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Fluorine in PDB 5xa9: Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E2-Alf-(Tg) Crystals of C2 Symmetry

Enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E2-Alf-(Tg) Crystals of C2 Symmetry

All present enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E2-Alf-(Tg) Crystals of C2 Symmetry:
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 E2-Alf-(Tg) Crystals of C2 Symmetry, PDB code: 5xa9 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) 135.70 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.400, 70.100, 141.900, 90.00, 107.00, 90.00
R / Rfree (%) 21.5 / 23.5

Other elements in 5xa9:

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E2-Alf-(Tg) Crystals of C2 Symmetry also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

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 E2-Alf-(Tg) Crystals of C2 Symmetry (pdb code 5xa9). 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 E2-Alf-(Tg) Crystals of C2 Symmetry, PDB code: 5xa9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5xa9

Go back to Fluorine Binding Sites List in 5xa9
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 E2-Alf-(Tg) Crystals of C2 Symmetry


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 E2-Alf-(Tg) Crystals of C2 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:79.0
occ:1.00
 F1 A:ALF1002 0.0 79.0 1.0
AL A:ALF1002 1.8 58.4 1.0
O A:HOH1136 2.5 65.8 1.0
F4 A:ALF1002 2.5 65.3 1.0
F3 A:ALF1002 2.5 66.8 1.0
ND2 A:ASN706 2.7 58.4 1.0
CA A:GLY182 3.1 64.2 1.0
O A:THR181 3.3 67.1 1.0
OD1 A:ASN706 3.3 67.8 1.0
OD1 A:ASP351 3.3 84.0 1.0
CG A:ASN706 3.4 60.0 1.0
O A:HOH1111 3.5 64.2 1.0
NZ A:LYS684 3.5 63.7 1.0
OD2 A:ASP351 3.5 75.5 1.0
F2 A:ALF1002 3.6 61.4 1.0
MG A:MG1001 3.7 67.7 1.0
CG A:ASP351 3.7 79.8 1.0
N A:GLY182 3.8 72.4 1.0
C A:THR181 3.8 63.1 1.0
OD1 A:ASP707 4.0 71.0 1.0
OD2 A:ASP707 4.0 71.6 1.0
C A:GLY182 4.0 70.8 1.0
O A:GLY182 4.2 66.3 1.0
CG A:ASP707 4.4 67.8 1.0
O A:HOH1129 4.5 71.4 1.0
CE A:LYS684 4.8 68.6 1.0
CB A:ASN706 4.8 66.0 1.0
N A:GLY626 4.9 65.5 1.0

Fluorine binding site 2 out of 4 in 5xa9

Go back to Fluorine Binding Sites List in 5xa9
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 E2-Alf-(Tg) Crystals of C2 Symmetry


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 E2-Alf-(Tg) Crystals of C2 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:61.4
occ:1.00
 F2 A:ALF1002 0.0 61.4 1.0
AL A:ALF1002 1.8 58.4 1.0
OD2 A:ASP351 2.3 75.5 1.0
F3 A:ALF1002 2.5 66.8 1.0
F4 A:ALF1002 2.5 65.3 1.0
OG1 A:THR625 2.6 68.1 1.0
O A:HOH1111 2.8 64.2 1.0
N A:THR353 3.1 75.5 1.0
CG A:ASP351 3.3 79.8 1.0
CB A:THR625 3.4 59.7 1.0
N A:LYS352 3.4 69.8 1.0
F1 A:ALF1002 3.6 79.0 1.0
OD1 A:ASP351 3.6 84.0 1.0
CB A:LYS352 3.7 59.6 1.0
CA A:THR625 3.7 69.6 1.0
OG1 A:THR353 3.8 63.9 1.0
CB A:THR353 3.8 65.2 1.0
CA A:LYS352 3.8 77.8 1.0
C A:LYS352 3.9 80.1 1.0
N A:GLY626 3.9 65.5 1.0
OE2 A:GLU183 4.0 65.5 1.0
CA A:THR353 4.0 69.5 1.0
NZ A:LYS352 4.3 64.4 1.0
O A:THR353 4.3 90.4 1.0
C A:THR625 4.4 63.0 1.0
MG A:MG1001 4.4 67.7 1.0
C A:ASP351 4.4 71.1 1.0
CB A:ASP351 4.6 72.8 1.0
O A:THR181 4.7 67.1 1.0
C A:THR353 4.7 81.3 1.0
CA A:ASP351 4.7 65.8 1.0
O A:ILE624 4.7 70.9 1.0
NZ A:LYS684 4.8 63.7 1.0
CG2 A:THR625 4.8 62.9 1.0
N A:ASP627 4.8 61.0 1.0
CG A:LYS352 4.9 62.2 1.0
N A:THR625 4.9 69.0 1.0
O A:HOH1136 4.9 65.8 1.0

Fluorine binding site 3 out of 4 in 5xa9

Go back to Fluorine Binding Sites List in 5xa9
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 E2-Alf-(Tg) Crystals of C2 Symmetry


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 E2-Alf-(Tg) Crystals of C2 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:66.8
occ:1.00
 F3 A:ALF1002 0.0 66.8 1.0
AL A:ALF1002 1.8 58.4 1.0
MG A:MG1001 2.2 67.7 1.0
F2 A:ALF1002 2.5 61.4 1.0
F1 A:ALF1002 2.5 79.0 1.0
OD1 A:ASP351 2.6 84.0 1.0
O A:THR353 2.8 90.4 1.0
O A:HOH1136 2.8 65.8 1.0
OD2 A:ASP351 3.1 75.5 1.0
CG A:ASP351 3.2 79.8 1.0
CB A:THR353 3.2 65.2 1.0
O A:HOH1129 3.2 71.4 1.0
O A:HOH1111 3.4 64.2 1.0
O A:GLY182 3.4 66.3 1.0
C A:THR353 3.5 81.3 1.0
F4 A:ALF1002 3.6 65.3 1.0
N A:THR353 3.6 75.5 1.0
CA A:THR353 3.6 69.5 1.0
CA A:GLY182 4.0 64.2 1.0
C A:GLY182 4.0 70.8 1.0
OG1 A:THR353 4.0 63.9 1.0
CG2 A:THR353 4.2 62.5 1.0
OD1 A:ASP703 4.2 88.6 1.0
OE2 A:GLU183 4.5 65.5 1.0
C A:LYS352 4.6 80.1 1.0
O A:THR181 4.6 67.1 1.0
CB A:ASP351 4.6 72.8 1.0
N A:LYS352 4.7 69.8 1.0
N A:GLY354 4.8 68.0 1.0
OD2 A:ASP707 5.0 71.6 1.0

Fluorine binding site 4 out of 4 in 5xa9

Go back to Fluorine Binding Sites List in 5xa9
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 E2-Alf-(Tg) Crystals of C2 Symmetry


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 E2-Alf-(Tg) Crystals of C2 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:65.3
occ:1.00
 F4 A:ALF1002 0.0 65.3 1.0
AL A:ALF1002 1.8 58.4 1.0
F1 A:ALF1002 2.5 79.0 1.0
F2 A:ALF1002 2.5 61.4 1.0
N A:GLY626 2.7 65.5 1.0
NZ A:LYS684 2.8 63.7 1.0
OD2 A:ASP351 2.9 75.5 1.0
O A:HOH1111 2.9 64.2 1.0
CA A:THR625 3.2 69.6 1.0
C A:THR625 3.3 63.0 1.0
O A:THR181 3.4 67.1 1.0
OG1 A:THR625 3.6 68.1 1.0
F3 A:ALF1002 3.6 66.8 1.0
CE A:LYS684 3.6 68.6 1.0
ND2 A:ASN706 3.7 58.4 1.0
CA A:GLY626 3.7 63.8 1.0
CG A:ASP351 3.8 79.8 1.0
O A:ILE624 3.9 70.9 1.0
CB A:THR625 3.9 59.7 1.0
OD1 A:ASP351 4.2 84.0 1.0
N A:THR625 4.3 69.0 1.0
C A:THR181 4.4 63.1 1.0
O A:THR625 4.5 64.7 1.0
C A:ILE624 4.5 74.1 1.0
O A:HOH1157 4.6 52.1 1.0
OD1 A:ASP707 4.6 71.0 1.0
N A:ASP627 4.7 61.0 1.0
C A:GLY626 4.7 62.4 1.0
O A:HOH1136 4.8 65.8 1.0
CG A:ASN706 4.8 60.0 1.0
CA A:GLY182 4.8 64.2 1.0
CB A:ASP351 5.0 72.8 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 Jul 15 09:07:28 2025

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