Fluorine in PDB 6lkn: Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State

Enzymatic activity of Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State

All present enzymatic activity of Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State:
7.6.2.1;

Protein crystallography data

The structure of Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State, PDB code: 6lkn was solved by K.Abe, K.Irie, K.Hasegawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.97 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.460, 232.830, 492.890, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 35

Other elements in 6lkn:

The structure of Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State (pdb code 6lkn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State, PDB code: 6lkn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6lkn

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Fluorine binding site 1 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:0.3
occ:1.00
F1 A:BFD409 0.0 0.3 1.0
BE A:BFD409 1.8 83.3 1.0
OG1 A:THR674 2.4 77.2 1.0
OG1 A:THR411 2.5 68.0 1.0
F3 A:BFD409 2.6 84.6 1.0
OD1 A:BFD409 3.0 74.4 1.0
F2 A:BFD409 3.0 78.7 1.0
N A:GLY675 3.4 94.2 1.0
N A:ASP676 3.4 0.1 1.0
N A:THR411 3.5 83.2 1.0
O A:GLY180 3.6 0.9 1.0
CB A:ASP676 3.6 0.2 1.0
CB A:THR411 3.7 68.4 1.0
C A:GLY675 3.7 0.6 1.0
CB A:THR674 3.8 78.2 1.0
CA A:GLY675 3.9 1.0 1.0
O A:THR411 4.0 65.4 1.0
CA A:THR411 4.0 70.4 1.0
CA A:ASP676 4.1 0.6 1.0
CG2 A:THR411 4.1 62.8 1.0
CG A:BFD409 4.2 75.0 1.0
CA A:GLY180 4.2 0.5 1.0
CB A:LYS410 4.2 0.3 1.0
OD2 A:BFD409 4.3 70.6 1.0
C A:GLY180 4.4 0.8 1.0
C A:THR674 4.4 84.2 1.0
N A:LYS410 4.4 96.6 1.0
CA A:THR674 4.4 82.0 1.0
O A:GLY675 4.4 99.2 1.0
C A:LYS410 4.5 95.5 1.0
C A:THR411 4.5 69.5 1.0
CG2 A:THR674 4.5 74.8 1.0
CA A:LYS410 4.6 97.0 1.0
O A:HOH1302 4.6 0.6 1.0
CG A:ASP676 4.8 0.1 1.0

Fluorine binding site 2 out of 12 in 6lkn

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Fluorine binding site 2 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:78.7
occ:1.00
F2 A:BFD409 0.0 78.7 1.0
BE A:BFD409 1.8 83.3 1.0
F3 A:BFD409 2.6 84.6 1.0
N A:GLY675 2.8 94.2 1.0
OD1 A:BFD409 3.0 74.4 1.0
OD1 A:ASP820 3.0 0.8 1.0
F1 A:BFD409 3.0 0.3 1.0
OD2 A:BFD409 3.1 70.6 1.0
OG1 A:THR674 3.2 77.2 1.0
CG A:BFD409 3.4 75.0 1.0
CA A:THR674 3.5 82.0 1.0
C A:THR674 3.5 84.2 1.0
ND2 A:ASN819 3.6 99.8 1.0
CA A:GLY675 3.6 1.0 1.0
CG A:ASP820 3.9 0.5 1.0
CB A:THR674 3.9 78.2 1.0
MG A:MG1202 4.0 0.4 1.0
O A:HOH1302 4.0 0.6 1.0
OD2 A:ASP820 4.0 0.4 1.0
CG A:ASN819 4.0 98.8 1.0
C A:GLY675 4.5 0.6 1.0
CB A:ASN819 4.5 89.0 1.0
O A:LEU673 4.5 85.0 1.0
OD1 A:ASN819 4.6 0.3 1.0
O A:THR674 4.6 75.9 1.0
CB A:BFD409 4.7 84.4 1.0
N A:THR674 4.8 91.2 1.0
O A:ASP179 4.8 72.3 1.0
N A:ASP676 4.9 0.1 1.0
CA A:GLY180 5.0 0.5 1.0

Fluorine binding site 3 out of 12 in 6lkn

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Fluorine binding site 3 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:84.6
occ:1.00
F3 A:BFD409 0.0 84.6 1.0
BE A:BFD409 1.8 83.3 1.0
OD2 A:BFD409 2.3 70.6 1.0
O A:HOH1302 2.3 0.6 1.0
OD1 A:BFD409 2.6 74.4 1.0
F1 A:BFD409 2.6 0.3 1.0
F2 A:BFD409 2.6 78.7 1.0
O A:THR411 2.7 65.4 1.0
CG A:BFD409 2.8 75.0 1.0
OG1 A:THR411 3.3 68.0 1.0
OD1 A:ASP816 3.3 89.8 1.0
MG A:MG1202 3.3 0.4 1.0
C A:THR411 3.7 69.5 1.0
OG1 A:THR674 4.0 77.2 1.0
N A:THR411 4.0 83.2 1.0
CG A:ASP816 4.1 91.8 1.0
OD2 A:ASP816 4.2 91.7 1.0
CA A:THR411 4.2 70.4 1.0
CB A:BFD409 4.3 84.4 1.0
CB A:THR411 4.3 68.4 1.0
OD1 A:ASP820 4.4 0.8 1.0
CA A:GLY180 4.4 0.5 1.0
O A:ALA176 4.6 89.5 1.0
N A:LYS410 4.6 96.6 1.0
N A:GLY675 4.8 94.2 1.0
C A:LYS410 4.8 95.5 1.0
N A:GLY412 4.9 68.6 1.0
O A:HOH1301 5.0 0.5 1.0

Fluorine binding site 4 out of 12 in 6lkn

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Fluorine binding site 4 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:87.5
occ:1.00
F1 E:BFD409 0.0 87.5 1.0
BE E:BFD409 1.8 78.5 1.0
N E:THR411 2.4 0.7 1.0
OG1 E:THR411 2.5 0.7 1.0
F3 E:BFD409 2.6 80.9 1.0
OG1 E:THR674 2.8 0.6 1.0
OD1 E:BFD409 3.0 73.8 1.0
F2 E:BFD409 3.1 74.8 1.0
CB E:LYS410 3.1 92.2 1.0
CB E:THR411 3.1 0.7 1.0
N E:LYS410 3.2 89.3 1.0
C E:LYS410 3.3 0.4 1.0
CG2 E:THR411 3.3 95.4 1.0
CA E:LYS410 3.3 92.3 1.0
CA E:THR411 3.3 0.1 1.0
CB E:THR674 3.7 93.9 1.0
CD E:LYS410 3.8 0.6 1.0
CG E:LYS410 3.8 98.4 1.0
O E:HOH1301 4.0 84.2 1.0
O E:HOH1302 4.1 79.9 1.0
CG E:BFD409 4.2 79.8 1.0
O E:LYS410 4.4 0.9 1.0
C E:THR411 4.4 1.0 1.0
CG2 E:THR674 4.5 80.3 1.0
C E:BFD409 4.5 86.4 1.0
N E:GLY412 4.5 0.4 1.0
OD1 E:ASP676 4.6 0.0 1.0
OD2 E:BFD409 4.9 88.1 1.0
CA E:THR674 4.9 99.6 1.0
CE E:LYS410 4.9 0.5 1.0
NZ E:LYS410 5.0 0.6 1.0

Fluorine binding site 5 out of 12 in 6lkn

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Fluorine binding site 5 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:74.8
occ:1.00
F2 E:BFD409 0.0 74.8 1.0
BE E:BFD409 1.8 78.5 1.0
O E:HOH1302 2.0 79.9 1.0
F3 E:BFD409 2.6 80.9 1.0
OD1 E:ASN819 2.8 0.4 1.0
OG1 E:THR674 2.8 0.6 1.0
OD1 E:BFD409 3.0 73.8 1.0
OD2 E:BFD409 3.1 88.1 1.0
F1 E:BFD409 3.1 87.5 1.0
CG E:BFD409 3.2 79.8 1.0
CB E:THR674 3.4 93.9 1.0
CA E:THR674 3.6 99.6 1.0
CG E:ASN819 3.7 0.4 1.0
NH1 E:ARG237 3.8 0.9 1.0
MG E:MG1203 3.9 91.2 1.0
O E:HOH1301 4.0 84.2 1.0
O E:LEU673 4.1 81.8 1.0
N E:LYS410 4.2 89.3 1.0
CB E:ASN819 4.5 1.0 1.0
CB E:BFD409 4.5 72.1 1.0
OG1 E:THR411 4.5 0.7 1.0
ND2 E:ASN819 4.5 0.1 1.0
CA E:BFD409 4.5 69.4 1.0
N E:GLY675 4.6 0.1 1.0
C E:THR674 4.6 0.8 1.0
N E:THR674 4.6 96.3 1.0
C E:LEU673 4.8 87.4 1.0
CG2 E:THR674 4.8 80.3 1.0
C E:BFD409 4.9 86.4 1.0
CZ E:ARG237 5.0 0.8 1.0

Fluorine binding site 6 out of 12 in 6lkn

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Fluorine binding site 6 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:80.9
occ:1.00
F3 E:BFD409 0.0 80.9 1.0
BE E:BFD409 1.8 78.5 1.0
O E:HOH1301 2.1 84.2 1.0
O E:HOH1302 2.1 79.9 1.0
OG1 E:THR411 2.3 0.7 1.0
F1 E:BFD409 2.6 87.5 1.0
F2 E:BFD409 2.6 74.8 1.0
OD1 E:BFD409 2.6 73.8 1.0
MG E:MG1203 2.9 91.2 1.0
CG E:BFD409 3.7 79.8 1.0
CB E:THR411 3.7 0.7 1.0
OD2 E:BFD409 3.7 88.1 1.0
N E:THR411 3.9 0.7 1.0
CA E:GLY180 4.1 0.5 1.0
OG1 E:THR674 4.2 0.6 1.0
OD1 E:ASP816 4.2 92.9 1.0
N E:GLY412 4.2 0.4 1.0
N E:GLY180 4.3 0.5 1.0
CA E:THR411 4.3 0.1 1.0
CG2 E:THR411 4.4 95.4 1.0
O E:ALA176 4.4 79.8 1.0
OD1 E:ASN819 4.5 0.4 1.0
N E:LYS410 4.7 89.3 1.0
C E:THR411 4.8 1.0 1.0
NH1 E:ARG237 4.8 0.9 1.0

Fluorine binding site 7 out of 12 in 6lkn

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Fluorine binding site 7 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F409

b:0.7
occ:1.00
F1 I:BFD409 0.0 0.7 1.0
BE I:BFD409 1.8 0.3 1.0
OG1 I:THR674 2.2 0.5 1.0
F3 I:BFD409 2.6 0.5 1.0
N I:GLY675 3.0 0.1 1.0
OG1 I:THR411 3.0 0.5 1.0
OD1 I:BFD409 3.0 0.3 1.0
F2 I:BFD409 3.0 0.2 1.0
CB I:THR674 3.2 0.9 1.0
CA I:THR674 3.2 0.8 1.0
C I:THR674 3.5 0.7 1.0
O I:ASP179 4.0 0.9 1.0
NH1 I:ARG237 4.0 0.4 1.0
CA I:GLY675 4.1 0.2 1.0
N I:THR411 4.2 0.3 1.0
N I:ASP676 4.3 0.6 1.0
CB I:THR411 4.3 0.2 1.0
CG I:BFD409 4.4 0.6 1.0
CG2 I:THR674 4.4 0.5 1.0
CA I:GLY180 4.5 0.3 1.0
N I:THR674 4.6 0.7 1.0
N I:LYS410 4.6 0.4 1.0
CB I:LYS410 4.6 0.8 1.0
C I:GLY675 4.6 0.8 1.0
O I:THR674 4.7 0.7 1.0
C I:ASP179 4.8 0.1 1.0
CG2 I:THR411 4.8 0.7 1.0
OD2 I:BFD409 4.8 0.6 1.0
CA I:THR411 4.9 0.8 1.0
O I:HOH1301 4.9 0.9 1.0
O I:LEU673 4.9 0.9 1.0
CA I:LYS410 5.0 0.3 1.0

Fluorine binding site 8 out of 12 in 6lkn

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Fluorine binding site 8 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F409

b:0.2
occ:1.00
F2 I:BFD409 0.0 0.2 1.0
BE I:BFD409 1.8 0.3 1.0
F3 I:BFD409 2.6 0.5 1.0
OD1 I:BFD409 3.0 0.3 1.0
F1 I:BFD409 3.0 0.7 1.0
OD2 I:ASP820 3.1 0.9 1.0
OD2 I:BFD409 3.1 0.6 1.0
CG I:BFD409 3.4 0.6 1.0
OD1 I:ASP820 3.8 0.4 1.0
CG I:ASP820 3.8 0.7 1.0
O I:LEU673 4.0 0.9 1.0
O I:HOH1302 4.1 0.8 1.0
O I:HOH1301 4.2 0.9 1.0
CA I:THR674 4.2 0.8 1.0
C I:THR674 4.4 0.7 1.0
N I:GLY675 4.4 0.1 1.0
O I:ASP179 4.4 0.9 1.0
MG I:MG1203 4.6 0.7 1.0
C I:ASP179 4.7 0.1 1.0
CB I:BFD409 4.7 1.0 1.0
OG1 I:THR411 4.8 0.5 1.0
OG1 I:THR674 4.8 0.5 1.0
C I:LEU673 4.9 1.0 1.0

Fluorine binding site 9 out of 12 in 6lkn

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Fluorine binding site 9 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F409

b:0.5
occ:1.00
F3 I:BFD409 0.0 0.5 1.0
BE I:BFD409 1.8 0.3 1.0
O I:HOH1301 2.4 0.9 1.0
F1 I:BFD409 2.6 0.7 1.0
OG1 I:THR411 2.6 0.5 1.0
OD1 I:BFD409 2.6 0.3 1.0
F2 I:BFD409 2.6 0.2 1.0
MG I:MG1203 2.9 0.7 1.0
O I:THR411 3.2 0.9 1.0
CG I:BFD409 3.4 0.6 1.0
N I:THR411 3.5 0.3 1.0
O I:HOH1302 3.7 0.8 1.0
CB I:THR411 3.8 0.2 1.0
CA I:THR411 3.9 0.8 1.0
C I:THR411 4.0 0.8 1.0
OD2 I:BFD409 4.0 0.6 1.0
N I:LYS410 4.1 0.4 1.0
CB I:BFD409 4.2 1.0 1.0
OD2 I:ASP820 4.2 0.9 1.0
C I:LYS410 4.3 0.2 1.0
OG1 I:THR674 4.4 0.5 1.0
CA I:GLY180 4.5 0.3 1.0
CA I:LYS410 4.6 0.3 1.0
OD1 I:ASP816 4.8 0.4 1.0
C I:BFD409 4.9 0.3 1.0
CA I:THR674 4.9 0.8 1.0
CG2 I:THR411 4.9 0.7 1.0
OD1 I:ASP820 5.0 0.4 1.0
O I:ASP179 5.0 0.9 1.0
N I:GLY180 5.0 0.8 1.0

Fluorine binding site 10 out of 12 in 6lkn

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Fluorine binding site 10 out of 12 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


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 ATP11C-CDC50A in Ptdser-Bound E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:F409

b:0.1
occ:1.00
F1 M:BFD409 0.0 0.1 1.0
BE M:BFD409 1.8 0.8 1.0
N M:GLY675 2.5 0.1 1.0
OG1 M:THR674 2.5 0.2 1.0
F3 M:BFD409 2.6 0.1 1.0
N M:ASP676 2.7 0.2 1.0
OG1 M:THR411 2.8 0.8 1.0
NH1 M:ARG237 2.9 0.2 1.0
NH2 M:ARG237 3.0 0.3 1.0
OD1 M:BFD409 3.0 0.7 1.0
CZ M:ARG237 3.0 0.8 1.0
F2 M:BFD409 3.0 0.3 1.0
CA M:GLY675 3.2 0.0 1.0
C M:GLY675 3.3 0.8 1.0
C M:THR674 3.5 0.1 1.0
CB M:ASP676 3.5 0.1 1.0
CA M:ASP676 3.6 1.0 1.0
CB M:THR674 3.6 0.9 1.0
CA M:THR674 3.6 0.2 1.0
NE M:ARG237 3.9 1.0 1.0
CB M:THR411 4.2 0.3 1.0
N M:THR411 4.3 0.1 1.0
CG M:BFD409 4.3 0.7 1.0
O M:GLY675 4.4 0.5 1.0
CG M:ASP676 4.4 0.2 1.0
OD1 M:ASP676 4.5 0.2 1.0
O M:THR674 4.6 0.0 1.0
OD2 M:BFD409 4.6 0.2 1.0
CG2 M:THR674 4.7 0.4 1.0
CD M:ARG237 4.8 0.7 1.0
O M:GLY180 4.8 1.0 1.0
CA M:THR411 4.8 0.7 1.0
C M:ASP676 4.9 0.7 1.0
CG2 M:THR411 4.9 0.6 1.0
N M:LYS410 4.9 0.3 1.0
O M:HOH1301 5.0 0.1 1.0
O M:THR411 5.0 1.0 1.0

Reference:

H.Nakanishi, K.Irie, K.Segawa, K.Hasegawa, Y.Fujiyoshi, S.Nagata, K.Abe. Crystal Structure of A Human Plasma Membrane Phospholipid Flippase J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Sun Dec 13 12:56:41 2020

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