Copper in PDB 5ytm: C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

Enzymatic activity of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

All present enzymatic activity of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source:
1.7.2.1;

Protein crystallography data

The structure of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source, PDB code: 5ytm was solved by Y.Fukuda, T.Matsusaki, K.M.Tse, E.Mizohata, M.E.P.Murphy, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	17.51 / 1.50
*Space group*	H 3
*Cell size a, b, c (Å), α, β, γ (°)*	115.078, 115.078, 84.043, 90.00, 90.00, 120.00
*R / R_free (%)*	11.7 / 15.3

Copper Binding Sites:

The binding sites of Copper atom in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source (pdb code 5ytm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source, PDB code: 5ytm:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5ytm

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Copper Binding Sites List in 5ytm

Copper binding site 1 out of 4 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cu401 b:19.0 occ:0.30	ND1	A:HIS95	2.0	17.0	1.0
	SD	A:MET148	2.1	20.1	1.0
	ND1	A:HIS143	2.1	17.3	1.0
	CE1	A:HIS95	2.8	18.5	1.0
	CG	A:HIS95	3.0	16.1	1.0
	CG	A:HIS143	3.1	16.9	1.0
	CE1	A:HIS143	3.1	17.8	1.0
	CE	A:MET148	3.4	22.5	1.0
	CB	A:HIS143	3.4	15.0	1.0
	CB	A:ALA135	3.4	17.6	1.0
	CB	A:HIS95	3.5	16.7	1.0
	CG	A:MET148	3.5	16.7	1.0
	NE2	A:HIS95	3.9	17.3	1.0
	CE3	A:TRP63	4.0	15.2	1.0
	CD2	A:HIS95	4.0	17.7	1.0
	CB	A:MET148	4.1	15.1	1.0
	CA	A:HIS95	4.2	17.0	1.0
	NE2	A:HIS143	4.2	16.4	1.0
	CD2	A:HIS143	4.3	16.0	1.0
	CA	A:HIS143	4.3	14.5	1.0
	O	A:PRO94	4.5	17.9	1.0
	CZ3	A:TRP63	4.6	16.3	1.0
	CB	A:TRP63	4.9	14.8	1.0
	O	A:HIS143	4.9	15.2	1.0
	CA	A:ALA135	4.9	14.1	1.0
	C	A:HIS143	5.0	14.6	1.0
	CD2	A:TRP63	5.0	15.0	1.0

Copper binding site 2 out of 4 in 5ytm

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Copper Binding Sites List in 5ytm

Copper binding site 2 out of 4 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cu402 b:18.5 occ:1.00	NE2	A:HIS100	2.0	13.7	1.0
	NE2	A:HIS134	2.1	13.7	1.0
	O	A:HOH506	2.2	42.5	1.0
	O	A:HOH753	2.3	22.2	1.0
	CE1	A:HIS100	2.9	14.4	1.0
	CD2	A:HIS134	3.0	15.6	1.0
	CE1	A:HIS134	3.1	15.7	1.0
	CD2	A:HIS100	3.1	13.9	1.0
	OD2	A:ASP98	3.9	19.5	1.0
	ND1	A:HIS100	4.1	14.2	1.0
	ND1	A:HIS134	4.1	15.3	1.0
	CG	A:HIS134	4.2	13.8	1.0
	CG	A:HIS100	4.2	13.1	1.0
	CG	A:ASP98	4.4	17.2	1.0
	OD1	A:ASP98	4.6	18.7	1.0
	O	A:HOH805	4.7	30.2	1.0
	O	A:HOH657	4.7	20.5	1.0

Copper binding site 3 out of 4 in 5ytm

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Copper Binding Sites List in 5ytm

Copper binding site 3 out of 4 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cu403 b:22.0 occ:0.70	ND1	A:HIS83	2.0	21.6	1.0
	NE2	A:HIS42	2.1	19.8	1.0
	O	A:HOH749	2.4	26.0	1.0
	CE1	A:HIS83	2.8	22.0	1.0
	CD2	A:HIS42	3.0	18.4	1.0
	CE1	A:HIS42	3.0	19.7	1.0
	CG	A:HIS83	3.0	19.6	1.0
	CB	A:HIS83	3.5	17.3	1.0
	NE2	A:HIS83	4.0	19.9	1.0
	CD2	A:HIS83	4.1	21.4	1.0
	O	A:HOH673	4.1	41.6	1.0
	ND1	A:HIS42	4.1	18.4	1.0
	CG	A:HIS42	4.1	16.3	1.0
	O	A:HOH775	4.3	23.8	1.0
	O	A:HOH803	4.6	46.0	1.0
	CG2	A:VAL36	4.6	18.9	1.0
	O	A:HOH788	4.7	28.7	1.0

Copper binding site 4 out of 4 in 5ytm

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Copper Binding Sites List in 5ytm

Copper binding site 4 out of 4 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Determined By in-Ouse Source within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cu404 b:32.7 occ:0.40	OD2	A:ASP167	2.1	20.5	1.0
	O	A:HOH505	2.3	50.4	1.0
	O	A:HOH619	2.5	39.3	1.0
	CG	A:ASP167	2.8	22.4	1.0
	O	A:HOH705	2.9	37.4	0.5
	OD1	A:ASP167	2.9	25.1	1.0
	O	A:GLY225	4.1	21.7	1.0
	O	A:GLU165	4.2	22.7	1.0
	N	A:LYS227	4.2	17.5	1.0
	CB	A:ASP167	4.3	19.5	1.0
	CA	A:GLU226	4.4	17.9	1.0
	O	A:HOH760	4.6	58.0	1.0
	O	A:HOH705	4.7	34.3	0.5
	C	A:GLU226	4.7	18.5	1.0
	CB	A:LYS227	4.8	19.3	1.0
	C	A:GLY225	5.0	18.3	1.0

Reference:

Y.Fukuda, T.Matsusaki, K.M.Tse, E.Mizohata, M.E.P.Murphy, T.Inoue. Crystallographic Study of Dioxygen Chemistry in A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans. Acta Crystallogr D Struct V. 74 769 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30082512
DOI: 10.1107/S2059798318010082

Page generated: Wed Jul 31 05:26:13 2024

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