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Fluorine 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:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Adp-Mg-F-Dtmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5xb2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5xb2

Go back to Fluorine Binding Sites List in 5xb2
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F204

b:28.6
occ:1.00
MG B:MG203 2.2 44.8 1.0
OD1 B:ASP89 2.7 17.0 1.0
O1P B:TMP202 2.8 24.2 1.0
O3B B:ADP201 2.8 16.4 1.0
CE B:LYS13 3.1 16.0 1.0
O B:HOH308 3.2 19.7 1.0
OG1 B:THR14 3.4 26.2 1.0
OD2 B:ASP89 3.4 18.3 1.0
CG B:ASP89 3.5 15.6 1.0
NZ B:LYS13 3.5 15.9 1.0
PB B:ADP201 3.7 19.1 1.0
O B:HOH348 3.7 23.8 1.0
CB B:LYS13 3.8 11.7 1.0
F B:F206 3.8 33.6 1.0
F B:F205 3.8 37.5 1.0
O1B B:ADP201 3.9 15.0 1.0
NE B:ARG90 4.0 22.2 1.0
P B:TMP202 4.0 28.1 1.0
N B:THR14 4.1 19.1 1.0
O2B B:ADP201 4.2 14.9 1.0
CD B:LYS13 4.3 18.8 1.0
O2P B:TMP202 4.3 27.2 1.0
CG B:ARG90 4.4 13.1 1.0
CG B:LYS13 4.5 14.1 1.0
CZ B:ARG90 4.6 19.5 1.0
O3P B:TMP202 4.6 32.9 1.0
NH2 B:ARG90 4.6 17.6 1.0
CD B:ARG90 4.6 16.9 1.0
CB B:THR14 4.6 21.9 1.0
C B:LYS13 4.7 16.0 1.0
CA B:LYS13 4.7 15.4 1.0
CA B:THR14 4.8 20.7 1.0
CB B:ASP89 5.0 18.0 1.0
N B:LYS13 5.0 22.5 1.0

Fluorine binding site 2 out of 3 in 5xb2

Go back to Fluorine Binding Sites List in 5xb2
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F binding site number 2 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:F205

b:37.5
occ:1.00
MG B:MG203 2.5 44.8 1.0
NH1 B:ARG145 3.1 23.9 0.5
O3P B:TMP202 3.2 32.9 1.0
NH2 B:ARG145 3.2 35.6 0.5
NH2 B:ARG145 3.3 37.5 0.5
O3B B:ADP201 3.4 16.4 1.0
O2B B:ADP201 3.5 14.9 1.0
CZ B:ARG145 3.5 29.8 0.5
OG1 B:THR14 3.6 26.2 1.0
O B:HOH308 3.7 19.7 1.0
P B:TMP202 3.8 28.1 1.0
O2P B:TMP202 3.8 27.2 1.0
F B:F204 3.8 28.6 1.0
O1P B:TMP202 3.8 24.2 1.0
F B:F206 3.9 33.6 1.0
PB B:ADP201 4.0 19.1 1.0
O2A B:ADP201 4.0 26.4 1.0
CZ B:ARG145 4.4 29.1 0.5
NE B:ARG145 4.7 21.5 0.5
NH1 B:ARG145 4.8 26.3 0.5
CB B:THR14 4.8 21.9 1.0
O3A B:ADP201 4.9 21.6 1.0

Fluorine binding site 3 out of 3 in 5xb2

Go back to Fluorine Binding Sites List in 5xb2
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F206

b:33.6
occ:1.00
MG B:MG203 2.0 44.8 1.0
OD2 B:ASP89 2.9 18.3 1.0
O B:HOH348 2.9 23.8 1.0
O2P B:TMP202 3.0 27.2 1.0
OG1 B:THR14 3.6 26.2 1.0
NH2 B:ARG47 3.8 17.1 1.0
F B:F204 3.8 28.6 1.0
CG B:ASP89 3.9 15.6 1.0
F B:F205 3.9 37.5 1.0
CD B:ARG35 4.0 18.6 1.0
O1P B:TMP202 4.0 24.2 1.0
P B:TMP202 4.1 28.1 1.0
CB B:ARG35 4.2 19.6 1.0
OD1 B:ASP89 4.3 17.0 1.0
NH1 B:ARG47 4.4 14.9 1.0
CZ B:ARG47 4.5 22.3 1.0
NH1 B:ARG35 4.5 21.4 1.0
CG2 B:THR14 4.6 13.1 1.0
CB B:THR14 4.7 21.9 1.0
CG B:ARG35 4.7 16.9 1.0
O3P B:TMP202 4.9 32.9 1.0
CB B:ASP89 5.0 18.0 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: Tue Jul 15 09:07:58 2025

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