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Magnesium in PDB 3hjn: Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima

Enzymatic activity of Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima

All present enzymatic activity of Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima:
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima, PDB code: 3hjn was solved by S.Yoshikawa, N.Nakagawa, M.Shirouzu, S.Yokoyama, S.Kuramitsu, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.80 / 2.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 51.587, 127.050, 133.519, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima (pdb code 3hjn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima, PDB code: 3hjn:

Magnesium binding site 1 out of 1 in 3hjn

Go back to Magnesium Binding Sites List in 3hjn
Magnesium binding site 1 out of 1 in the Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima


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 Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:37.7
occ:1.00
 O3B A:TYD401 2.1 15.0 0.7
O2B A:ADP301 2.2 27.1 1.0
OG A:SER14 2.2 27.3 1.0
O A:HOH243 2.3 29.1 1.0
O A:HOH242 2.3 27.9 1.0
O A:HOH239 2.4 38.5 1.0
PB A:ADP301 3.4 26.1 1.0
CB A:SER14 3.4 29.7 1.0
PB A:TYD401 3.5 16.9 0.7
O3B A:ADP301 3.7 25.4 1.0
O1B A:TYD401 3.9 24.9 0.7
NZ A:LYS139 4.0 35.2 1.0
O1A A:TYD401 4.0 13.3 0.7
OD2 A:ASP88 4.0 32.5 1.0
N A:SER14 4.0 27.6 1.0
O A:HOH234 4.1 32.4 1.0
O1A A:ADP301 4.2 34.8 1.0
PA A:TYD401 4.2 20.9 0.7
CA A:SER14 4.3 37.9 1.0
O3A A:TYD401 4.4 18.1 0.7
OD1 A:ASP88 4.4 25.7 1.0
O1B A:ADP301 4.4 33.3 1.0
O3A A:ADP301 4.5 25.6 1.0
PA A:ADP301 4.6 30.3 1.0
O2B A:TYD401 4.6 16.9 0.7
O2A A:TYD401 4.6 23.3 0.7
CG A:ASP88 4.6 37.0 1.0
NZ A:LYS13 4.7 24.6 1.0
CE A:LYS13 4.8 21.5 1.0
CB A:LYS13 4.9 28.0 1.0

Reference:

S.Yoshikawa, N.Nakagawa, M.Shirouzu, S.Yokoyama, S.Kuramitsu. Crystal Structure of Thymidylate Kinase in Complex with Dtdp and Adp From Thermotoga Maritima To Be Published.
Page generated: Sun Aug 10 21:57:14 2025

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