Sodium in PDB 1kr3: Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

Enzymatic activity of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

All present enzymatic activity of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050., PDB code: 1kr3 was solved by D.J.Payne, J.A.Hueso-Rodrguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Cheever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Dez, P.Prez, J.De La Fuente, M.Rees, A.Rivera-Sagredo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.07 / 2.50
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	41.800, 44.200, 58.500, 92.80, 95.30, 98.00
*R / R_free (%)*	n/a / n/a

Other elements in 1kr3:

The structure of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. (pdb code 1kr3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050., PDB code: 1kr3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1kr3

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Sodium Binding Sites List in 1kr3

Sodium binding site 1 out of 2 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na501 b:3.1 occ:1.00	O	A:HOH616	2.9	13.4	1.0
	O	A:ASP103	3.1	23.9	1.0
	OH	A:TYR40	3.1	15.8	1.0
	O	A:THR70	3.1	25.2	1.0
	O	A:ASN55	3.1	19.7	1.0
	C	A:THR70	3.6	21.4	1.0
	CB	A:ASP69	3.6	16.9	1.0
	C	A:ASN55	3.7	21.8	1.0
	CB	A:SER54	3.9	29.6	1.0
	CZ	A:TYR40	3.9	11.4	1.0
	N	A:THR70	4.0	19.2	1.0
	CE1	A:TYR40	4.0	12.1	1.0
	C	A:ASP103	4.0	26.5	1.0
	OD2	A:ASP69	4.1	16.1	1.0
	N	A:PRO71	4.1	22.3	1.0
	C	A:SER54	4.1	25.5	1.0
	O	A:SER54	4.2	22.9	1.0
	CA	A:PRO71	4.2	25.5	1.0
	N	A:ASN55	4.2	25.6	1.0
	C	A:ASP69	4.3	20.4	1.0
	CG	A:ASP69	4.3	15.2	1.0
	N	A:GLY56	4.3	21.0	1.0
	CA	A:THR70	4.3	21.0	1.0
	CA	A:ASN55	4.4	23.6	1.0
	OG	A:SER42	4.5	36.7	1.0
	CA	A:GLY56	4.5	20.7	1.0
	CA	A:ASP69	4.6	17.0	1.0
	CA	A:SER54	4.7	28.2	1.0
	CA	A:ASP103	4.7	29.1	1.0
	O	A:ASP69	4.8	18.5	1.0
	CB	A:ASP103	4.8	29.4	1.0
	OG	A:SER54	4.9	32.2	1.0
	N	A:CYS104	5.0	24.4	1.0
	C	A:PRO71	5.0	26.6	1.0

Sodium binding site 2 out of 2 in 1kr3

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Sodium Binding Sites List in 1kr3

Sodium binding site 2 out of 2 in the Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Metallo Beta-Lactamase From Bacteroides Fragilis (Cfia) in Complex with the Tricyclic Inhibitor Sb-236050. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na502 b:3.1 occ:1.00	O	B:ASP103	2.3	19.1	1.0
	O	B:ASN55	2.7	18.4	1.0
	O	B:THR70	3.3	19.9	1.0
	C	B:ASN55	3.5	19.4	1.0
	C	B:ASP103	3.5	15.7	1.0
	O	B:HOH617	3.6	14.4	1.0
	CB	B:SER54	3.6	23.4	1.0
	CB	B:ASP69	3.8	6.1	1.0
	OD2	B:ASP69	3.8	11.1	1.0
	N	B:ASN55	3.8	24.7	1.0
	C	B:SER54	4.0	25.9	1.0
	CA	B:ASN55	4.2	19.2	1.0
	CG	B:ASP69	4.2	4.5	1.0
	OH	B:TYR40	4.2	7.8	1.0
	N	B:GLY56	4.3	19.9	1.0
	CA	B:ASP103	4.3	16.6	1.0
	CB	B:ASP103	4.3	13.3	1.0
	OG	B:SER54	4.3	26.6	1.0
	O	B:SER54	4.4	25.9	1.0
	C	B:THR70	4.4	13.8	1.0
	CA	B:SER54	4.4	25.8	1.0
	N	B:CYS104	4.5	18.8	1.0
	CA	B:GLY56	4.5	19.9	1.0
	N	B:THR70	4.6	17.1	1.0
	CA	B:CYS104	4.7	16.9	1.0
	C	B:ASP69	4.8	13.5	1.0
	OD2	B:ASP103	4.9	14.7	1.0
	CZ	B:TYR40	4.9	6.9	1.0
	CA	B:ASP69	4.9	10.8	1.0
	CE1	B:TYR40	4.9	3.3	1.0

Reference:

D.J.Payne, J.A.Hueso-Rodrguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Cheever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Dez, P.Prez, J.De La Fuente, M.Rees, A.Rivera-Sagredo. Identification of A Series of Tricyclic Natural Products As Potent Broad-Spectrum Inhibitors of Metallo-Beta-Lactamases Antimicrob.Agents Chemother. V. 46 1880 2002.
ISSN: ISSN 0066-4804
PubMed: 12019104
DOI: 10.1128/AAC.46.6.1880-1886.2002

Page generated: Sun Oct 6 19:39:32 2024

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