Calcium in PDB 5h56: Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

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

The structure of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h56 was solved by A.Biswas, J.Jeyakanthan, K.Sekar, S.Kuramitsu, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.482, 62.414, 76.144, 90.00, 91.02, 90.00
R / Rfree (%)	15.6 / 18.5

The structure of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Calcium atom in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 5h56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h56:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:13.3 occ:1.00 O A:HOH374 2.3 24.4 1.0 OE1 A:GLU142 2.4 17.2 1.0 O A:HOH397 2.4 11.6 1.0 O A:HOH427 2.5 13.8 1.0 OE2 A:GLU142 2.9 24.9 1.0 CD A:GLU142 3.0 18.8 1.0 O A:HOH350 4.5 10.4 1.0 CG A:GLU142 4.5 16.7 1.0 O A:HOH434 4.6 24.2 1.0 CG A:ARG139 4.8 9.2 1.0 N3 A:ADP201 4.8 9.0 1.0 CA A:ARG139 4.8 9.4 1.0 C2 A:ADP201 4.9 9.4 1.0

Calcium binding site 2 out of 2 in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:16.9 occ:1.00 O A:HOH376 2.3 24.5 1.0 O A:HOH421 2.4 20.7 1.0 OE2 A:GLU180 2.4 17.1 1.0 O A:HOH433 2.7 26.0 1.0 CD A:GLU180 3.4 15.3 1.0 OE1 A:GLU180 3.6 14.6 1.0 O A:HOH314 4.5 30.2 1.0 CA A:GLY176 4.6 14.0 1.0 OD2 A:ASP173 4.7 14.4 1.0 CG A:GLU180 4.7 14.3 1.0 O A:HOH307 4.9 31.5 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