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Fluorine in PDB 3ar9: Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium

Enzymatic activity of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium

All present enzymatic activity of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium:
3.6.3.8;

Protein crystallography data

The structure of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium, PDB code: 3ar9 was solved by C.Toyoshima, S.Yonekura, J.Tsueda, S.Iwasawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.97 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.388, 135.807, 105.425, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.7

Other elements in 3ar9:

The structure of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium (pdb code 3ar9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium, PDB code: 3ar9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3ar9

Go back to Fluorine Binding Sites List in 3ar9
Fluorine binding site 1 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:42.6
occ:1.00
 F1 A:BEF998 0.0 42.6 1.0
BE A:BEF998 1.4 44.0 1.0
F2 A:BEF998 2.4 43.2 1.0
F3 A:BEF998 2.4 41.5 1.0
OD2 A:ASP351 2.6 30.4 1.0
N A:GLY626 2.8 38.3 1.0
NZ A:LYS684 2.9 40.9 1.0
ND2 A:ASN706 3.0 34.2 1.0
CA A:THR625 3.4 37.4 1.0
OG1 A:THR625 3.6 34.6 1.0
C A:THR625 3.6 39.1 1.0
CA A:GLY182 3.7 46.3 1.0
CA A:GLY626 3.8 41.4 1.0
CG A:ASP351 3.9 33.7 1.0
O A:HOH2105 3.9 48.6 1.0
CE A:LYS684 3.9 42.0 1.0
CB A:THR625 4.0 35.2 1.0
MG A:MG997 4.0 38.4 1.0
CG A:ASN706 4.1 40.3 1.0
O A:ILE624 4.1 41.5 1.0
O A:THR181 4.2 50.6 1.0
OD1 A:ASN706 4.4 42.1 1.0
N A:GLY182 4.5 47.6 1.0
O A:GLY182 4.5 41.5 1.0
C A:GLY182 4.6 44.9 1.0
OD1 A:ASP707 4.6 44.8 1.0
N A:THR625 4.6 39.0 1.0
N A:ASP627 4.6 44.4 1.0
C A:THR181 4.7 49.5 1.0
OD1 A:ASP351 4.7 30.7 1.0
CB A:ASP351 4.7 33.9 1.0
N A:LYS352 4.8 32.6 1.0
C A:GLY626 4.8 43.1 1.0
O A:THR625 4.8 37.2 1.0
C A:ILE624 4.8 42.1 1.0

Fluorine binding site 2 out of 3 in 3ar9

Go back to Fluorine Binding Sites List in 3ar9
Fluorine binding site 2 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:43.2
occ:1.00
 F2 A:BEF998 0.0 43.2 1.0
BE A:BEF998 1.4 44.0 1.0
MG A:MG997 2.0 38.4 1.0
F1 A:BEF998 2.4 42.6 1.0
F3 A:BEF998 2.4 41.5 1.0
OD2 A:ASP351 2.5 30.4 1.0
O A:HOH2105 2.8 48.6 1.0
CA A:GLY182 3.0 46.3 1.0
O A:HOH2114 3.1 28.0 1.0
O A:THR353 3.3 41.7 1.0
CG A:ASP351 3.3 33.7 1.0
CB A:THR353 3.4 34.8 1.0
OD1 A:ASP351 3.5 30.7 1.0
N A:THR353 3.7 33.3 1.0
O A:GLY182 3.7 41.5 1.0
CA A:THR353 3.8 35.5 1.0
C A:GLY182 3.9 44.9 1.0
ND2 A:ASN706 4.0 34.2 1.0
OG1 A:THR353 4.0 35.8 1.0
C A:THR353 4.0 38.4 1.0
O A:SER178 4.1 52.3 1.0
N A:GLY182 4.2 47.6 1.0
OD1 A:ASP703 4.2 35.6 1.0
CG2 A:THR353 4.4 35.2 1.0
OD1 A:ASN706 4.4 42.1 1.0
NZ A:LYS684 4.6 40.9 1.0
OG1 A:THR625 4.6 34.6 1.0
C A:LYS352 4.7 33.7 1.0
N A:LYS352 4.7 32.6 1.0
CG A:ASN706 4.7 40.3 1.0
CB A:ASP351 4.8 33.9 1.0
N A:GLY626 4.9 38.3 1.0
OD2 A:ASP707 5.0 47.0 1.0
C A:THR181 5.0 49.5 1.0

Fluorine binding site 3 out of 3 in 3ar9

Go back to Fluorine Binding Sites List in 3ar9
Fluorine binding site 3 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Calcium Pump Crystal Structure with Bound BEF3, Tnp-Amp and Tg in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:41.5
occ:1.00
 F3 A:BEF998 0.0 41.5 1.0
BE A:BEF998 1.4 44.0 1.0
F1 A:BEF998 2.4 42.6 1.0
F2 A:BEF998 2.4 43.2 1.0
OD2 A:ASP351 2.5 30.4 1.0
OG1 A:THR625 2.6 34.6 1.0
N A:THR353 2.8 33.3 1.0
N A:LYS352 3.0 32.6 1.0
CB A:THR625 3.2 35.2 1.0
CB A:LYS352 3.3 28.4 1.0
CA A:LYS352 3.4 32.5 1.0
CG A:ASP351 3.4 33.7 1.0
C A:LYS352 3.5 33.7 1.0
CA A:THR625 3.6 37.4 1.0
OG1 A:THR353 3.7 35.8 1.0
CB A:THR353 3.7 34.8 1.0
CA A:THR353 3.8 35.5 1.0
OD1 A:ASP351 3.9 30.7 1.0
MG A:MG997 3.9 38.4 1.0
N A:GLY626 4.0 38.3 1.0
O A:GLY182 4.0 41.5 1.0
C A:ASP351 4.1 32.1 1.0
C A:THR625 4.3 39.1 1.0
O A:THR353 4.4 41.7 1.0
O A:ILE624 4.4 41.5 1.0
CA A:GLY182 4.4 46.3 1.0
CG A:LYS352 4.4 33.3 1.0
CB A:ASP351 4.4 33.9 1.0
CA A:ASP351 4.5 35.6 1.0
NZ A:LYS352 4.5 30.8 1.0
CE A:LYS352 4.5 33.7 1.0
C A:THR353 4.6 38.4 1.0
CG2 A:THR625 4.6 35.0 1.0
O A:LYS352 4.7 36.4 1.0
NZ A:LYS684 4.7 40.9 1.0
C A:GLY182 4.7 44.9 1.0
N A:THR625 4.7 39.0 1.0
O A:HOH2105 4.8 48.6 1.0
N A:ASP627 4.8 44.4 1.0
C A:ILE624 5.0 42.1 1.0

Reference:

C.Toyoshima, S.Yonekura, J.Tsueda, S.Iwasawa. Trinitrophenyl Derivatives Bind Differently From Parent Adenine Nucleotides to CA2+-Atpase in the Absence of CA2+ Proc.Natl.Acad.Sci.Usa V. 108 1833 2011.
ISSN: ISSN 0027-8424
PubMed: 21239683
DOI: 10.1073/PNAS.1017659108
Page generated: Sun Dec 13 11:43:03 2020

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