Calcium in PDB 1daf: Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium

Enzymatic activity of Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium

All present enzymatic activity of Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium:
6.3.3.3;

Protein crystallography data

The structure of Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium, PDB code: 1daf was solved by W.Huang, J.Jia, G.Schneider, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	6.00 / 1.70
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	73.200, 49.200, 61.800, 90.00, 107.10, 90.00
*R / R_free (%)*	17.2 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium (pdb code 1daf). 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 Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium, PDB code: 1daf:

Calcium binding site 1 out of 1 in 1daf

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Calcium Binding Sites List in 1daf

Calcium binding site 1 out of 1 in the Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dethiobiotin Synthetase Complexed with 7-(Carboxyamino)-8- Amino-Nonanoic Acid, Adp, and Calcium within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca227 b:23.2 occ:1.00	O	A:HOH363	2.2	27.3	1.0
	O1A	A:ADP226	2.3	17.4	1.0
	OD1	A:ASP54	2.5	23.3	1.0
	O	A:HOH374	2.5	35.5	1.0
	O	A:HOH380	2.6	26.7	1.0
	O	A:HOH370	2.7	34.1	1.0
	OD2	A:ASP54	2.8	24.7	1.0
	CG	A:ASP54	3.0	21.6	1.0
	PA	A:ADP226	3.7	17.4	1.0
	OE2	A:GLU12	4.2	38.8	1.0
	O	A:HOH369	4.2	34.5	1.0
	O3A	A:ADP226	4.3	20.2	1.0
	O3B	A:ADP226	4.3	17.6	1.0
	CB	A:ASP54	4.5	21.4	1.0
	OG1	A:THR16	4.5	14.2	1.0
	O5'	A:ADP226	4.5	19.6	1.0
	C5'	A:ADP226	4.5	19.0	1.0
	OG	A:SER53	4.6	28.1	1.0
	O2B	A:ADP226	4.6	16.3	1.0
	O	A:HOH285	4.6	23.3	1.0
	O	A:HOH367	4.7	24.1	1.0
	PB	A:ADP226	4.7	18.8	1.0
	O2A	A:ADP226	4.7	17.8	1.0

Reference:

W.Huang, J.Jia, K.J.Gibson, W.S.Taylor, A.R.Rendina, G.Schneider, Y.Lindqvist. Mechanism of An Atp-Dependent Carboxylase, Dethiobiotin Synthetase, Based on Crystallographic Studies of Complexes with Substrates and A Reaction Intermediate. Biochemistry V. 34 10985 1995.
ISSN: ISSN 0006-2960
PubMed: 7669756
DOI: 10.1021/BI00035A004

Page generated: Mon Jul 7 14:21:21 2025

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