Sodium in PDB 6r78: Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)

Enzymatic activity of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)

All present enzymatic activity of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed):
3.5.2.6;

Protein crystallography data

The structure of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed), PDB code: 6r78 was solved by K.M.Zak, C.Softley, M.Kolonko, M.Sattler, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	59.25 / 2.21
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	60.790, 73.120, 64.210, 90.00, 112.67, 90.00
*R / R_free (%)*	17.9 / 21.6

Other elements in 6r78:

The structure of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) (pdb code 6r78). 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 Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed), PDB code: 6r78:

Sodium binding site 1 out of 1 in 6r78

Go back to

Sodium Binding Sites List in 6r78

Sodium binding site 1 out of 1 in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na409 b:66.7 occ:1.00	OG1	A:THR42	2.5	40.2	1.0
	OD1	A:ASP43	2.5	56.3	1.0
	OE2	A:GLU69	2.9	61.2	1.0
	O	A:THR42	3.1	47.1	1.0
	C	A:THR42	3.3	45.7	1.0
	CB	A:THR42	3.5	39.6	1.0
	N	A:ASP43	3.7	44.4	1.0
	O	B:HOH450	3.7	57.4	1.0
	CG	A:ASP43	3.7	51.1	1.0
	CD	A:GLU69	3.7	62.6	1.0
	CG	A:GLU69	3.8	55.8	1.0
	CA	A:THR42	3.9	42.4	1.0
	CB	A:GLU69	3.9	49.9	1.0
	CA	A:ASP43	4.1	44.7	1.0
	O	A:HOH538	4.2	47.1	1.0
	CE	A:LYS71	4.3	58.8	1.0
	NZ	A:LYS71	4.4	61.1	1.0
	CB	A:ASP43	4.5	50.2	1.0
	N	A:THR42	4.5	41.3	1.0
	N	A:GLU69	4.6	44.2	1.0
	OD2	A:ASP43	4.6	50.8	1.0
	CG2	A:THR42	4.8	44.1	1.0
	CA	A:GLU69	4.8	44.5	1.0
	OE1	A:GLU69	4.9	64.0	1.0
	O	A:GLU69	5.0	39.6	1.0

Reference:

C.Softley, K.M.Zak, R.Fino, M.Kolonko, R.Mejdi-Nitiu, H.Meyer, M.Sattler, G.M.Popowicz. Structure and Molecular Recognition Mechanism of Imp-13 B-Lactamase To Be Published.

Page generated: Mon Aug 18 06:52:44 2025

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