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 / R_free (%)*	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

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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

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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

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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: Thu Aug 1 16:47:52 2024

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