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Fluorine in PDB 3n5k: Structure of the (Sr)CA2+-Atpase E2-ALF4- Form

Enzymatic activity of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form

All present enzymatic activity of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form:
3.6.3.8;

Protein crystallography data

The structure of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form, PDB code: 3n5k was solved by M.Bublitz, C.Olesen, H.Poulsen, J.P.Morth, J.V.Moller, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.930, 109.420, 276.092, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.6

Other elements in 3n5k:

The structure of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms
Potassium (K) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form (pdb code 3n5k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form, PDB code: 3n5k:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3n5k

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Fluorine binding site 1 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:27.4
occ:1.00
 F1 A:ALF2002 0.0 27.4 1.0
AL A:ALF2002 1.8 24.9 1.0
F4 A:ALF2002 2.5 25.1 1.0
O A:HOH1279 2.5 23.0 1.0
F3 A:ALF2002 2.5 23.1 1.0
OD1 A:ASP351 2.7 23.8 1.0
O A:HOH1365 2.7 23.3 1.0
ND2 A:ASN706 2.7 20.9 1.0
CA A:GLY182 3.1 23.2 1.0
OD1 A:ASN706 3.3 24.9 1.0
O A:THR181 3.4 22.4 1.0
CG A:ASN706 3.4 25.1 1.0
MG A:MG2001 3.5 26.7 1.0
NZ A:LYS684 3.5 22.9 1.0
F2 A:ALF2002 3.6 23.4 1.0
CG A:ASP351 3.6 24.2 1.0
N A:GLY182 3.6 21.9 1.0
C A:THR181 3.8 23.8 1.0
OD2 A:ASP351 4.1 23.9 1.0
C A:GLY182 4.1 27.3 1.0
OD1 A:ASP707 4.2 26.2 1.0
OD2 A:ASP707 4.2 25.4 1.0
O A:HOH1366 4.4 21.1 1.0
N A:GLY626 4.5 24.8 1.0
O A:GLY182 4.5 25.8 1.0
CG A:ASP707 4.5 25.2 1.0
CE A:LYS684 4.6 26.1 1.0
CB A:ASP351 4.7 21.3 1.0
CB A:ASN706 4.9 21.8 1.0

Fluorine binding site 2 out of 8 in 3n5k

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Fluorine binding site 2 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:23.4
occ:1.00
 F2 A:ALF2002 0.0 23.4 1.0
AL A:ALF2002 1.8 24.9 1.0
F3 A:ALF2002 2.5 23.1 1.0
F4 A:ALF2002 2.6 25.1 1.0
OG1 A:THR625 2.6 19.3 1.0
OD1 A:ASP351 2.6 23.8 1.0
O A:HOH1365 2.6 23.3 1.0
N A:THR353 2.8 21.7 1.0
N A:LYS352 3.0 22.6 1.0
CB A:LYS352 3.4 17.9 1.0
CB A:THR625 3.4 22.2 1.0
CA A:LYS352 3.5 22.3 1.0
CG A:ASP351 3.5 24.2 1.0
F1 A:ALF2002 3.6 27.4 1.0
C A:LYS352 3.6 23.4 1.0
OG1 A:THR353 3.6 21.5 1.0
CB A:THR353 3.7 19.1 1.0
OE2 A:GLU183 3.7 22.2 1.0
CA A:THR625 3.8 25.9 1.0
CA A:THR353 3.8 21.3 1.0
OD2 A:ASP351 4.0 23.9 1.0
N A:GLY626 4.0 24.8 1.0
C A:ASP351 4.1 24.0 1.0
MG A:MG2001 4.3 26.7 1.0
CG A:LYS352 4.4 21.9 1.0
C A:THR625 4.4 25.7 1.0
CA A:ASP351 4.5 21.4 1.0
CB A:ASP351 4.6 21.3 1.0
O A:ILE624 4.6 24.8 1.0
O A:THR353 4.7 23.7 1.0
CE A:LYS352 4.7 27.4 1.0
C A:THR353 4.8 26.5 1.0
NZ A:LYS684 4.8 22.9 1.0
O A:LYS352 4.8 24.1 1.0
N A:ASP627 4.8 24.2 1.0
CG2 A:THR625 4.8 20.8 1.0
NZ A:LYS352 4.8 25.0 1.0
CD A:GLU183 5.0 26.0 1.0
O A:THR181 5.0 22.4 1.0
N A:THR625 5.0 23.9 1.0

Fluorine binding site 3 out of 8 in 3n5k

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Fluorine binding site 3 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:23.1
occ:1.00
 F3 A:ALF2002 0.0 23.1 1.0
AL A:ALF2002 1.8 24.9 1.0
MG A:MG2001 2.0 26.7 1.0
F2 A:ALF2002 2.5 23.4 1.0
OD1 A:ASP351 2.5 23.8 1.0
F1 A:ALF2002 2.5 27.4 1.0
O A:HOH1365 2.7 23.3 1.0
OD2 A:ASP351 2.9 23.9 1.0
O A:HOH1279 3.0 23.0 1.0
CG A:ASP351 3.0 24.2 1.0
O A:THR353 3.1 23.7 1.0
O A:HOH1366 3.1 21.1 1.0
CB A:THR353 3.1 19.1 1.0
N A:THR353 3.2 21.7 1.0
CA A:THR353 3.4 21.3 1.0
F4 A:ALF2002 3.5 25.1 1.0
C A:THR353 3.7 26.5 1.0
O A:GLY182 3.7 25.8 1.0
CA A:GLY182 3.9 23.2 1.0
OG1 A:THR353 3.9 21.5 1.0
C A:GLY182 4.1 27.3 1.0
OE2 A:GLU183 4.1 22.2 1.0
CG2 A:THR353 4.2 15.0 1.0
OD1 A:ASP703 4.2 30.0 1.0
C A:LYS352 4.2 23.4 1.0
N A:LYS352 4.3 22.6 1.0
CB A:ASP351 4.5 21.3 1.0
O A:THR181 4.7 22.4 1.0
CA A:LYS352 4.8 22.3 1.0
OG1 A:THR625 4.9 19.3 1.0
N A:GLY354 5.0 25.0 1.0

Fluorine binding site 4 out of 8 in 3n5k

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Fluorine binding site 4 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:25.1
occ:1.00
 F4 A:ALF2002 0.0 25.1 1.0
AL A:ALF2002 1.8 24.9 1.0
N A:GLY626 2.5 24.8 1.0
F1 A:ALF2002 2.5 27.4 1.0
F2 A:ALF2002 2.6 23.4 1.0
OD1 A:ASP351 2.7 23.8 1.0
NZ A:LYS684 2.7 22.9 1.0
O A:HOH1365 2.7 23.3 1.0
CA A:THR625 2.9 25.9 1.0
C A:THR625 3.1 25.7 1.0
OG1 A:THR625 3.3 19.3 1.0
F3 A:ALF2002 3.5 23.1 1.0
O A:ILE624 3.6 24.8 1.0
CA A:GLY626 3.6 21.3 1.0
CB A:THR625 3.6 22.2 1.0
CE A:LYS684 3.7 26.1 1.0
O A:THR181 3.8 22.4 1.0
ND2 A:ASN706 3.9 20.9 1.0
CG A:ASP351 3.9 24.2 1.0
N A:THR625 4.0 23.9 1.0
C A:ILE624 4.2 24.0 1.0
O A:THR625 4.3 26.2 1.0
N A:LYS352 4.5 22.6 1.0
N A:ASP627 4.6 24.2 1.0
C A:GLY626 4.6 23.0 1.0
CB A:ASP351 4.6 21.3 1.0
O A:HOH1279 4.7 23.0 1.0
OD1 A:ASP707 4.7 26.2 1.0
C A:THR181 4.7 23.8 1.0
CA A:ASP351 4.7 21.4 1.0
OD2 A:ASP351 4.8 23.9 1.0
OE2 A:GLU183 5.0 22.2 1.0

Fluorine binding site 5 out of 8 in 3n5k

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Fluorine binding site 5 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:28.6
occ:1.00
 F1 B:ALF2002 0.0 28.6 1.0
AL B:ALF2002 1.8 24.9 1.0
F4 B:ALF2002 2.5 25.2 1.0
O B:HOH1311 2.5 22.3 1.0
F3 B:ALF2002 2.5 23.6 1.0
O B:HOH1228 2.6 29.4 1.0
ND2 B:ASN706 2.7 20.1 1.0
OD1 B:ASP351 2.8 22.7 1.0
CA B:GLY182 3.0 25.6 1.0
O B:THR181 3.3 24.9 1.0
OD1 B:ASN706 3.3 25.9 1.0
CG B:ASN706 3.4 24.9 1.0
MG B:MG2001 3.4 28.4 1.0
N B:GLY182 3.5 22.5 1.0
F2 B:ALF2002 3.6 23.3 1.0
NZ B:LYS684 3.6 23.0 1.0
CG B:ASP351 3.7 26.1 1.0
C B:THR181 3.7 23.3 1.0
C B:GLY182 4.0 24.2 1.0
OD2 B:ASP351 4.0 25.4 1.0
OD2 B:ASP707 4.2 26.6 1.0
O B:GLY182 4.3 22.6 1.0
OD1 B:ASP707 4.3 24.5 1.0
O B:HOH1226 4.3 27.0 1.0
N B:GLY626 4.5 22.4 1.0
CE B:LYS684 4.6 26.1 1.0
CG B:ASP707 4.6 27.1 1.0
CB B:ASN706 4.9 24.1 1.0
CB B:ASP351 4.9 23.1 1.0
N B:GLU183 4.9 25.9 1.0
CA B:THR181 5.0 21.5 1.0

Fluorine binding site 6 out of 8 in 3n5k

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Fluorine binding site 6 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:23.3
occ:1.00
 F2 B:ALF2002 0.0 23.3 1.0
AL B:ALF2002 1.8 24.9 1.0
F3 B:ALF2002 2.5 23.6 1.0
OD1 B:ASP351 2.5 22.7 1.0
F4 B:ALF2002 2.6 25.2 1.0
O B:HOH1311 2.6 22.3 1.0
OG1 B:THR625 2.7 22.5 1.0
N B:THR353 2.8 26.4 1.0
N B:LYS352 2.9 22.2 1.0
CB B:LYS352 3.3 21.0 1.0
CA B:LYS352 3.3 24.2 1.0
CB B:THR625 3.4 23.1 1.0
CG B:ASP351 3.4 26.1 1.0
C B:LYS352 3.5 25.7 1.0
F1 B:ALF2002 3.6 28.6 1.0
OG1 B:THR353 3.7 25.4 1.0
CA B:THR625 3.8 22.1 1.0
CB B:THR353 3.8 23.9 1.0
OE2 B:GLU183 3.8 24.6 1.0
CA B:THR353 3.9 22.4 1.0
OD2 B:ASP351 3.9 25.4 1.0
C B:ASP351 4.0 24.0 1.0
N B:GLY626 4.2 22.4 1.0
MG B:MG2001 4.3 28.4 1.0
CA B:ASP351 4.4 23.4 1.0
CG B:LYS352 4.4 23.9 1.0
CB B:ASP351 4.5 23.1 1.0
C B:THR625 4.5 22.2 1.0
O B:ILE624 4.5 27.2 1.0
NZ B:LYS684 4.6 23.0 1.0
CE B:LYS352 4.7 21.0 1.0
O B:LYS352 4.7 27.7 1.0
O B:THR353 4.7 25.9 1.0
CG2 B:THR625 4.8 18.6 1.0
C B:THR353 4.8 23.0 1.0
N B:THR625 4.9 25.1 1.0
N B:ASP627 4.9 24.7 1.0

Fluorine binding site 7 out of 8 in 3n5k

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Fluorine binding site 7 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:23.6
occ:1.00
 F3 B:ALF2002 0.0 23.6 1.0
AL B:ALF2002 1.8 24.9 1.0
MG B:MG2001 2.0 28.4 1.0
F2 B:ALF2002 2.5 23.3 1.0
F1 B:ALF2002 2.5 28.6 1.0
OD1 B:ASP351 2.5 22.7 1.0
O B:HOH1311 2.6 22.3 1.0
OD2 B:ASP351 2.8 25.4 1.0
O B:THR353 3.0 25.9 1.0
CG B:ASP351 3.0 26.1 1.0
O B:HOH1228 3.1 29.4 1.0
CB B:THR353 3.1 23.9 1.0
N B:THR353 3.1 26.4 1.0
O B:HOH1226 3.1 27.0 1.0
CA B:THR353 3.4 22.4 1.0
F4 B:ALF2002 3.6 25.2 1.0
C B:THR353 3.6 23.0 1.0
O B:GLY182 3.8 22.6 1.0
OG1 B:THR353 3.8 25.4 1.0
CA B:GLY182 4.1 25.6 1.0
OE2 B:GLU183 4.1 24.6 1.0
C B:LYS352 4.1 25.7 1.0
CG2 B:THR353 4.1 20.4 1.0
OD1 B:ASP703 4.2 28.1 1.0
C B:GLY182 4.2 24.2 1.0
N B:LYS352 4.3 22.2 1.0
CB B:ASP351 4.5 23.1 1.0
O B:THR181 4.7 24.9 1.0
CA B:LYS352 4.7 24.2 1.0
OG1 B:THR625 4.9 22.5 1.0
N B:GLY354 4.9 24.6 1.0
OD2 B:ASP707 4.9 26.6 1.0
CD B:GLU183 4.9 24.7 1.0
O B:LYS352 5.0 27.7 1.0

Fluorine binding site 8 out of 8 in 3n5k

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Fluorine binding site 8 out of 8 in the Structure of the (Sr)CA2+-Atpase E2-ALF4- Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the (Sr)CA2+-Atpase E2-ALF4- Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:25.2
occ:1.00
 F4 B:ALF2002 0.0 25.2 1.0
AL B:ALF2002 1.8 24.9 1.0
F1 B:ALF2002 2.5 28.6 1.0
N B:GLY626 2.6 22.4 1.0
F2 B:ALF2002 2.6 23.3 1.0
NZ B:LYS684 2.6 23.0 1.0
O B:HOH1311 2.6 22.3 1.0
OD1 B:ASP351 2.7 22.7 1.0
CA B:THR625 2.9 22.1 1.0
C B:THR625 3.2 22.2 1.0
OG1 B:THR625 3.4 22.5 1.0
CE B:LYS684 3.5 26.1 1.0
O B:ILE624 3.6 27.2 1.0
F3 B:ALF2002 3.6 23.6 1.0
CB B:THR625 3.7 23.1 1.0
CA B:GLY626 3.7 23.4 1.0
ND2 B:ASN706 3.8 20.1 1.0
O B:THR181 3.9 24.9 1.0
CG B:ASP351 3.9 26.1 1.0
N B:THR625 4.0 25.1 1.0
C B:ILE624 4.2 23.0 1.0
O B:THR625 4.4 22.5 1.0
N B:LYS352 4.5 22.2 1.0
N B:ASP627 4.6 24.7 1.0
OD1 B:ASP707 4.7 24.5 1.0
O B:HOH1228 4.7 29.4 1.0
C B:GLY626 4.7 25.8 1.0
C B:THR181 4.7 23.3 1.0
CB B:ASP351 4.7 23.1 1.0
CA B:ASP351 4.8 23.4 1.0
OD2 B:ASP351 4.8 25.4 1.0
CD B:LYS684 4.9 25.9 1.0
O B:HOH1003 4.9 24.8 1.0
CG B:ASN706 5.0 24.9 1.0

Reference:

M.Bublitz, M.Musgaard, H.Poulsen, L.Thogersen, C.Olesen, B.Schiott, J.P.Morth, J.V.Moller, P.Nissen. Ion Pathways in the Sarcoplasmic Reticulum CA2+-Atpase. J.Biol.Chem. V. 288 10759 2013.
ISSN: ISSN 0021-9258
PubMed: 23400778
DOI: 10.1074/JBC.R112.436550
Page generated: Sun Dec 13 11:51:18 2020

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