Fluorine in PDB 6vcm: Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-

Enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-

All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-:
5.1.1.7;

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-, PDB code: 6vcm was solved by A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.90 / 2.35
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	162.357, 192.948, 51.100, 90.00, 90.00, 90.00
*R / R_free (%)*	21.2 / 23.5

Other elements in 6vcm:

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F- also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F- (pdb code 6vcm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-, PDB code: 6vcm:

Fluorine binding site 1 out of 1 in 6vcm

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Fluorine Binding Sites List in 6vcm

Fluorine binding site 1 out of 1 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F- within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F207 b:76.5 occ:1.00	MG	B:MG203	2.0	80.5	1.0
	MG	B:MG205	2.2	69.6	1.0
	MG	B:MG204	2.4	81.8	1.0
	OE1	B:GLU53	3.1	42.0	1.0
	O	B:GLN37	3.1	46.6	1.0
	O2G	B:GTP206	3.1	73.0	0.6
	CA	B:GLY38	3.2	49.3	1.0
	O3G	B:GTP206	3.4	68.4	0.6
	MG	B:MG202	3.6	79.4	1.0
	OE2	B:GLU53	3.6	55.0	1.0
	CD	B:GLU53	3.7	55.3	1.0
	PG	B:GTP206	3.8	64.3	0.6
	C	B:GLN37	4.0	47.8	1.0
	N	B:GLY38	4.1	46.2	1.0
	N	B:GLY39	4.2	51.9	1.0
	C	B:GLY38	4.3	44.4	1.0
	O1G	B:GTP206	4.5	54.5	0.6
	CG	B:GLU120	4.6	80.2	1.0

Reference:

A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov. Principles of Rna and Nucleotide Discrimination By the Rna Processing Enzyme Rpph. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 31960065
DOI: 10.1093/NAR/GKAA024

Page generated: Tue Jul 15 16:36:38 2025

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