Chlorine in PDB 6vi5: Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

Enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

All present enzymatic activity of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure:
1.13.11.6;

Protein crystallography data

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure, PDB code: 6vi5 was solved by Y.Wang, F.Liu, Y.Yang, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	46.03 / 1.60
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	57.930, 57.930, 231.440, 90.00, 90.00, 120.00
*R / R_free (%)*	19.9 / 22.9

Other elements in 6vi5:

The structure of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure (pdb code 6vi5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure, PDB code: 6vi5:

Chlorine binding site 1 out of 1 in 6vi5

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Chlorine Binding Sites List in 6vi5

Chlorine binding site 1 out of 1 in the Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Observing A Ring-Cleaving Dioxygenase in Action Through A Crystalline Lens - A Resting State Structure within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl204 b:22.1 occ:1.00	O	A:HOH482	2.8	58.9	1.0
	O	A:HOH554	3.0	46.8	1.0
	NH2	A:ARG99	3.2	13.6	1.0
	O	A:HOH448	3.2	24.4	1.0
	NE	A:ARG99	3.3	12.0	1.0
	CB	A:PRO97	3.6	13.7	1.0
	CG	A:PRO97	3.6	17.5	1.0
	CZ	A:ARG99	3.6	16.8	1.0
	O	A:HOH460	4.2	55.7	1.0
	CG2	A:VAL41	4.2	11.4	1.0
	CG1	A:VAL41	4.2	8.5	1.0
	CE2	A:PHE59	4.2	9.2	1.0
	CG2	A:VAL108	4.3	9.9	1.0
	CB	A:VAL41	4.5	8.5	1.0
	CD	A:ARG99	4.5	10.5	1.0
	O	A:HOH504	4.8	29.7	1.0
	CD	A:PRO97	4.9	9.7	1.0
	NH1	A:ARG99	5.0	12.0	1.0
	O	A:HOH488	5.0	27.3	1.0

Reference:

Y.Wang, F.Liu, Y.Yang, A.Liu. Probing Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Reaction Cycle Intermediates Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2005327117

Page generated: Mon Jul 29 16:20:56 2024

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