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Fluorine in PDB 1wpg: Crystal Structure of the Sr CA2+-Atpase with MGF4

Enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with MGF4

All present enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with MGF4:
3.6.3.8;

Protein crystallography data

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg was solved by C.Toyoshima, H.Nomura, T.Tsuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.210, 275.394, 109.945, 90.00, 90.01, 90.00
R / Rfree (%) 22.3 / 24.5

Other elements in 1wpg:

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4 also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Sodium (Na) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sr CA2+-Atpase with MGF4 (pdb code 1wpg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 1wpg

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Fluorine binding site 1 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:26.7
occ:1.00
F1 A:MF4998 0.0 26.7 1.0
MG A:MF4998 1.8 31.2 1.0
OD2 A:ASP351 2.5 22.8 1.0
NZ A:LYS684 2.7 22.7 1.0
F2 A:MF4998 2.9 32.7 1.0
F4 A:MF4998 2.9 22.3 1.0
F3 A:MF4998 2.9 25.4 1.0
ND2 A:ASN706 3.0 22.5 1.0
N A:GLY626 3.0 22.9 1.0
O A:THR181 3.5 24.8 1.0
CA A:THR625 3.6 22.6 1.0
CE A:LYS684 3.6 24.3 1.0
CG A:ASP351 3.7 26.2 1.0
C A:THR625 3.8 21.4 1.0
OG1 A:THR625 3.9 24.6 1.0
O A:HOH2105 4.0 30.1 1.0
CA A:GLY626 4.0 25.1 1.0
CG A:ASN706 4.1 29.4 1.0
O A:ILE624 4.1 25.2 1.0
CB A:THR625 4.3 21.9 1.0
OD1 A:ASN706 4.3 30.2 1.0
C A:THR181 4.3 25.8 1.0
OD1 A:ASP707 4.4 27.2 1.0
OD1 A:ASP351 4.4 22.4 1.0
CA A:GLY182 4.4 23.1 1.0
MG A:MG997 4.6 25.5 1.0
O A:HOH2098 4.7 20.8 1.0
N A:THR625 4.7 22.2 1.0
N A:GLY182 4.7 24.8 1.0
CB A:ASP351 4.8 22.1 1.0
C A:ILE624 4.8 26.1 1.0
O A:THR625 4.9 24.7 1.0
N A:LYS352 5.0 26.8 1.0

Fluorine binding site 2 out of 16 in 1wpg

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Fluorine binding site 2 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:32.7
occ:1.00
F2 A:MF4998 0.0 32.7 1.0
MG A:MF4998 1.8 31.2 1.0
OE1 A:GLU183 2.7 38.3 1.0
O A:THR181 2.8 24.8 1.0
F1 A:MF4998 2.9 26.7 1.0
F4 A:MF4998 2.9 22.3 1.0
F3 A:MF4998 2.9 25.4 1.0
OG1 A:THR625 3.1 24.6 1.0
N A:GLY626 3.4 22.9 1.0
CD A:GLU183 3.4 35.8 1.0
N A:ASP627 3.6 23.7 1.0
OG1 A:THR353 3.6 31.9 1.0
CG A:GLU183 3.7 28.5 1.0
C A:GLY182 3.8 25.5 1.0
CB A:THR353 3.9 27.7 1.0
CA A:GLY182 3.9 23.1 1.0
C A:THR181 3.9 25.8 1.0
CA A:GLY626 3.9 25.1 1.0
N A:GLU183 4.0 25.2 1.0
C A:GLY626 4.0 22.0 1.0
O A:GLY182 4.2 21.5 1.0
CB A:ASP627 4.3 25.5 1.0
OD2 A:ASP351 4.3 22.8 1.0
CB A:THR625 4.4 21.9 1.0
N A:GLY182 4.4 24.8 1.0
CA A:ASP627 4.4 25.0 1.0
C A:THR625 4.4 21.4 1.0
OE2 A:GLU183 4.5 29.1 1.0
CA A:THR625 4.6 22.6 1.0
N A:THR353 4.6 28.1 1.0
CA A:GLU183 4.7 28.3 1.0
CB A:GLU183 4.8 26.1 1.0
MG A:MG997 4.8 25.5 1.0
CA A:THR353 4.9 28.1 1.0
ND2 A:ASN706 4.9 22.5 1.0
CG2 A:THR353 4.9 28.4 1.0

Fluorine binding site 3 out of 16 in 1wpg

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Fluorine binding site 3 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:25.4
occ:1.00
F3 A:MF4998 0.0 25.4 1.0
MG A:MF4998 1.8 31.2 1.0
OG1 A:THR625 2.5 24.6 1.0
OD2 A:ASP351 2.5 22.8 1.0
N A:LYS352 2.7 26.8 1.0
F4 A:MF4998 2.9 22.3 1.0
F2 A:MF4998 2.9 32.7 1.0
F1 A:MF4998 2.9 26.7 1.0
N A:THR353 2.9 28.1 1.0
CB A:THR625 3.0 21.9 1.0
CB A:LYS352 3.2 24.6 1.0
CA A:LYS352 3.3 27.5 1.0
CG A:ASP351 3.4 26.2 1.0
CA A:THR625 3.5 22.6 1.0
C A:LYS352 3.5 28.5 1.0
C A:ASP351 3.9 27.8 1.0
OD1 A:ASP351 3.9 22.4 1.0
OG1 A:THR353 3.9 31.9 1.0
CB A:THR353 4.0 27.7 1.0
CA A:THR353 4.0 28.1 1.0
N A:GLY626 4.1 22.9 1.0
CA A:ASP351 4.2 26.2 1.0
O A:ILE624 4.2 25.2 1.0
CG A:LYS352 4.3 25.9 1.0
C A:THR625 4.3 21.4 1.0
CB A:ASP351 4.4 22.1 1.0
MG A:MG997 4.4 25.5 1.0
CG2 A:THR625 4.5 15.3 1.0
OE1 A:GLU183 4.5 38.3 1.0
N A:THR625 4.6 22.2 1.0
O A:THR353 4.6 25.9 1.0
NZ A:LYS684 4.6 22.7 1.0
O A:LYS352 4.7 29.5 1.0
NZ A:LYS352 4.8 23.1 1.0
C A:THR353 4.8 28.8 1.0
C A:ILE624 4.8 26.1 1.0
O A:ASP351 4.9 26.0 1.0
N A:ASP627 5.0 23.7 1.0

Fluorine binding site 4 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 4 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:22.3
occ:1.00
F4 A:MF4998 0.0 22.3 1.0
MG A:MF4998 1.8 31.2 1.0
MG A:MG997 2.0 25.5 1.0
OD2 A:ASP351 2.6 22.8 1.0
O A:HOH2105 2.8 30.1 1.0
OD1 A:ASP351 2.9 22.4 1.0
F3 A:MF4998 2.9 25.4 1.0
F2 A:MF4998 2.9 32.7 1.0
F1 A:MF4998 2.9 26.7 1.0
O A:HOH2100 3.0 25.3 1.0
CG A:ASP351 3.1 26.2 1.0
O A:THR353 3.1 25.9 1.0
CB A:THR353 3.4 27.7 1.0
CA A:GLY182 3.7 23.1 1.0
N A:THR353 3.8 28.1 1.0
O A:GLY182 3.8 21.5 1.0
CA A:THR353 3.8 28.1 1.0
C A:THR353 3.9 28.8 1.0
OD1 A:ASP703 4.0 27.5 1.0
C A:GLY182 4.0 25.5 1.0
OG1 A:THR353 4.2 31.9 1.0
O A:THR181 4.3 24.8 1.0
CG2 A:THR353 4.4 28.4 1.0
OD1 A:ASN706 4.5 30.2 1.0
CB A:ASP351 4.6 22.1 1.0
N A:LYS352 4.6 26.8 1.0
ND2 A:ASN706 4.6 22.5 1.0
C A:LYS352 4.6 28.5 1.0
N A:GLY182 4.8 24.8 1.0
OE1 A:GLU183 4.8 38.3 1.0
NZ A:LYS684 4.8 22.7 1.0
OD2 A:ASP707 4.9 27.8 1.0
OG1 A:THR625 4.9 24.6 1.0
C A:THR181 5.0 25.8 1.0
N A:GLU183 5.0 25.2 1.0

Fluorine binding site 5 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 5 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:20.7
occ:1.00
F1 B:MF41098 0.0 20.7 1.0
MG B:MF41098 1.8 27.1 1.0
OD2 B:ASP351 2.5 16.8 1.0
OG1 B:THR625 2.6 21.4 1.0
N B:THR353 2.8 18.9 1.0
N B:LYS352 2.8 17.6 1.0
F2 B:MF41098 2.9 23.8 1.0
F4 B:MF41098 2.9 22.4 1.0
F3 B:MF41098 2.9 25.7 1.0
CB B:THR625 3.2 22.1 1.0
CB B:LYS352 3.2 15.5 1.0
CA B:LYS352 3.3 18.3 1.0
CG B:ASP351 3.4 16.6 1.0
C B:LYS352 3.5 20.3 1.0
CA B:THR625 3.6 22.3 1.0
OG1 B:THR353 3.7 22.4 1.0
CB B:THR353 3.8 20.1 1.0
CA B:THR353 3.8 20.9 1.0
C B:ASP351 3.9 21.0 1.0
OD1 B:ASP351 4.0 14.0 1.0
N B:GLY626 4.1 23.2 1.0
CG B:LYS352 4.2 20.6 1.0
CA B:ASP351 4.3 21.0 1.0
O B:ILE624 4.3 24.1 1.0
OE1 B:GLU183 4.4 23.7 1.0
C B:THR625 4.4 20.5 1.0
MG B:MG997 4.4 22.6 1.0
CB B:ASP351 4.5 18.8 1.0
NZ B:LYS352 4.6 27.9 1.0
CG2 B:THR625 4.6 16.4 1.0
O B:THR353 4.6 25.4 1.0
O B:LYS352 4.7 17.1 1.0
NZ B:LYS684 4.7 17.4 1.0
C B:THR353 4.7 21.9 1.0
N B:THR625 4.7 24.3 1.0
CD B:LYS352 4.7 27.2 1.0
N B:ASP627 4.9 20.5 1.0
C B:ILE624 4.9 25.6 1.0
O B:ASP351 5.0 18.8 1.0

Fluorine binding site 6 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 6 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:23.8
occ:1.00
F2 B:MF41098 0.0 23.8 1.0
MG B:MF41098 1.7 27.1 1.0
OD2 B:ASP351 2.5 16.8 1.0
NZ B:LYS684 2.8 17.4 1.0
F3 B:MF41098 2.9 25.7 1.0
F1 B:MF41098 2.9 20.7 1.0
F4 B:MF41098 2.9 22.4 1.0
ND2 B:ASN706 3.0 18.3 1.0
N B:GLY626 3.1 23.2 1.0
O B:THR181 3.6 17.4 1.0
CG B:ASP351 3.6 16.6 1.0
CE B:LYS684 3.7 21.4 1.0
CA B:THR625 3.7 22.3 1.0
O B:HOH3105 3.9 20.1 1.0
C B:THR625 3.9 20.5 1.0
OG1 B:THR625 4.0 21.4 1.0
CG B:ASN706 4.0 23.1 1.0
CA B:GLY626 4.1 17.3 1.0
O B:ILE624 4.1 24.1 1.0
OD1 B:ASN706 4.2 25.9 1.0
C B:THR181 4.4 18.9 1.0
OD1 B:ASP351 4.4 14.0 1.0
CB B:THR625 4.4 22.1 1.0
CA B:GLY182 4.4 21.5 1.0
OD1 B:ASP707 4.4 25.0 1.0
MG B:MG997 4.5 22.6 1.0
CB B:ASP351 4.6 18.8 1.0
N B:GLY182 4.8 20.1 1.0
O B:HOH3098 4.8 22.3 1.0
N B:THR625 4.8 24.3 1.0
N B:LYS352 4.8 17.6 1.0
C B:ILE624 4.9 25.6 1.0
CA B:ASP351 4.9 21.0 1.0

Fluorine binding site 7 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 7 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:25.7
occ:1.00
F3 B:MF41098 0.0 25.7 1.0
MG B:MF41098 1.8 27.1 1.0
OE1 B:GLU183 2.6 23.7 1.0
O B:THR181 2.6 17.4 1.0
F2 B:MF41098 2.9 23.8 1.0
F1 B:MF41098 2.9 20.7 1.0
F4 B:MF41098 2.9 22.4 1.0
OG1 B:THR625 3.4 21.4 1.0
CD B:GLU183 3.4 27.7 1.0
N B:GLY626 3.5 23.2 1.0
N B:ASP627 3.6 20.5 1.0
OG1 B:THR353 3.7 22.4 1.0
CA B:GLY182 3.7 21.5 1.0
CG B:GLU183 3.7 22.3 1.0
C B:THR181 3.7 18.9 1.0
C B:GLY182 3.8 24.8 1.0
CA B:GLY626 3.9 17.3 1.0
CB B:THR353 3.9 20.1 1.0
N B:GLU183 3.9 22.8 1.0
C B:GLY626 4.0 17.5 1.0
N B:GLY182 4.2 20.1 1.0
OD2 B:ASP351 4.2 16.8 1.0
O B:GLY182 4.3 25.1 1.0
CB B:ASP627 4.4 20.7 1.0
CA B:ASP627 4.5 20.1 1.0
C B:THR625 4.5 20.5 1.0
OE2 B:GLU183 4.5 28.6 1.0
CB B:THR625 4.6 22.1 1.0
N B:THR353 4.6 18.9 1.0
CA B:GLU183 4.6 26.4 1.0
CA B:THR625 4.7 22.3 1.0
ND2 B:ASN706 4.7 18.3 1.0
CB B:GLU183 4.8 22.1 1.0
CA B:THR353 4.9 20.9 1.0
CG2 B:THR353 4.9 16.4 1.0
MG B:MG997 4.9 22.6 1.0
O B:GLY626 4.9 19.9 1.0

Fluorine binding site 8 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 8 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1098

b:22.4
occ:1.00
F4 B:MF41098 0.0 22.4 1.0
MG B:MF41098 1.8 27.1 1.0
MG B:MG997 2.0 22.6 1.0
OD2 B:ASP351 2.5 16.8 1.0
O B:HOH3105 2.7 20.1 1.0
O B:HOH3100 2.9 22.0 1.0
OD1 B:ASP351 2.9 14.0 1.0
F2 B:MF41098 2.9 23.8 1.0
F1 B:MF41098 2.9 20.7 1.0
F3 B:MF41098 2.9 25.7 1.0
CG B:ASP351 3.1 16.6 1.0
O B:THR353 3.1 25.4 1.0
CB B:THR353 3.4 20.1 1.0
CA B:GLY182 3.6 21.5 1.0
N B:THR353 3.7 18.9 1.0
CA B:THR353 3.8 20.9 1.0
C B:THR353 3.8 21.9 1.0
O B:GLY182 3.8 25.1 1.0
C B:GLY182 3.9 24.8 1.0
OD1 B:ASP703 4.1 29.1 1.0
OG1 B:THR353 4.2 22.4 1.0
O B:THR181 4.4 17.4 1.0
CG2 B:THR353 4.4 16.4 1.0
OD1 B:ASN706 4.5 25.9 1.0
CB B:ASP351 4.6 18.8 1.0
N B:LYS352 4.6 17.6 1.0
C B:LYS352 4.6 20.3 1.0
ND2 B:ASN706 4.7 18.3 1.0
OE1 B:GLU183 4.7 23.7 1.0
N B:GLY182 4.7 20.1 1.0
N B:GLU183 4.9 22.8 1.0
OD2 B:ASP707 4.9 22.8 1.0
C B:THR181 5.0 18.9 1.0

Fluorine binding site 9 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 9 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1198

b:20.6
occ:1.00
F1 C:MF41198 0.0 20.6 1.0
MG C:MF41198 1.8 27.7 1.0
OD2 C:ASP351 2.5 15.5 1.0
OG1 C:THR625 2.6 22.3 1.0
N C:THR353 2.7 20.4 1.0
N C:LYS352 2.8 19.1 1.0
F2 C:MF41198 2.9 24.7 1.0
F4 C:MF41198 2.9 22.3 1.0
F3 C:MF41198 2.9 25.4 1.0
CB C:THR625 3.2 23.7 1.0
CB C:LYS352 3.3 17.6 1.0
CA C:LYS352 3.3 19.1 1.0
CG C:ASP351 3.4 17.9 1.0
C C:LYS352 3.5 21.0 1.0
CA C:THR625 3.6 23.1 1.0
OG1 C:THR353 3.7 22.5 1.0
CB C:THR353 3.8 20.8 1.0
CA C:THR353 3.8 21.6 1.0
C C:ASP351 4.0 22.0 1.0
OD1 C:ASP351 4.0 16.3 1.0
N C:GLY626 4.0 22.6 1.0
CG C:LYS352 4.2 21.1 1.0
CA C:ASP351 4.3 21.6 1.0
OE1 C:GLU183 4.3 23.2 1.0
C C:THR625 4.4 21.7 1.0
O C:ILE624 4.4 24.1 1.0
MG C:MG997 4.5 21.1 1.0
CB C:ASP351 4.5 19.9 1.0
NZ C:LYS352 4.6 28.3 1.0
O C:THR353 4.6 24.7 1.0
CG2 C:THR625 4.6 19.2 1.0
O C:LYS352 4.6 18.3 1.0
CD C:LYS352 4.7 28.1 1.0
C C:THR353 4.7 22.6 1.0
N C:THR625 4.7 24.0 1.0
NZ C:LYS684 4.7 20.3 1.0
N C:ASP627 4.9 21.3 1.0
C C:ILE624 4.9 25.3 1.0

Fluorine binding site 10 out of 16 in 1wpg

Go back to Fluorine Binding Sites List in 1wpg
Fluorine binding site 10 out of 16 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1198

b:24.7
occ:1.00
F2 C:MF41198 0.0 24.7 1.0
MG C:MF41198 1.7 27.7 1.0
OD2 C:ASP351 2.4 15.5 1.0
NZ C:LYS684 2.8 20.3 1.0
F3 C:MF41198 2.9 25.4 1.0
F4 C:MF41198 2.9 22.3 1.0
F1 C:MF41198 2.9 20.6 1.0
ND2 C:ASN706 3.0 18.5 1.0
N C:GLY626 3.1 22.6 1.0
O C:THR181 3.6 14.7 1.0
CG C:ASP351 3.6 17.9 1.0
CE C:LYS684 3.7 23.6 1.0
CA C:THR625 3.8 23.1 1.0
O C:HOH4105 3.9 18.7 1.0
C C:THR625 3.9 21.7 1.0
CG C:ASN706 4.0 23.2 1.0
OG1 C:THR625 4.0 22.3 1.0
CA C:GLY626 4.1 18.8 1.0
O C:ILE624 4.1 24.1 1.0
OD1 C:ASN706 4.2 24.2 1.0
OD1 C:ASP351 4.4 16.3 1.0
C C:THR181 4.4 17.4 1.0
CA C:GLY182 4.4 22.1 1.0
CB C:THR625 4.4 23.7 1.0
OD1 C:ASP707 4.4 24.6 1.0
MG C:MG997 4.6 21.1 1.0
CB C:ASP351 4.6 19.9 1.0
N C:GLY182 4.8 20.3 1.0
N C:THR625 4.8 24.0 1.0
O C:HOH4098 4.8 22.4 1.0
N C:LYS352 4.8 19.1 1.0
C C:ILE624 4.9 25.3 1.0
CA C:ASP351 4.9 21.6 1.0

Reference:

C.Toyoshima, H.Nomura, T.Tsuda. Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Nature V. 432 361 2004.
ISSN: ISSN 0028-0836
PubMed: 15448704
DOI: 10.1038/NATURE02981
Page generated: Sun Dec 13 11:33:49 2020

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Zn in 7M4N
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