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

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

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

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-, PDB code: 6vck 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)*	28.93 / 2.69
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	161.840, 193.601, 51.037, 90.00, 90.00, 90.00
*R / R_free (%)*	22.6 / 26.8

Other elements in 6vck:

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

Magnesium	(Mg)	3 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 Gdp, MG2+ and F- (pdb code 6vck). 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 Gdp, MG2+ and F-, PDB code: 6vck:

Fluorine binding site 1 out of 1 in 6vck

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Fluorine Binding Sites List in 6vck

Fluorine binding site 1 out of 1 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, 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 Gdp, MG2+ and F- within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F206 b:0.5 occ:1.00	MG	B:MG202	2.2	89.0	1.0
	MG	B:MG201	2.2	91.2	1.0
	O	B:HOH353	2.3	93.6	1.0
	O2B	B:GDP204	2.6	89.9	1.0
	O3B	B:GDP204	3.1	94.6	1.0
	OE2	B:GLU53	3.1	75.5	1.0
	PB	B:GDP204	3.2	97.6	1.0
	OE1	B:GLU53	3.2	72.5	1.0
	O1B	B:GDP204	3.5	95.9	1.0
	CD	B:GLU53	3.6	71.8	1.0
	O	B:HOH342	3.7	96.5	1.0
	OE1	B:GLU120	3.7	89.0	1.0
	OE1	B:GLU56	3.8	77.6	1.0
	OE2	B:GLU57	4.2	79.0	0.4
	O	B:HOH313	4.2	76.7	1.0
	O3A	B:GDP204	4.7	0.6	1.0
	NH2	B:ARG52	4.8	66.4	1.0
	CD	B:GLU120	4.9	95.5	1.0
	CD	B:GLU56	5.0	81.5	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: Fri Aug 2 02:58:28 2024

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