Calcium in PDB 4ghf: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf was solved by E.G.Kovaleva, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	89.04 / 1.67
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	110.519, 150.318, 96.105, 90.00, 90.00, 90.00
*R / R_free (%)*	15.1 / 18.1

Other elements in 4ghf:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution (pdb code 4ghf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf:

Calcium binding site 1 out of 1 in 4ghf

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Calcium Binding Sites List in 4ghf

Calcium binding site 1 out of 1 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca403 b:21.1 occ:1.00	OE2	B:GLU185	2.2	33.4	1.0
	OD1	B:ASP184	2.3	20.1	1.0
	O	B:HOH501	2.5	26.9	1.0
	CG	B:ASP184	3.2	20.7	1.0
	CD	B:GLU185	3.3	33.2	1.0
	OD2	B:ASP184	3.5	19.3	1.0
	CG	B:GLU185	3.8	29.6	1.0
	O	B:HOH567	4.3	39.2	1.0
	O	B:HOH758	4.3	40.4	1.0
	NE2	B:HIS288	4.4	21.1	1.0
	OE1	B:GLU185	4.4	39.2	1.0
	N	B:ASP184	4.6	20.0	1.0
	CB	B:ASP184	4.6	19.7	1.0
	CB	B:GLU185	4.7	27.1	1.0
	OD2	B:ASP183	4.8	25.0	1.0
	N	B:GLU185	4.8	22.7	1.0
	CB	B:ASP183	4.9	20.4	1.0
	CA	B:ASP184	4.9	20.5	1.0
	CD2	B:HIS288	5.0	20.1	1.0
	CG	B:ASP183	5.0	21.8	1.0

Reference:

E.G.Kovaleva, J.D.Lipscomb. Structural Basis For the Role of Tyrosine 257 of Homoprotocatechuate 2,3-Dioxygenase in Substrate and Oxygen Activation. Biochemistry V. 51 8755 2012.
ISSN: ISSN 0006-2960
PubMed: 23066739
DOI: 10.1021/BI301115C

Page generated: Sun Jul 14 07:13:13 2024

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