Sodium in PDB 6l46: High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

Enzymatic activity of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

All present enzymatic activity of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans:
1.7.2.1;

Protein crystallography data

The structure of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 6l46 was solved by Y.Fukuda, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	N/A / 1.30
*Space group*	H 3
*Cell size a, b, c (Å), α, β, γ (°)*	114.212, 114.212, 83.688, 90.00, 90.00, 120.00
*R / R_free (%)*	14.2 / 15.9

Other elements in 6l46:

The structure of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Copper	(Cu)	4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 6l46). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 6l46:

Sodium binding site 1 out of 1 in 6l46

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Sodium Binding Sites List in 6l46

Sodium binding site 1 out of 1 in the High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na405 b:6.0 occ:0.16	D1	A:DOD781	1.6	15.5	0.7
	O	A:DOD807	1.8	27.9	0.9
	D1	A:DOD520	1.9	19.6	1.0
	O	A:DOD781	2.0	19.9	0.7
	D2	A:DOD807	2.0	23.7	0.9
	OD2	A:ASP98	2.1	12.3	1.0
	D2	A:DOD526	2.1	25.5	0.7
	O	A:DOD520	2.1	15.1	1.0
	CL	A:CL406	2.3	7.3	0.3
	D1	A:DOD807	2.4	33.0	0.9
	O	A:DOD526	2.5	25.5	0.7
	HE1	A:HIS134	2.6	8.7	1.0
	D2	A:DOD781	2.7	24.6	0.7
	CU	A:CU402	3.1	8.6	1.0
	CE1	A:HIS134	3.2	8.0	1.0
	D1	A:DOD526	3.2	26.5	0.7
	CG	A:ASP98	3.3	9.7	1.0
	NE2	A:HIS134	3.4	8.3	1.0
	O	A:DOD871	3.8	34.1	0.7
	D2	A:DOD871	3.9	35.5	0.7
	CU	A:CU404	4.0	6.3	0.1
	D2	A:DOD871	4.0	34.9	0.3
	OD1	A:ASP98	4.0	10.4	1.0
	HB2	A:ASP98	4.1	12.3	1.0
	D1	A:DOD871	4.1	31.2	0.7
	D1	A:DOD640	4.2	14.7	0.9
	CB	A:ASP98	4.2	9.4	1.0
	HB3	A:ASP98	4.2	11.5	1.0
	O	A:DOD871	4.2	34.7	0.3
	D2	A:DOD958	4.3	38.4	1.0
	D1	A:DOD871	4.3	36.4	0.3
	ND1	A:HIS134	4.4	7.9	1.0
	O	A:DOD640	4.4	11.0	0.9
	HG12	A:VAL140	4.5	9.6	1.0
	HD2	A:HIS100	4.6	8.5	1.0
	NE2	A:HIS100	4.6	7.6	1.0
	CD2	A:HIS134	4.7	7.8	1.0
	HD2	A:PHE110	4.8	9.0	1.0
	O	A:DOD891	4.8	28.5	0.7
	HD1	A:HIS134	4.8	9.0	0.7
	DD1	A:HIS134	4.9	2.7	0.3
	HA2	A:GLY136	4.9	13.1	1.0
	D2	A:DOD891	5.0	27.1	0.7
	HE2	A:PHE110	5.0	12.4	1.0
	CD2	A:HIS100	5.0	7.3	1.0

Reference:

Y.Fukuda, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada. High-Resolution Neutron Crystallography Visualizes An Oh-Bound Resting State of A Copper-Containing Nitrite Reductase Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1918125117

Page generated: Tue Oct 8 11:35:36 2024

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