Erbium in PDB 6the: Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

All present enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the was solved by D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	39.57 / 2.87
*Space group*	I 2 3
*Cell size a, b, c (Å), α, β, γ (°)*	125.141, 125.141, 125.141, 90.00, 90.00, 90.00
*R / R_free (%)*	22.5 / 23.4

Other elements in 6the:

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 also contains other interesting chemical elements:

Ytterbium	(Yb)	3 atoms
Yttrium	(Y)	2 atoms
Terbium	(Tb)	1 atom
Chlorine	(Cl)	1 atom
Copper	(Cu)	2 atoms

Erbium Binding Sites:

The binding sites of Erbium atom in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (pdb code 6the). This binding sites where shown within 5.0 Angstroms radius around Erbium atom.
In total 4 binding sites of Erbium where determined in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the:
Jump to Erbium binding site number: 1; 2; 3; 4;

Erbium binding site 1 out of 4 in 6the

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Erbium Binding Sites List in 6the

Erbium binding site 1 out of 4 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Mono view

Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 1 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Er506 b:21.4 occ:0.20	N	A:ARG30	3.6	25.5	1.0
	O	A:ARG30	3.8	25.4	1.0
	CG1	A:VAL29	4.1	25.5	1.0
	CA	A:VAL29	4.3	25.6	1.0
	CA	A:ARG30	4.3	25.5	1.0
	CB	A:ARG30	4.4	25.5	1.0
	O01	A:9JE515	4.4	35.1	1.0
	O	A:HOH650	4.4	18.7	1.0
	C	A:VAL29	4.4	25.6	1.0
	C	A:ARG30	4.5	25.4	1.0
	CB	A:VAL29	4.8	25.5	1.0
	O	A:HOH635	4.8	10.8	1.0
	O	A:THR28	5.0	25.6	1.0

Erbium binding site 2 out of 4 in 6the

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Erbium Binding Sites List in 6the

Erbium binding site 2 out of 4 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Mono view

Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 2 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Er507 b:34.0 occ:0.20	TB	A:TB510	2.9	38.6	0.6
A:Er507 b:34.0 occ:0.20	Y	A:YT3511	3.8	39.1	0.5

Erbium binding site 3 out of 4 in 6the

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Erbium Binding Sites List in 6the

Erbium binding site 3 out of 4 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Mono view

Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 3 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Er508 b:26.1 occ:0.20	O	A:GLY49	3.4	20.3	1.0
	N	A:PHE178	3.7	26.8	1.0
	CB	A:PHE178	4.0	26.4	1.0
	CA	A:GLY49	4.1	20.4	1.0
	C	A:GLY49	4.2	20.2	1.0
	CA	A:GLU177	4.3	27.2	1.0
	ND2	A:ASN136	4.4	18.7	1.0
	C	A:GLU177	4.5	27.1	1.0
	CA	A:PHE178	4.5	26.5	1.0
	NE1	A:TRP51	4.5	19.1	1.0
	CB	A:GLU177	4.5	27.5	1.0
	N	A:GLY49	4.7	20.6	1.0
	CG	A:ASN136	4.7	18.6	1.0
	OD1	A:ASN136	4.8	18.6	1.0
	CZ2	A:TRP51	4.8	19.1	1.0
	CE2	A:TRP51	4.9	19.1	1.0
	CZ	A:PHE48	4.9	20.6	1.0

Erbium binding site 4 out of 4 in 6the

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Erbium Binding Sites List in 6the

Erbium binding site 4 out of 4 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Mono view

Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 4 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Er509 b:58.4 occ:0.25	OD1	A:ASP303	4.3	44.9	1.0
A:Er509 b:58.4 occ:0.25	OD2	A:ASP303	4.9	44.9	1.0

Reference:

D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain. Reverse Protein Engineering of A Novel 4-Domain Copper Nitrite Reductase Reveals Functional Regulation By Protein-Protein Interaction. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32255260
DOI: 10.1111/FEBS.15324

Page generated: Wed Jul 31 10:38:35 2024

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