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

Go back to

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

Go back to

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

Go back to

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

Go back to

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy