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Magnesium in PDB 5xb2: Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

Enzymatic activity of Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

All present enzymatic activity of Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5:
2.7.4.9;

Protein crystallography data

The structure of Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5xb2 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) 49.94 / 2.16
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.620, 52.990, 54.019, 88.90, 90.83, 70.53
R / Rfree (%) 19.5 / 25.9

Other elements in 5xb2:

The structure of Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 5xb2). 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 Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5xb2:

Magnesium binding site 1 out of 1 in 5xb2

Go back to Magnesium Binding Sites List in 5xb2
Magnesium binding site 1 out of 1 in the Adp-Mg-F-Dtmp 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 Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:44.8
occ:1.00
 F B:F206 2.0 33.6 1.0
F B:F204 2.2 28.6 1.0
F B:F205 2.5 37.5 1.0
OG1 B:THR14 2.8 26.2 1.0
O1P B:TMP202 2.8 24.2 1.0
O2P B:TMP202 2.9 27.2 1.0
P B:TMP202 3.3 28.1 1.0
OD2 B:ASP89 3.3 18.3 1.0
O B:HOH348 3.4 23.8 1.0
O3B B:ADP201 3.4 16.4 1.0
O3P B:TMP202 3.7 32.9 1.0
OD1 B:ASP89 3.9 17.0 1.0
CG B:ASP89 4.0 15.6 1.0
O B:HOH308 4.1 19.7 1.0
CB B:THR14 4.2 21.9 1.0
PB B:ADP201 4.6 19.1 1.0
NH2 B:ARG47 4.7 17.1 1.0
O2B B:ADP201 4.7 14.9 1.0
CG2 B:THR14 4.8 13.1 1.0
O5' B:TMP202 4.8 27.3 1.0
N B:THR14 4.9 19.1 1.0
CA B:THR14 5.0 20.7 1.0

Reference:

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
Page generated: Mon Sep 30 09:15:48 2024

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