Fluorine in PDB 5xaa: Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E2-Alf-(Tg) Crystals of P21212 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 P21212 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 P21212 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 P21212 Symmetry, PDB code: 5xaa 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) 91.56 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.900, 87.700, 140.200, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 26

Other elements in 5xaa:

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 P21212 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 P21212 Symmetry (pdb code 5xaa). 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 P21212 Symmetry, PDB code: 5xaa:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5xaa

Go back to Fluorine Binding Sites List in 5xaa
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 P21212 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 P21212 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:61.4
occ:1.00
 F1 A:ALF1002 0.0 61.4 1.0
AL A:ALF1002 1.8 47.6 1.0
O A:HOH1121 2.4 54.9 1.0
ND2 A:ASN706 2.5 55.7 1.0
F3 A:ALF1002 2.5 64.3 1.0
F4 A:ALF1002 2.5 52.0 1.0
OD1 A:ASN706 3.1 65.2 1.0
CG A:ASN706 3.1 68.9 1.0
OD2 A:ASP351 3.2 59.6 1.0
CA A:GLY182 3.2 56.0 1.0
NZ A:LYS684 3.3 41.9 1.0
OD1 A:ASP351 3.5 86.7 1.0
O A:THR181 3.5 54.5 1.0
F2 A:ALF1002 3.6 45.2 1.0
CG A:ASP351 3.6 70.6 1.0
OD1 A:ASP707 3.7 53.8 1.0
O A:HOH1108 3.7 53.6 1.0
OD2 A:ASP707 3.7 52.2 1.0
MG A:MG1001 3.8 47.7 1.0
N A:GLY182 3.8 55.7 1.0
C A:THR181 4.0 55.0 1.0
CG A:ASP707 4.0 57.7 1.0
O A:HOH1104 4.0 59.0 1.0
C A:GLY182 4.2 56.2 1.0
O A:GLY182 4.4 56.5 1.0
CE A:LYS684 4.6 49.0 1.0
CB A:ASN706 4.6 63.9 1.0
CB A:ASP351 4.9 58.1 1.0
O A:HOH1266 4.9 66.0 1.0

Fluorine binding site 2 out of 4 in 5xaa

Go back to Fluorine Binding Sites List in 5xaa
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 P21212 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 P21212 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:45.2
occ:1.00
 F2 A:ALF1002 0.0 45.2 1.0
AL A:ALF1002 1.8 47.6 1.0
OD1 A:ASP351 2.3 86.7 1.0
O A:HOH1108 2.4 53.6 1.0
F4 A:ALF1002 2.5 52.0 1.0
F3 A:ALF1002 2.5 64.3 1.0
OG1 A:THR625 2.7 62.1 1.0
N A:THR353 3.0 63.7 1.0
CG A:ASP351 3.2 70.6 1.0
OG1 A:THR353 3.4 53.1 1.0
OD2 A:ASP351 3.5 59.6 1.0
CB A:THR353 3.5 57.5 1.0
N A:LYS352 3.5 69.1 1.0
F1 A:ALF1002 3.6 61.4 1.0
CB A:THR625 3.6 48.7 1.0
OE2 A:GLU183 3.7 54.6 1.0
CA A:THR353 3.7 71.3 1.0
CB A:LYS352 3.8 53.4 1.0
C A:LYS352 3.9 65.8 1.0
CA A:LYS352 3.9 68.0 1.0
CA A:THR625 4.0 54.9 1.0
N A:GLY626 4.1 49.5 1.0
O A:THR353 4.2 73.4 1.0
MG A:MG1001 4.3 47.7 1.0
C A:THR353 4.5 66.2 1.0
O A:THR181 4.5 54.5 1.0
C A:ASP351 4.6 55.0 1.0
CB A:ASP351 4.6 58.1 1.0
C A:THR625 4.6 64.9 1.0
CG A:LYS352 4.7 54.5 1.0
O A:HOH1121 4.7 54.9 1.0
O A:HOH1104 4.7 59.0 1.0
O A:GLY182 4.8 56.5 1.0
CD A:GLU183 4.8 55.1 1.0
CA A:ASP351 4.8 54.1 1.0
NZ A:LYS684 4.8 41.9 1.0
N A:ASP627 4.9 43.9 1.0
CG2 A:THR353 4.9 54.9 1.0

Fluorine binding site 3 out of 4 in 5xaa

Go back to Fluorine Binding Sites List in 5xaa
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 P21212 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 P21212 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:64.3
occ:1.00
 F3 A:ALF1002 0.0 64.3 1.0
AL A:ALF1002 1.8 47.6 1.0
MG A:MG1001 2.1 47.7 1.0
O A:HOH1104 2.3 59.0 1.0
F1 A:ALF1002 2.5 61.4 1.0
F2 A:ALF1002 2.5 45.2 1.0
OD2 A:ASP351 2.5 59.6 1.0
O A:HOH1121 2.6 54.9 1.0
O A:THR353 2.9 73.4 1.0
O A:GLY182 3.2 56.5 1.0
OD1 A:ASP351 3.2 86.7 1.0
CB A:THR353 3.3 57.5 1.0
CG A:ASP351 3.3 70.6 1.0
O A:HOH1108 3.4 53.6 1.0
F4 A:ALF1002 3.6 52.0 1.0
CA A:GLY182 3.6 56.0 1.0
C A:THR353 3.7 66.2 1.0
C A:GLY182 3.7 56.2 1.0
CA A:THR353 3.7 71.3 1.0
N A:THR353 3.8 63.7 1.0
OG1 A:THR353 4.0 53.1 1.0
OD1 A:ASP703 4.1 61.0 1.0
O A:HOH1126 4.2 58.9 1.0
CG2 A:THR353 4.2 54.9 1.0
O A:HOH1266 4.4 66.0 1.0
O A:THR181 4.5 54.5 1.0
OE2 A:GLU183 4.5 54.6 1.0
OD2 A:ASP707 4.6 52.2 1.0
CB A:ASP351 4.7 58.1 1.0
N A:GLY182 4.8 55.7 1.0
C A:LYS352 4.8 65.8 1.0
ND2 A:ASN706 4.9 55.7 1.0
N A:GLY354 4.9 56.9 1.0
N A:GLU183 4.9 56.2 1.0
N A:LYS352 5.0 69.1 1.0

Fluorine binding site 4 out of 4 in 5xaa

Go back to Fluorine Binding Sites List in 5xaa
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 P21212 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 P21212 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:52.0
occ:1.00
 F4 A:ALF1002 0.0 52.0 1.0
AL A:ALF1002 1.8 47.6 1.0
F2 A:ALF1002 2.5 45.2 1.0
F1 A:ALF1002 2.5 61.4 1.0
OD1 A:ASP351 2.7 86.7 1.0
NZ A:LYS684 2.7 41.9 1.0
N A:GLY626 2.8 49.5 1.0
O A:HOH1108 2.9 53.6 1.0
CA A:THR625 3.2 54.9 1.0
C A:THR625 3.4 64.9 1.0
OG1 A:THR625 3.5 62.1 1.0
O A:THR181 3.5 54.5 1.0
CE A:LYS684 3.5 49.0 1.0
CG A:ASP351 3.6 70.6 1.0
F3 A:ALF1002 3.6 64.3 1.0
ND2 A:ASN706 3.6 55.7 1.0
CA A:GLY626 3.8 45.5 1.0
CB A:THR625 3.9 48.7 1.0
O A:ILE624 3.9 56.5 1.0
OD2 A:ASP351 4.0 59.6 1.0
N A:THR625 4.4 55.0 1.0
OD1 A:ASP707 4.4 53.8 1.0
C A:THR181 4.5 55.0 1.0
C A:ILE624 4.6 71.6 1.0
O A:THR625 4.6 55.3 1.0
O A:HOH1121 4.6 54.9 1.0
CB A:ASP351 4.7 58.1 1.0
CG A:ASN706 4.7 68.9 1.0
N A:ASP627 4.8 43.9 1.0
CA A:GLY182 4.8 56.0 1.0
O A:HOH1123 4.8 40.6 1.0
C A:GLY626 4.8 49.6 1.0
N A:LYS352 4.9 69.1 1.0
CD A:LYS684 5.0 57.0 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: Sun Dec 13 12:42:22 2020

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