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Calcium 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 / Rfree (%) 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:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where 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:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5xa7

Go back to Calcium Binding Sites List in 5xa7
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca1001

b:37.9
occ:1.00
 OE2 A:GLU309 2.3 45.5 1.0
O A:VAL304 2.4 45.7 1.0
OD1 A:ASN796 2.5 56.9 1.0
O A:ILE307 2.5 41.7 1.0
OD2 A:ASP800 2.6 48.7 1.0
O A:ALA305 2.6 38.4 1.0
C A:ALA305 2.9 45.3 1.0
CD A:GLU309 3.1 44.8 1.0
OE1 A:GLU309 3.2 49.5 1.0
CA A:ALA305 3.4 42.5 1.0
C A:VAL304 3.5 45.6 1.0
C A:ILE307 3.5 40.1 1.0
CG A:ASN796 3.6 57.4 1.0
CG A:ASP800 3.7 47.1 1.0
N A:ILE307 3.7 47.7 1.0
N A:ALA306 3.8 48.6 1.0
ND2 A:ASN768 3.8 39.3 1.0
O A:HOH1106 3.8 43.2 1.0
N A:ALA305 3.9 40.1 1.0
C A:ALA306 4.0 48.4 1.0
CA A:ILE307 4.1 40.8 1.0
CB A:ASP800 4.2 46.1 1.0
CB A:ASN796 4.3 54.8 1.0
CA A:ALA306 4.3 53.5 1.0
O A:ALA306 4.5 44.6 1.0
N A:PRO308 4.6 38.6 1.0
CG A:GLU309 4.6 59.2 1.0
CB A:ILE307 4.6 33.3 1.0
OD1 A:ASP800 4.7 42.5 1.0
ND2 A:ASN796 4.7 48.0 1.0
CB A:ALA305 4.7 39.5 1.0
OE2 A:GLU58 4.8 60.0 1.0
CA A:ASN796 4.8 43.1 1.0
CA A:VAL304 4.8 52.1 1.0
N A:GLU309 4.9 32.3 1.0
CA A:PRO308 4.9 38.1 1.0
CG A:ASN768 4.9 47.1 1.0
O A:ALA303 5.0 36.0 1.0

Calcium binding site 2 out of 2 in 5xa7

Go back to Calcium Binding Sites List in 5xa7
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca1002

b:39.3
occ:1.00
 OD1 A:ASP800 2.4 42.5 1.0
OE2 A:GLU771 2.4 53.4 1.0
OD1 A:ASN768 2.5 55.9 1.0
OG1 A:THR799 2.5 43.9 1.0
OE1 A:GLU908 2.5 48.9 1.0
O A:HOH1116 2.6 36.3 1.0
O A:HOH1106 2.8 43.2 1.0
CG A:ASP800 3.4 47.1 1.0
CD A:GLU771 3.4 46.3 1.0
CB A:THR799 3.5 44.3 1.0
CD A:GLU908 3.5 52.4 1.0
CG A:ASN768 3.5 47.1 1.0
OD2 A:ASP800 3.8 48.7 1.0
OE2 A:GLU908 3.8 52.8 1.0
OE1 A:GLU771 3.9 43.9 1.0
ND2 A:ASN768 4.1 39.3 1.0
CB A:SER767 4.2 39.6 1.0
C A:THR799 4.4 46.0 1.0
CG2 A:THR799 4.4 46.0 1.0
N A:ASP800 4.4 50.3 1.0
N A:ASN768 4.5 49.2 1.0
CG1 A:VAL795 4.5 42.9 1.0
O A:ALA305 4.5 38.4 1.0
CG A:GLU771 4.5 44.4 1.0
CA A:THR799 4.6 50.0 1.0
O A:VAL795 4.6 51.3 1.0
C A:SER767 4.6 59.7 1.0
CA A:ASN768 4.6 57.1 1.0
CB A:ASP800 4.7 46.1 1.0
CB A:ASN768 4.7 45.5 1.0
O A:THR799 4.7 43.4 1.0
CG A:GLU908 4.9 50.6 1.0
CA A:ASP800 4.9 50.6 1.0
O A:SER767 4.9 70.0 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: Wed Jul 9 11:37:10 2025

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