9 1.0 OP1 A:2DT301 5.0 29.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Thymidylate Kinase with D4TMP + 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 D4TMP + Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.0 occ:0.50 O A:HOH501 1.9 24.8 1.0 O A:HOH502 2.1 23.4 1.0 O A:HOH503 2.2 28.1 1.0 OE1 A:GLN119 4.2 13.1 1.0 OD1 A:ASP115 4.5 21.6 1.0 CD A:GLN119 4.5 11.9 1.0 OD2 A:ASP115 4.6 22.4 1.0 O A:HOH666 4.7 34.4 1.0 NE2 A:GLN119 4.8 14.9 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