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Calcium in PDB 5xa8: Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals

Enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-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-ALF4-Adp-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-ALF4-Adp-2CA2+ Crystals, PDB code: 5xa8 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) 79.64 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.970, 75.020, 152.240, 90.00, 109.31, 90.00
R / Rfree (%) 21.3 / 24.1

Other elements in 5xa8:

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Magnesium (Mg) 2 atoms
Aluminium (Al) 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-ALF4-Adp-2CA2+ Crystals (pdb code 5xa8). 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-ALF4-Adp-2CA2+ Crystals, PDB code: 5xa8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5xa8

Go back to Calcium Binding Sites List in 5xa8
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-ALF4-Adp-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-ALF4-Adp-2CA2+ Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:73.9
occ:1.00
 OE2 A:GLU771 2.4 86.2 1.0
OD1 A:ASP800 2.4 75.8 1.0
OD1 A:ASN768 2.5 84.3 1.0
OE2 A:GLU908 2.5 85.9 1.0
O A:HOH1139 2.6 63.4 1.0
O A:HOH1112 2.6 78.9 1.0
OG1 A:THR799 2.7 80.9 1.0
CD A:GLU771 3.3 82.6 1.0
CG A:ASP800 3.4 71.1 1.0
CD A:GLU908 3.4 88.7 1.0
CB A:THR799 3.5 81.2 1.0
OE1 A:GLU908 3.6 90.4 1.0
OD2 A:ASP800 3.7 70.9 1.0
CG A:ASN768 3.7 95.2 1.0
OE1 A:GLU771 3.8 81.2 1.0
CB A:SER767 4.1 81.9 1.0
N A:ASN768 4.3 79.9 1.0
CG A:GLU771 4.4 85.3 1.0
CA A:ASN768 4.4 80.1 1.0
C A:SER767 4.5 98.5 1.0
CG2 A:THR799 4.5 84.4 1.0
ND2 A:ASN768 4.5 97.8 1.0
O A:ALA305 4.5 89.0 1.0
N A:ASP800 4.5 97.3 1.0
C A:THR799 4.5 76.1 1.0
CG1 A:VAL795 4.6 85.5 1.0
CB A:ASP800 4.7 69.5 1.0
O A:SER767 4.7 0.2 1.0
CA A:THR799 4.7 79.2 1.0
CB A:ASN768 4.7 0.4 1.0
O A:VAL795 4.7 92.1 1.0
CG A:GLU908 4.8 90.2 1.0
O A:THR799 4.9 74.9 1.0
CA A:SER767 5.0 96.7 1.0

Calcium binding site 2 out of 2 in 5xa8

Go back to Calcium Binding Sites List in 5xa8
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-ALF4-Adp-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-ALF4-Adp-2CA2+ Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:72.6
occ:1.00
 OD1 A:ASN796 2.4 87.2 1.0
O A:ILE307 2.5 0.8 1.0
OD2 A:ASP800 2.6 70.9 1.0
OE2 A:GLU309 2.6 86.1 1.0
O A:VAL304 2.6 76.2 1.0
O A:ALA305 2.8 89.0 1.0
OE1 A:GLU309 3.1 90.4 1.0
CD A:GLU309 3.1 93.9 1.0
C A:ALA305 3.1 96.8 1.0
C A:ILE307 3.4 0.5 1.0
CG A:ASP800 3.5 71.1 1.0
CG A:ASN796 3.6 93.0 1.0
C A:VAL304 3.7 80.5 1.0
CA A:ALA305 3.7 92.8 1.0
N A:ILE307 3.7 0.0 1.0
CB A:ASP800 3.7 69.5 1.0
ND2 A:ASN768 3.8 97.8 1.0
N A:ALA306 3.8 0.2 1.0
C A:ALA306 3.8 86.8 1.0
O A:ALA306 4.1 86.3 1.0
O A:HOH1139 4.1 63.4 1.0
CA A:ILE307 4.1 0.2 1.0
N A:ALA305 4.2 89.6 1.0
CA A:ALA306 4.2 0.1 1.0
ND2 A:ASN796 4.3 90.8 1.0
N A:PRO308 4.3 0.7 1.0
CG A:GLU309 4.5 86.2 1.0
CA A:PRO308 4.6 96.6 1.0
CB A:ASN796 4.7 83.1 1.0
OD1 A:ASP800 4.7 75.8 1.0
CG A:ASN768 4.8 95.2 1.0
N A:GLU309 4.8 91.8 1.0
CB A:ILE307 4.9 67.2 1.0
CA A:VAL304 5.0 80.0 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 11:37:40 2025

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