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Fluorine in PDB 2zbe: Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg

Enzymatic activity of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg

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

Protein crystallography data

The structure of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg, PDB code: 2zbe was solved by C.Toyoshima, H.Ogawa, Y.Norimatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.869, 91.592, 248.464, 90.00, 90.00, 90.00
R / Rfree (%) 29.3 / 32.7

Other elements in 2zbe:

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

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg (pdb code 2zbe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg, PDB code: 2zbe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 1 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


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 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:0.5
occ:1.00
 F1 A:BEF998 0.0 0.5 1.0
BE A:BEF998 1.3 0.8 1.0
F2 A:BEF998 2.2 0.0 1.0
OD2 A:ASP351 2.2 0.6 1.0
F3 A:BEF998 2.3 0.1 1.0
NZ A:LYS684 2.5 90.3 1.0
N A:GLY626 2.8 0.7 1.0
CA A:THR625 2.9 0.6 1.0
C A:THR625 3.3 0.3 1.0
CG A:ASP351 3.3 0.4 1.0
OG1 A:THR625 3.4 76.5 1.0
CE A:LYS684 3.4 94.9 1.0
O A:ILE624 3.5 64.5 1.0
ND2 A:ASN706 3.5 0.5 1.0
CB A:THR625 3.6 72.5 1.0
OD1 A:ASP351 3.8 0.7 1.0
MG A:MG997 3.9 89.4 1.0
CA A:GLY626 3.9 0.1 1.0
N A:THR625 4.0 0.3 1.0
C A:ILE624 4.2 67.0 1.0
OD1 A:ASP707 4.4 0.7 1.0
O A:THR625 4.4 1.0 1.0
N A:LYS352 4.5 0.8 1.0
CA A:GLY182 4.5 0.2 1.0
CG A:ASN706 4.5 0.9 1.0
CB A:ASP351 4.6 0.3 1.0
OD1 A:ASN706 4.8 0.1 1.0
CD A:LYS684 4.8 97.8 1.0
N A:ASP627 4.9 84.9 1.0
O A:THR181 4.9 0.6 1.0
C A:GLY626 5.0 0.4 1.0
CG2 A:THR625 5.0 66.9 1.0

Fluorine binding site 2 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 2 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


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 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:0.0
occ:1.00
 F2 A:BEF998 0.0 0.0 1.0
BE A:BEF998 1.3 0.8 1.0
MG A:MG997 1.9 89.4 1.0
F1 A:BEF998 2.2 0.5 1.0
F3 A:BEF998 2.3 0.1 1.0
OD1 A:ASP351 2.6 0.7 1.0
OD2 A:ASP351 2.6 0.6 1.0
CG A:ASP351 3.0 0.4 1.0
CA A:GLY182 3.3 0.2 1.0
O A:THR353 3.3 95.1 1.0
N A:THR353 3.8 91.6 1.0
ND2 A:ASN706 3.8 0.5 1.0
CB A:THR353 3.9 0.4 1.0
NZ A:LYS684 3.9 90.3 1.0
C A:THR353 4.1 93.4 1.0
OG1 A:THR353 4.1 0.2 1.0
CA A:THR353 4.1 91.5 1.0
OG1 A:THR625 4.2 76.5 1.0
N A:GLY182 4.3 0.1 1.0
N A:LYS352 4.3 0.8 1.0
C A:GLY182 4.4 0.2 1.0
OD1 A:ASN706 4.4 0.1 1.0
N A:GLY626 4.4 0.7 1.0
O A:GLY182 4.4 0.2 1.0
OD1 A:ASP703 4.5 0.2 1.0
CB A:ASP351 4.5 0.3 1.0
C A:LYS352 4.6 0.4 1.0
CG A:ASN706 4.6 0.9 1.0
OD1 A:ASP707 4.8 0.7 1.0
CA A:THR625 4.8 0.6 1.0
CA A:LYS352 4.8 0.2 1.0
OD2 A:ASP707 4.8 0.2 1.0
CB A:THR625 4.8 72.5 1.0
O A:THR181 4.9 0.6 1.0
C A:THR181 4.9 0.8 1.0
CB A:LYS352 4.9 71.7 1.0

Fluorine binding site 3 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 3 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


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 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:0.1
occ:1.00
 F3 A:BEF998 0.0 0.1 1.0
BE A:BEF998 1.5 0.8 1.0
F1 A:BEF998 2.3 0.5 1.0
F2 A:BEF998 2.3 0.0 1.0
OD2 A:ASP351 2.4 0.6 1.0
OG1 A:THR625 2.4 76.5 1.0
CB A:THR625 2.8 72.5 1.0
N A:LYS352 2.9 0.8 1.0
CB A:LYS352 2.9 71.7 1.0
N A:THR353 3.0 91.6 1.0
CG A:ASP351 3.2 0.4 1.0
CA A:THR625 3.2 0.6 1.0
CA A:LYS352 3.2 0.2 1.0
OD1 A:ASP351 3.5 0.7 1.0
C A:LYS352 3.6 0.4 1.0
OG1 A:THR353 3.6 0.2 1.0
N A:GLY626 3.8 0.7 1.0
MG A:MG997 3.8 89.4 1.0
CA A:THR353 4.0 91.5 1.0
C A:THR625 4.0 0.3 1.0
CB A:THR353 4.0 0.4 1.0
O A:ILE624 4.1 64.5 1.0
C A:ASP351 4.1 92.8 1.0
CG A:LYS352 4.2 78.2 1.0
CG2 A:THR625 4.3 66.9 1.0
N A:THR625 4.3 0.3 1.0
CB A:ASP351 4.4 0.3 1.0
NZ A:LYS684 4.4 90.3 1.0
O A:THR353 4.4 95.1 1.0
CA A:ASP351 4.5 96.5 1.0
O A:GLY182 4.6 0.2 1.0
C A:ILE624 4.6 67.0 1.0
CA A:GLY182 4.6 0.2 1.0
C A:THR353 4.6 93.4 1.0
O A:LYS352 4.8 0.9 1.0
N A:ASP627 4.9 84.9 1.0
CD A:LYS352 5.0 78.5 1.0
CE A:LYS352 5.0 82.7 1.0

Fluorine binding site 4 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 4 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:0.6
occ:1.00
 F1 B:BEF1098 0.0 0.6 1.0
BE B:BEF1098 1.3 0.9 1.0
F3 B:BEF1098 2.3 0.3 1.0
F2 B:BEF1098 2.3 0.1 1.0
OD2 B:ASP351 2.4 0.8 1.0
ND2 B:ASN706 3.0 92.1 1.0
NZ B:LYS684 3.2 87.3 1.0
N B:GLY626 3.4 0.7 1.0
CG B:ASP351 3.4 0.7 1.0
CA B:GLY182 3.8 1.0 1.0
OG1 B:THR625 3.8 96.0 1.0
OD1 B:ASP351 3.9 1.0 1.0
MG B:MG997 3.9 68.0 1.0
CG B:ASN706 3.9 96.5 1.0
CA B:THR625 4.0 76.8 1.0
OD1 B:ASN706 4.1 96.8 1.0
CE B:LYS684 4.2 91.9 1.0
C B:THR625 4.2 77.6 1.0
O B:THR181 4.3 0.1 1.0
CA B:GLY626 4.3 0.2 1.0
CB B:THR625 4.4 92.0 1.0
N B:GLY182 4.5 0.9 1.0
OD1 B:ASP707 4.6 96.3 1.0
O B:GLY182 4.6 1.0 1.0
C B:THR181 4.6 0.2 1.0
O B:ILE624 4.7 89.6 1.0
N B:LYS352 4.7 0.7 1.0
CB B:ASP351 4.7 0.6 1.0
C B:GLY182 4.7 1.0 1.0
O B:THR353 4.9 76.1 1.0
N B:THR353 4.9 72.6 1.0

Fluorine binding site 5 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 5 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:0.1
occ:1.00
 F2 B:BEF1098 0.0 0.1 1.0
BE B:BEF1098 1.3 0.9 1.0
MG B:MG997 1.9 68.0 1.0
F3 B:BEF1098 2.3 0.3 1.0
F1 B:BEF1098 2.3 0.6 1.0
OD2 B:ASP351 2.6 0.8 1.0
O B:THR353 2.7 76.1 1.0
OD1 B:ASP351 2.7 1.0 1.0
CG B:ASP351 3.0 0.7 1.0
CA B:GLY182 3.4 1.0 1.0
CB B:THR353 3.5 0.5 1.0
C B:THR353 3.6 74.4 1.0
N B:THR353 3.6 72.6 1.0
OD1 B:ASP703 3.7 92.8 1.0
CA B:THR353 3.8 72.5 1.0
OG1 B:THR353 4.0 0.3 1.0
C B:GLY182 4.4 1.0 1.0
O B:GLY182 4.4 1.0 1.0
N B:GLY182 4.4 0.9 1.0
C B:LYS352 4.4 0.4 1.0
ND2 B:ASN706 4.4 92.1 1.0
N B:LYS352 4.5 0.7 1.0
O B:SER178 4.5 0.8 1.0
CB B:ASP351 4.5 0.6 1.0
OD1 B:ASN706 4.6 96.8 1.0
CG B:ASP703 4.8 95.3 1.0
OD2 B:ASP707 4.8 97.8 1.0
N B:GLY354 4.8 87.2 1.0
NZ B:LYS684 4.8 87.3 1.0
CG2 B:THR353 4.9 1.0 1.0
CA B:LYS352 4.9 0.2 1.0
OG1 B:THR625 4.9 96.0 1.0
OD2 B:ASP703 4.9 99.5 1.0
CG B:ASN706 5.0 96.5 1.0

Fluorine binding site 6 out of 6 in 2zbe

Go back to Fluorine Binding Sites List in 2zbe
Fluorine binding site 6 out of 6 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:0.3
occ:1.00
 F3 B:BEF1098 0.0 0.3 1.0
BE B:BEF1098 1.5 0.9 1.0
F2 B:BEF1098 2.3 0.1 1.0
F1 B:BEF1098 2.3 0.6 1.0
OD2 B:ASP351 2.3 0.8 1.0
N B:THR353 2.8 72.6 1.0
OG1 B:THR625 2.9 96.0 1.0
N B:LYS352 3.0 0.7 1.0
CB B:LYS352 3.1 73.0 1.0
CG B:ASP351 3.2 0.7 1.0
CA B:LYS352 3.3 0.2 1.0
C B:LYS352 3.4 0.4 1.0
CB B:THR625 3.5 92.0 1.0
OG1 B:THR353 3.6 0.3 1.0
OD1 B:ASP351 3.7 1.0 1.0
CA B:THR353 3.7 72.5 1.0
CB B:THR353 3.8 0.5 1.0
MG B:MG997 3.8 68.0 1.0
CA B:THR625 3.9 76.8 1.0
O B:THR353 3.9 76.1 1.0
C B:ASP351 4.0 99.5 1.0
N B:GLY626 4.1 0.7 1.0
CG B:LYS352 4.2 79.5 1.0
C B:THR353 4.2 74.4 1.0
O B:GLY182 4.3 1.0 1.0
CA B:ASP351 4.4 0.2 1.0
CB B:ASP351 4.4 0.6 1.0
CA B:GLY182 4.4 1.0 1.0
CE B:LYS352 4.4 84.0 1.0
C B:THR625 4.6 77.6 1.0
O B:LYS352 4.6 0.8 1.0
NZ B:LYS684 4.6 87.3 1.0
O B:ILE624 4.6 89.6 1.0
CD B:LYS352 4.7 79.8 1.0
C B:GLY182 4.8 1.0 1.0
O B:ASP351 4.9 0.6 1.0
CG2 B:THR625 4.9 86.4 1.0
N B:THR625 5.0 74.5 1.0

Reference:

C.Toyoshima, Y.Norimatsu, S.Iwasawa, T.Tsuda, H.Ogawa. How Processing of Aspartylphosphate Is Coupled to Lumenal Gating of the Ion Pathway in the Calcium Pump Proc.Natl.Acad.Sci.Usa V. 104 19831 2007.
ISSN: ISSN 0027-8424
PubMed: 18077416
DOI: 10.1073/PNAS.0709978104
Page generated: Mon Jul 14 15:04:54 2025

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