Sodium in PDB 5xa7: Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals

Enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals

All present enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals:
3.6.3.8;

Protein crystallography data

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals, PDB code: 5xa7 was solved by Y.Norimatsu, K.Hasegawa, N.Shimizu, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	82.27 / 3.20
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	166.200, 64.545, 146.220, 90.00, 98.12, 90.00
*R / R_free (%)*	22.5 / 24.4

Other elements in 5xa7:

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals (pdb code 5xa7). 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 Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals, PDB code: 5xa7:

Sodium binding site 1 out of 1 in 5xa7

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Sodium Binding Sites List in 5xa7

Sodium binding site 1 out of 1 in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-2CA2+ Crystals within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1003 b:32.2 occ:1.00	OE1	A:GLU732	2.5	39.4	1.0
	O	A:LEU711	2.6	28.4	1.0
	O	A:LYS712	2.6	30.7	1.0
	O	A:ALA714	2.7	25.8	1.0
	OE2	A:GLU732	2.7	48.8	1.0
	CD	A:GLU732	2.9	46.9	1.0
	C	A:LYS712	3.2	33.1	1.0
	O	A:HOH1184	3.3	45.6	1.0
	CA	A:LYS712	3.3	39.8	1.0
	C	A:LEU711	3.6	36.5	1.0
	C	A:ALA714	3.9	31.4	1.0
	N	A:LYS712	4.0	36.4	1.0
	N	A:GLY717	4.1	23.4	1.0
	O	A:ALA730	4.2	44.6	1.0
	O	A:GLU715	4.3	20.6	1.0
	N	A:LYS713	4.3	39.6	1.0
	CG	A:GLU732	4.3	35.1	1.0
	N	A:ALA714	4.4	29.8	1.0
	CA	A:GLY717	4.5	28.2	1.0
	C	A:GLU715	4.5	31.9	1.0
	C	A:LYS713	4.6	34.6	1.0
	CB	A:LYS712	4.6	69.4	1.0
	CA	A:ALA714	4.7	26.4	1.0
	N	A:GLU715	4.9	21.7	1.0
	C	A:ILE716	5.0	30.9	1.0
	CA	A:GLU715	5.0	28.4	1.0
	CA	A:LYS713	5.0	42.8	1.0

Reference:

Y.Norimatsu, K.Hasegawa, N.Shimizu, C.Toyoshima. Protein-Phospholipid Interplay Revealed with Crystals of A Calcium Pump. Nature V. 545 193 2017.
ISSN: ESSN 1476-4687
PubMed: 28467821
DOI: 10.1038/NATURE22357

Page generated: Tue Oct 8 01:10:28 2024

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