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Fluorine 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:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5xa8

Go back to Fluorine Binding Sites List in 5xa8
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F1004

b:38.2
occ:1.00
 F1 A:ALF1004 0.0 38.2 1.0
AL A:ALF1004 1.8 31.8 1.0
O1B A:ADP1006 2.4 49.0 1.0
N A:THR353 2.5 38.8 1.0
F3 A:ALF1004 2.5 34.5 1.0
F4 A:ALF1004 2.5 27.9 1.0
OD1 A:ASP351 2.7 35.6 1.0
OD2 A:ASP351 2.8 18.4 1.0
CG A:ASP351 2.9 30.0 1.0
OG1 A:THR625 3.0 31.2 1.0
N A:LYS352 3.0 41.9 1.0
CB A:THR353 3.3 39.9 1.0
CA A:THR353 3.4 46.6 1.0
C A:LYS352 3.4 29.2 1.0
CA A:LYS352 3.5 34.5 1.0
F2 A:ALF1004 3.6 51.2 1.0
CB A:LYS352 3.6 38.6 1.0
OG1 A:THR353 3.6 36.3 1.0
O A:THR353 3.7 32.3 1.0
PB A:ADP1006 3.8 37.1 1.0
CB A:THR625 3.9 33.0 1.0
C A:THR353 4.0 28.0 1.0
C A:ASP351 4.1 57.8 1.0
CB A:ASP351 4.2 17.4 1.0
O3A A:ADP1006 4.2 35.3 1.0
CA A:THR625 4.3 42.7 1.0
MG A:MG1005 4.3 28.2 1.0
CA A:ASP351 4.4 52.7 1.0
O A:LYS352 4.5 30.1 1.0
O A:HOH1122 4.6 26.7 1.0
O3B A:ADP1006 4.6 27.2 1.0
MG A:MG1003 4.6 22.0 1.0
CE A:LYS352 4.7 61.1 1.0
CG A:LYS352 4.7 47.8 1.0
N A:GLY626 4.7 29.8 1.0
CG2 A:THR353 4.7 32.0 1.0
O2B A:ADP1006 4.8 39.1 1.0
O A:ILE624 4.9 33.5 1.0
NZ A:LYS684 4.9 25.1 1.0
NZ A:LYS352 4.9 54.2 1.0

Fluorine binding site 2 out of 4 in 5xa8

Go back to Fluorine Binding Sites List in 5xa8
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F 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:F1004

b:51.2
occ:1.00
 F2 A:ALF1004 0.0 51.2 1.0
AL A:ALF1004 1.8 31.8 1.0
ND2 A:ASN706 2.4 48.9 1.0
F4 A:ALF1004 2.5 27.9 1.0
F3 A:ALF1004 2.5 34.5 1.0
O3A A:ADP1006 2.8 35.3 1.0
O A:HOH1122 2.8 26.7 1.0
MG A:MG1003 2.9 22.0 1.0
O A:HOH1141 3.0 33.8 1.0
OD1 A:ASP351 3.1 35.6 1.0
CG A:ASN706 3.3 52.2 1.0
OD1 A:ASN706 3.4 57.7 1.0
O1A A:ADP1006 3.5 34.0 1.0
O1B A:ADP1006 3.5 49.0 1.0
F1 A:ALF1004 3.6 38.2 1.0
PA A:ADP1006 3.6 28.0 1.0
PB A:ADP1006 3.7 37.1 1.0
NZ A:LYS684 3.8 25.1 1.0
CG A:ASP351 3.9 30.0 1.0
OD2 A:ASP351 3.9 18.4 1.0
MG A:MG1005 4.0 28.2 1.0
O3B A:ADP1006 4.1 27.2 1.0
O A:HOH1211 4.2 37.8 1.0
O2A A:ADP1006 4.3 30.3 1.0
O A:HOH1159 4.5 51.7 1.0
CB A:ASN706 4.8 37.7 1.0
OD2 A:ASP707 4.8 25.1 1.0
OD1 A:ASP707 4.8 26.9 1.0
NE A:ARG489 4.8 27.2 1.0
CE A:LYS684 5.0 28.1 1.0
N A:GLY626 5.0 29.8 1.0
O2B A:ADP1006 5.0 39.1 1.0

Fluorine binding site 3 out of 4 in 5xa8

Go back to Fluorine Binding Sites List in 5xa8
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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:F1004

b:34.5
occ:1.00
 F3 A:ALF1004 0.0 34.5 1.0
AL A:ALF1004 1.8 31.8 1.0
OD1 A:ASP351 2.4 35.6 1.0
F1 A:ALF1004 2.5 38.2 1.0
F2 A:ALF1004 2.5 51.2 1.0
O1B A:ADP1006 2.9 49.0 1.0
N A:GLY626 3.0 29.8 1.0
NZ A:LYS684 3.1 25.1 1.0
O3A A:ADP1006 3.1 35.3 1.0
OG1 A:THR625 3.1 31.2 1.0
CA A:THR625 3.2 42.7 1.0
C A:THR625 3.5 37.9 1.0
CG A:ASP351 3.5 30.0 1.0
F4 A:ALF1004 3.6 27.9 1.0
PB A:ADP1006 3.6 37.1 1.0
CB A:THR625 3.7 33.0 1.0
ND2 A:ASN706 3.9 48.9 1.0
CE A:LYS684 3.9 28.1 1.0
O A:ILE624 4.0 33.5 1.0
CA A:GLY626 4.1 30.7 1.0
OD2 A:ASP351 4.1 18.4 1.0
O A:HOH1159 4.4 51.7 1.0
N A:THR625 4.4 50.5 1.0
PA A:ADP1006 4.4 28.0 1.0
O2B A:ADP1006 4.4 39.1 1.0
MG A:MG1003 4.6 22.0 1.0
N A:LYS352 4.6 41.9 1.0
O2A A:ADP1006 4.6 30.3 1.0
C A:ILE624 4.6 44.4 1.0
O A:HOH1122 4.7 26.7 1.0
O A:THR625 4.7 38.7 1.0
CB A:ASP351 4.7 17.4 1.0
O3B A:ADP1006 4.8 27.2 1.0
N A:ASP627 4.9 33.5 1.0
C A:GLY626 4.9 30.1 1.0

Fluorine binding site 4 out of 4 in 5xa8

Go back to Fluorine Binding Sites List in 5xa8
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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:F1004

b:27.9
occ:1.00
 F4 A:ALF1004 0.0 27.9 1.0
AL A:ALF1004 1.8 31.8 1.0
MG A:MG1005 2.2 28.2 1.0
F2 A:ALF1004 2.5 51.2 1.0
F1 A:ALF1004 2.5 38.2 1.0
OD2 A:ASP351 2.6 18.4 1.0
O A:THR353 2.6 32.3 1.0
O A:HOH1122 2.7 26.7 1.0
O A:HOH1211 2.8 37.8 1.0
MG A:MG1003 3.0 22.0 1.0
O1B A:ADP1006 3.1 49.0 1.0
CB A:THR353 3.1 39.9 1.0
OD1 A:ASP351 3.2 35.6 1.0
CG A:ASP351 3.3 30.0 1.0
C A:THR353 3.4 28.0 1.0
F3 A:ALF1004 3.6 34.5 1.0
CA A:THR353 3.6 46.6 1.0
N A:THR353 3.7 38.8 1.0
CG2 A:THR353 3.8 32.0 1.0
PB A:ADP1006 3.9 37.1 1.0
O3B A:ADP1006 3.9 27.2 1.0
OD1 A:ASP703 4.0 49.2 1.0
O3A A:ADP1006 4.0 35.3 1.0
OG1 A:THR353 4.1 36.3 1.0
O A:HOH1141 4.1 33.8 1.0
N A:GLY354 4.7 30.9 1.0
C A:LYS352 4.7 29.2 1.0
CB A:ASP351 4.8 17.4 1.0
OD2 A:ASP703 4.8 47.1 1.0
CG A:ASP703 4.9 41.4 1.0
ND2 A:ASN706 4.9 48.9 1.0
N A:LYS352 4.9 41.9 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 Jul 15 09:07:16 2025

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