Copper in PDB 1qle: Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

All present enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment:
1.9.3.1;

Protein crystallography data

The structure of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle was solved by A.Harrenga, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	6.00 / 3.00
*Space group*	P 4
*Cell size a, b, c (Å), α, β, γ (°)*	205.200, 205.200, 81.100, 90.00, 90.00, 90.00
*R / R_free (%)*	23.5 / 30.9

Other elements in 1qle:

Manganese	(Mn)	1 atom
Iron	(Fe)	2 atoms
Calcium	(Ca)	1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment (pdb code 1qle). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1qle

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Copper Binding Sites List in 1qle

Copper binding site 1 out of 3 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cu603 b:11.8 occ:1.00	NE2	A:HIS326	2.1	20.7	1.0
	ND1	A:HIS276	2.1	12.1	1.0
	NE2	A:HIS325	2.2	27.5	1.0
	CE1	A:HIS326	2.9	26.3	1.0
	CE1	A:HIS325	3.1	31.3	1.0
	CG	A:HIS276	3.1	10.6	1.0
	CE1	A:HIS276	3.2	12.0	1.0
	CD2	A:HIS326	3.2	20.3	1.0
	CD2	A:HIS325	3.3	30.7	1.0
	CB	A:HIS276	3.4	9.6	1.0
	CA	A:HIS276	3.9	17.5	1.0
	ND1	A:HIS326	4.1	27.5	1.0
	CG	A:HIS326	4.2	24.0	1.0
	CD2	A:HIS276	4.3	14.4	1.0
	ND1	A:HIS325	4.3	32.7	1.0
	NE2	A:HIS276	4.3	12.3	1.0
	CG	A:HIS325	4.4	29.9	1.0
	NA	A:HEA602	4.5	19.1	1.0
	C1A	A:HEA602	4.5	23.1	1.0
	N	A:HIS276	4.7	16.1	1.0
	C4A	A:HEA602	4.7	15.6	1.0
	CHA	A:HEA602	4.8	25.3	1.0
	ND	A:HEA602	4.9	20.6	1.0
	C2A	A:HEA602	4.9	19.3	1.0
	C	A:HIS276	5.0	22.9	1.0
	CG1	A:VAL279	5.0	8.3	1.0

Copper binding site 2 out of 3 in 1qle

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Copper Binding Sites List in 1qle

Copper binding site 2 out of 3 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cu301 b:32.5 occ:1.00	CU1	B:CUA301	0.0	32.5	1.0
	ND1	B:HIS224	2.0	18.5	1.0
	SG	B:CYS220	2.1	35.3	1.0
	SG	B:CYS216	2.1	25.7	1.0
	CU2	B:CUA301	2.5	26.7	1.0
	CE1	B:HIS224	3.0	18.5	1.0
	CG	B:HIS224	3.1	25.5	1.0
	O	B:GLU218	3.1	36.8	1.0
	CB	B:CYS220	3.3	39.0	1.0
	CB	B:CYS216	3.3	19.3	1.0
	CB	B:HIS224	3.5	35.7	1.0
	CA	B:HIS224	3.6	40.0	1.0
	N	B:CYS220	3.6	35.4	1.0
	O	B:HIS224	3.9	39.9	1.0
	CA	B:CYS220	4.1	34.2	1.0
	C	B:GLU218	4.1	34.8	1.0
	NE2	B:HIS224	4.2	22.3	1.0
	C	B:HIS224	4.2	40.0	1.0
	CD2	B:HIS224	4.2	21.3	1.0
	SD	B:MET227	4.3	44.6	1.0
	C	B:LEU219	4.4	35.5	1.0
	ND1	B:HIS181	4.4	30.8	1.0
	CA	B:CYS216	4.6	21.9	1.0
	CA	B:LEU219	4.6	33.1	1.0
	CG	B:MET227	4.6	41.3	1.0
	C	B:CYS216	4.7	21.4	1.0
	N	B:LEU219	4.7	31.7	1.0
	N	B:GLU218	4.7	29.9	1.0
	O	B:CYS216	4.8	28.6	1.0
	N	B:HIS224	4.8	43.2	1.0
	C	B:CYS220	4.9	36.0	1.0

Copper binding site 3 out of 3 in 1qle

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Copper Binding Sites List in 1qle

Copper binding site 3 out of 3 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Mono view

Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cu301 b:26.7 occ:1.00	CU2	B:CUA301	0.0	26.7	1.0
	ND1	B:HIS181	2.1	30.8	1.0
	SG	B:CYS220	2.1	35.3	1.0
	SG	B:CYS216	2.2	25.7	1.0
	CU1	B:CUA301	2.5	32.5	1.0
	SD	B:MET227	2.6	44.6	1.0
	CE1	B:HIS181	3.0	32.7	1.0
	CG	B:HIS181	3.2	32.7	1.0
	CB	B:CYS220	3.3	39.0	1.0
	CE	B:MET227	3.5	46.6	1.0
	CB	B:HIS181	3.6	26.9	1.0
	CG	B:MET227	3.8	41.3	1.0
	CB	B:CYS216	3.8	19.3	1.0
	CA	B:HIS181	4.2	29.9	1.0
	NE2	B:HIS181	4.2	29.0	1.0
	CD2	B:HIS181	4.3	31.4	1.0
	ND1	B:HIS224	4.5	18.5	1.0
	O	B:GLU218	4.5	36.8	1.0
	CA	B:CYS220	4.7	34.2	1.0
	O	B:HIS119	4.7	46.7	1.0

Reference:

A.Harrenga, H.Michel. The Cytochrome C Oxidase From Paracoccus Denitrificans Does Not Change the Metal Center Ligation Upon Reduction J.Biol.Chem. V. 274 33296 1999.
ISSN: ISSN 0021-9258
PubMed: 10559205
DOI: 10.1074/JBC.274.47.33296

Page generated: Tue Jul 30 22:37:16 2024

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