Magnesium in PDB 5h5k: Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

All present enzymatic activity of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5:
2.7.4.9;

The structure of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h5k was solved by A.Biswas, J.Jeyakanthan, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.840, 51.863, 53.595, 92.00, 92.30, 112.22
R / Rfree (%)	19.4 / 25.1

The binding sites of Magnesium atom in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 5h5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:48.9 occ:1.00 O1G A:ATP202 2.1 58.5 1.0 OG1 A:THR14 2.1 38.5 1.0 O A:HOH314 2.2 40.5 1.0 O1B A:ATP202 2.5 42.3 1.0 O A:HOH308 2.6 40.7 1.0 CB A:THR14 3.2 37.4 1.0 O1A A:ATP202 3.3 57.1 1.0 PG A:ATP202 3.4 66.0 1.0 O1P A:C5P206 3.5 81.3 1.0 PB A:ATP202 3.7 39.3 1.0 O3B A:ATP202 3.7 49.7 1.0 CG2 A:THR14 4.0 38.1 1.0 P A:C5P206 4.1 76.4 1.0 O2P A:C5P206 4.1 73.2 1.0 O2G A:ATP202 4.1 54.0 1.0 OD2 A:ASP89 4.2 46.5 1.0 O3P A:C5P206 4.4 82.5 1.0 CA A:THR14 4.4 35.7 1.0 O A:HOH301 4.5 53.2 1.0 PA A:ATP202 4.5 52.6 1.0 N A:THR14 4.5 35.5 1.0 O A:HOH335 4.5 38.6 1.0 O3G A:ATP202 4.5 66.1 1.0 O3A A:ATP202 4.6 46.8 1.0 OD1 A:ASP89 4.7 46.9 1.0 CG A:ASP89 4.9 41.2 1.0 O2B A:ATP202 4.9 41.8 1.0

Magnesium binding site 2 out of 2 in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:56.5 occ:1.00 O1G B:ATP202 2.1 80.7 1.0 OG1 B:THR14 2.1 47.0 1.0 O1B B:ATP202 2.4 53.0 1.0 O1P B:C5P203 2.8 62.7 1.0 PG B:ATP202 3.3 86.8 1.0 CB B:THR14 3.4 42.8 1.0 O2G B:ATP202 3.7 59.0 1.0 PB B:ATP202 3.7 50.6 1.0 O2P B:C5P203 3.7 63.5 1.0 O3B B:ATP202 3.8 62.5 1.0 P B:C5P203 3.8 64.3 1.0 OD2 B:ASP89 3.9 41.9 1.0 CG2 B:THR14 4.2 40.6 1.0 O1A B:ATP202 4.2 58.9 1.0 N B:THR14 4.4 37.0 1.0 CA B:THR14 4.4 42.1 1.0 OD1 B:ASP89 4.5 42.5 1.0 O3G B:ATP202 4.6 76.5 1.0 CG B:ASP89 4.7 39.5 1.0 O3A B:ATP202 4.7 56.9 1.0 O2B B:ATP202 4.8 42.2 1.0 PA B:ATP202 4.9 61.6 1.0 O3P B:C5P203 4.9 73.6 1.0 O5' B:C5P203 4.9 68.5 1.0

A.Biswas, A.Shukla, S.K.Chaudhary, R.Santhosh, J.Jeyakanthan, K.Sekar. Structural Studies of A Hyperthermophilic Thymidylate Kinase Enzyme Reveal Conformational Substates Along the Reaction Coordinate Febs J. V. 284 2527 2017.
ISSN: ISSN 1742-4658
PubMed: 28627020
DOI: 10.1111/FEBS.14140