Ytterbium 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:

Yttrium	(Y)	2 atoms
Erbium	(Er)	4 atoms
Terbium	(Tb)	1 atom
Chlorine	(Cl)	1 atom
Copper	(Cu)	2 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium 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 Ytterbium atom.
In total 3 binding sites of Ytterbium 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 Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 6the

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Ytterbium Binding Sites List in 6the

Ytterbium binding site 1 out of 3 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 Ytterbium with other atoms in the Yb 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:Yb503 b:33.4 occ:1.00	OE1	A:GLU104	4.2	24.9	1.0
	OE2	A:GLU104	4.6	24.9	1.0
	CD1	A:ILE83	4.6	26.8	1.0
	CD	A:GLU104	4.8	24.8	1.0
	CG1	A:ILE83	4.9	26.8	1.0

Ytterbium binding site 2 out of 3 in 6the

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Ytterbium Binding Sites List in 6the

Ytterbium binding site 2 out of 3 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 Ytterbium with other atoms in the Yb 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:Yb504 b:24.3 occ:0.20	N	A:THR275	3.8	24.7	1.0
	OG1	A:THR275	3.9	24.3	1.0
	CB	A:THR275	4.1	24.4	1.0
	CA	A:GLY274	4.3	25.2	1.0
	C	A:GLY274	4.5	24.9	1.0
	CA	A:THR275	4.6	24.4	1.0

Ytterbium binding site 3 out of 3 in 6the

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Ytterbium Binding Sites List in 6the

Ytterbium binding site 3 out of 3 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 Ytterbium with other atoms in the Yb 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:Yb505 b:32.9 occ:0.20	O	A:HOH650	2.8	18.7	1.0
	N	A:ARG63	3.5	21.6	1.0
	O01	A:9JE517	3.8	42.3	1.0
	O	A:ARG63	3.8	22.1	1.0
	CA	A:LEU62	3.9	21.1	1.0
	CD2	A:LEU62	4.1	21.1	1.0
	CB	A:LEU62	4.1	21.1	1.0
	C	A:LEU62	4.2	21.3	1.0
	C	A:ARG63	4.4	22.1	1.0
	CA	A:ARG63	4.4	21.9	1.0
	C03	A:9JE517	4.4	42.1	1.0
	CG2	A:VAL31	4.7	25.3	1.0
	C02	A:9JE517	4.7	42.2	1.0
	CG1	A:VAL29	4.7	25.5	1.0
	CG	A:LEU62	4.8	21.1	1.0
	CB	A:ARG63	4.9	21.9	1.0
	O	A:LEU61	4.9	20.8	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: Sat Oct 12 21:23:25 2024

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