Calcium in PDB 2v5d: Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.

Enzymatic activity of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.

All present enzymatic activity of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.:
3.2.1.52;

Protein crystallography data

The structure of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens., PDB code: 2v5d was solved by E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, S.J.Smith, M.Czjzek, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	141.42 / 3.30
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.851, 69.546, 136.780, 90.00, 95.78, 90.00
*R / R_free (%)*	32.249 / 36.981

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens. (pdb code 2v5d). 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 A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens., PDB code: 2v5d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2v5d

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Calcium Binding Sites List in 2v5d

Calcium binding site 1 out of 3 in the Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca1768 b:49.2 occ:1.00	O	A:ALA597	2.5	42.2	1.0
	O	A:ALA602	2.5	37.6	1.0
	O	A:SER600	2.8	39.2	1.0
	OE1	A:GLU557	3.1	34.3	1.0
	C	A:ALA602	3.6	37.7	1.0
	C	A:ALA597	3.6	42.2	1.0
	CG2	A:VAL603	3.7	37.0	1.0
	C	A:SER600	4.0	39.3	1.0
	CA	A:VAL603	4.0	37.1	1.0
	CD	A:GLU557	4.1	34.4	1.0
	CA	A:LEU598	4.2	41.6	1.0
	N	A:VAL603	4.2	37.4	1.0
	CB	A:VAL603	4.3	37.1	1.0
	N	A:LEU598	4.4	41.9	1.0
	C	A:LEU598	4.4	41.4	1.0
	O	A:LEU598	4.4	41.4	1.0
	O	A:PHE601	4.4	38.5	1.0
	C	A:PHE601	4.5	38.5	1.0
	OE2	A:GLU557	4.6	34.4	1.0
	N	A:ALA602	4.7	38.3	1.0
	N	A:SER600	4.7	40.0	1.0
	CA	A:ALA597	4.7	42.5	1.0
	CA	A:SER600	4.7	39.6	0.2
	CG1	A:VAL603	4.8	37.1	1.0
	CA	A:ALA602	4.8	38.0	1.0
	OE1	A:GLN610	4.8	36.1	1.0
	CB	A:SER600	4.9	39.6	0.2
	N	A:PHE601	4.9	39.0	1.0
	CG	A:GLU557	5.0	34.5	1.0

Calcium binding site 2 out of 3 in 2v5d

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Calcium Binding Sites List in 2v5d

Calcium binding site 2 out of 3 in the Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca1769 b:0.0 occ:1.00	OE2	A:GLU108	2.6	75.5	1.0
	O	A:GLU73	3.0	73.9	1.0
	OD1	A:ASP111	3.0	76.0	1.0
	OD2	A:ASP111	3.4	75.9	1.0
	CG	A:ASP111	3.6	76.0	1.0
	CD	A:GLU108	3.7	75.6	1.0
	OD1	A:ASP110	4.0	76.0	1.0
	C	A:GLU73	4.2	73.9	1.0
	CG	A:GLU108	4.3	75.6	1.0
	CB	A:GLU108	4.4	75.6	1.0
	CB	A:ASP110	4.7	76.0	1.0
	C	A:ALA74	4.8	73.8	1.0
	OE1	A:GLU108	4.8	75.5	1.0
	CG	A:ASP110	4.8	76.0	1.0
	CA	A:ALA74	4.8	73.8	1.0
	O	A:ALA74	4.9	73.8	1.0
	N	A:ALA74	5.0	73.9	1.0

Calcium binding site 3 out of 3 in 2v5d

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Calcium Binding Sites List in 2v5d

Calcium binding site 3 out of 3 in the Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Family 84 Glycoside Hydrolase and A Family 32 Carbohydrate-Binding Module in Tandem From Clostridium Perfringens. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca1770 b:34.4 occ:1.00	O	A:PHE647	2.2	40.7	1.0
	O	A:ALA761	2.4	34.6	1.0
	O	A:ASP652	2.6	40.5	1.0
	OG1	A:THR655	2.6	39.4	1.0
	OE1	A:GLU762	2.7	34.8	1.0
	O	A:THR655	2.8	39.1	1.0
	C	A:PHE647	3.4	40.7	1.0
	C	A:THR655	3.5	39.1	1.0
	C	A:ALA761	3.6	34.6	1.0
	CD	A:GLU762	3.6	34.9	1.0
	CG	A:GLU762	3.8	34.9	1.0
	CB	A:ASP650	3.8	41.0	1.0
	C	A:ASP652	3.8	40.5	1.0
	CB	A:THR655	3.8	39.3	1.0
	CA	A:THR655	4.1	39.3	1.0
	CA	A:PHE647	4.2	40.8	1.0
	CB	A:PHE647	4.3	40.8	1.0
	N	A:ASP650	4.3	40.9	1.0
	N	A:PHE656	4.4	39.0	1.0
	N	A:THR655	4.4	39.5	1.0
	N	A:ALA648	4.4	40.7	1.0
	N	A:ASP652	4.5	40.7	1.0
	N	A:GLU762	4.5	34.7	1.0
	O	A:ALA648	4.5	40.7	1.0
	CA	A:GLU762	4.5	34.7	1.0
	CA	A:ALA761	4.5	34.5	1.0
	C	A:ALA648	4.5	40.8	1.0
	CA	A:ASP652	4.6	40.6	1.0
	CA	A:ASP650	4.6	41.0	1.0
	N	A:GLY651	4.6	40.8	1.0
	CA	A:ALA648	4.6	40.7	1.0
	CA	A:PHE656	4.7	38.8	1.0
	CB	A:GLU762	4.7	34.8	1.0
	OD1	A:ASP650	4.7	41.5	1.0
	N	A:MET653	4.8	40.4	1.0
	OE2	A:GLU762	4.8	34.9	1.0
	CB	A:ASP652	4.8	40.6	1.0
	CG	A:ASP650	4.8	41.2	1.0
	CA	A:MET653	4.9	40.4	1.0
	C	A:MET653	4.9	40.2	1.0
	O	A:MET653	5.0	40.2	1.0

Reference:

E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, S.J.Smith, M.Czjzek, A.B.Boraston. Portrait of An Enzyme: A Complete Structural Analysis of A Multi-Modular Beta-N- Acetylglucosaminidase From Clostridium Perfringens J.Biol.Chem. V. 284 9876 2009.
ISSN: ISSN 0021-9258
PubMed: 19193644
DOI: 10.1074/JBC.M808954200

Page generated: Tue Jul 8 08:30:34 2025

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