Sodium in PDB 1kcc: Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution.

Enzymatic activity of Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution.

All present enzymatic activity of Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution.:
3.2.1.15;

Protein crystallography data

The structure of Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution., PDB code: 1kcc was solved by T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, H.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.00
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.515, 52.138, 37.187, 72.31, 69.09, 70.35
*R / R_free (%)*	11.4 / 14

Other elements in 1kcc:

The structure of Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution. (pdb code 1kcc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution., PDB code: 1kcc:

Sodium binding site 1 out of 1 in 1kcc

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Sodium Binding Sites List in 1kcc

Sodium binding site 1 out of 1 in the Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endopolygalacturonase I From Stereum Purpureum Complexed with A Galacturonate at 1.00 A Resolution. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na2004 b:10.9 occ:1.00	OG	A:SER158	3.0	8.9	1.0
	O	A:HOH2059	3.2	11.7	1.0
	OD1	A:ASN179	3.2	16.9	1.0
	O	A:HOH2451	3.3	39.4	1.0
	O	A:HOH2151	3.3	19.5	1.0
	CB	A:ASP156	3.7	6.2	1.0
	C	A:ASP156	3.7	5.5	1.0
	N	A:VAL157	3.8	5.8	1.0
	C	A:VAL157	3.8	5.8	1.0
	CB	A:SER158	3.8	8.2	1.0
	N	A:SER158	3.8	6.3	1.0
	O	A:ASP156	3.9	6.9	1.0
	CG	A:ASN179	4.1	12.2	1.0
	CB	A:ASN179	4.1	8.4	1.0
	O	A:VAL157	4.1	6.7	1.0
	CA	A:ASP156	4.2	5.6	1.0
	CA	A:VAL157	4.3	5.6	1.0
	CA	A:SER158	4.4	7.0	1.0
	O	A:HOH2464	4.6	24.2	0.5
	O	A:HOH2262	4.7	26.1	0.5
	O	A:HOH2071	4.7	14.1	1.0
	CG	A:ASP156	4.8	6.4	1.0
	OG	A:SER123	4.9	8.7	1.0
	O	A:HOH2322	5.0	29.9	1.0

Reference:

T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, H.Kato. Active-Site Architecture of Endopolygalacturonase I From Stereum Purpureum Revealed By Crystal Structures in Native and Ligand-Bound Forms at Atomic Resolution. Biochemistry V. 41 6651 2002.
ISSN: ISSN 0006-2960
PubMed: 12022868
DOI: 10.1021/BI025541A

Page generated: Sun Oct 6 19:35:24 2024

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