Calcium in PDB 2ydp: Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

Enzymatic activity of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

All present enzymatic activity of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor:
3.2.1.55;

Protein crystallography data

The structure of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor, PDB code: 2ydp was solved by E.D.Goddard-Borger, R.Carapito, J.M.Jeltsch, V.Phalip, R.V.Stick, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	33.97 / 1.85
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	56.930, 57.800, 91.600, 90.14, 93.55, 114.50
*R / R_free (%)*	17.1 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor (pdb code 2ydp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor, PDB code: 2ydp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2ydp

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Calcium Binding Sites List in 2ydp

Calcium binding site 1 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca502 b:31.9 occ:1.00	O	A:PRO33	2.3	20.0	1.0
	O	A:HOH2029	2.4	31.1	1.0
	O	A:HOH2025	2.4	33.8	1.0
	OD1	A:ASP32	2.5	27.3	1.0
	OD1	B:ASN248	2.5	25.7	1.0
	O	A:HOH2024	2.7	17.0	1.0
	O	A:HOH2392	3.2	49.8	1.0
	C	A:PRO33	3.5	20.8	1.0
	CG	A:ASP32	3.5	23.9	1.0
	CG	B:ASN248	3.6	22.6	1.0
	N	A:PRO33	3.9	20.6	1.0
	ND2	B:ASN248	4.0	19.4	1.0
	OD2	A:ASP32	4.1	27.8	1.0
	CG	A:PRO33	4.1	20.1	1.0
	CD	A:PRO33	4.1	19.8	1.0
	O	A:GLY364	4.1	19.4	1.0
	C	A:ASP32	4.2	20.4	1.0
	CA	A:PRO33	4.2	20.0	1.0
	C	A:PRO34	4.5	23.0	1.0
	OE1	A:GLN41	4.5	18.1	1.0
	N	A:PRO34	4.5	21.0	1.0
	O	A:ASP32	4.6	20.7	1.0
	CB	A:ASP32	4.7	21.5	1.0
	N	A:THR35	4.7	24.0	1.0
	CA	A:PRO34	4.7	22.2	1.0
	CB	A:PRO33	4.7	20.4	1.0
	O	A:PRO34	4.7	22.4	1.0
	CA	A:ASP32	4.8	20.4	1.0
	CB	B:ASN248	4.9	20.5	1.0
	O	A:HOH2023	4.9	40.2	1.0
	O	A:ASN366	5.0	12.4	1.0

Calcium binding site 2 out of 3 in 2ydp

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Calcium Binding Sites List in 2ydp

Calcium binding site 2 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca502 b:41.0 occ:1.00	OD1	B:ASP32	2.3	31.6	1.0
	O	B:HOH2006	2.3	34.5	1.0
	O	B:PRO33	2.4	28.7	1.0
	CG	B:ASP32	3.4	30.9	1.0
	C	B:PRO33	3.6	29.0	1.0
	OD2	B:ASP32	3.9	33.0	1.0
	O	B:GLY364	4.0	29.3	1.0
	N	B:PRO33	4.0	28.8	1.0
	CD	B:PRO33	4.0	29.0	1.0
	C	B:ASP32	4.2	29.2	1.0
	CG	B:PRO33	4.2	28.4	1.0
	CA	B:PRO33	4.3	28.9	1.0
	OE1	B:GLN41	4.5	27.1	1.0
	CB	B:ASP32	4.6	29.4	1.0
	N	B:PRO34	4.6	30.1	1.0
	O	B:ASP32	4.6	29.4	1.0
	C	B:PRO34	4.7	32.1	1.0
	CA	B:ASP32	4.7	28.7	1.0
	N	B:THR35	4.8	33.0	1.0
	CB	B:PRO33	4.8	27.9	1.0
	CA	B:PRO34	4.9	31.2	1.0
	O	B:ASN366	4.9	22.9	1.0
	CG2	B:THR35	4.9	34.2	1.0

Calcium binding site 3 out of 3 in 2ydp

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Calcium Binding Sites List in 2ydp

Calcium binding site 3 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Ca502 b:24.1 occ:1.00	O	A:HOH2290	2.2	24.6	1.0
	O	C:PRO33	2.3	15.6	1.0
	OD1	A:ASN248	2.4	18.3	1.0
	OD1	C:ASP32	2.4	14.7	1.0
	O	C:HOH2009	2.6	38.9	1.0
	O	A:HOH2287	2.6	17.8	1.0
	O	A:HOH2289	2.8	32.6	1.0
	CG	A:ASN248	3.3	19.3	1.0
	CG	C:ASP32	3.5	16.9	1.0
	C	C:PRO33	3.5	16.4	1.0
	ND2	A:ASN248	3.7	20.1	1.0
	N	C:PRO33	3.9	15.1	1.0
	OD2	C:ASP32	4.0	20.1	1.0
	O	C:GLY364	4.0	18.3	1.0
	C	C:ASP32	4.1	15.8	1.0
	CD	C:PRO33	4.2	14.6	1.0
	CG	C:PRO33	4.2	14.6	1.0
	CA	C:PRO33	4.3	15.7	1.0
	O	C:ASP32	4.4	15.9	1.0
	OE1	C:GLN41	4.4	18.8	1.0
	O	A:HOH2288	4.5	49.8	1.0
	CB	A:ASN248	4.5	16.1	1.0
	C	C:PRO34	4.5	17.7	1.0
	N	C:PRO34	4.6	17.3	1.0
	CA	A:ASN248	4.6	16.8	1.0
	CB	C:ASP32	4.7	16.5	1.0
	O	C:HOH2283	4.7	39.6	1.0
	CA	C:PRO34	4.7	17.1	1.0
	CA	C:ASP32	4.7	15.6	1.0
	O	C:PRO34	4.7	17.9	1.0
	CB	C:PRO33	4.8	15.3	1.0
	N	C:THR35	4.8	17.8	1.0
	O	C:ASN366	4.9	13.0	1.0
	N	A:ASN248	5.0	15.8	1.0

Reference:

E.D.Goddard-Borger, R.Carapito, J.Jeltsch, V.Phalip, R.V.Stick, A.Varrot. Alpha-L-Arabinofuranosylated Pyrrolidines As Arabinanase Inhibitors. Chem.Commun.(Camb.) V. 47 9684 2011.
ISSN: ISSN 1359-7345
PubMed: 21773614
DOI: 10.1039/C1CC13675E

Page generated: Fri Jul 12 19:28:11 2024

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