Magnesium in PDB 6lkn: 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;

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

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

Fluorine

(F)

12 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State, PDB code: 6lkn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1202 b:0.4 occ:1.00 O A:HOH1301 2.2 0.5 1.0 O A:HOH1302 2.2 0.6 1.0 OD2 A:BFD409 2.7 70.6 1.0 OD1 A:ASP820 2.9 0.8 1.0 OD1 A:ASP816 3.0 89.8 1.0 F3 A:BFD409 3.3 84.6 1.0 N A:GLY817 3.5 0.2 1.0 CG A:ASP816 3.6 91.8 1.0 N A:ASP820 3.6 96.7 1.0 CG A:ASP820 3.7 0.5 1.0 CB A:ASN819 3.7 89.0 1.0 N A:ASP816 3.8 0.8 1.0 CG A:BFD409 3.9 75.0 1.0 OD2 A:ASP816 3.9 91.7 1.0 CB A:ASP820 3.9 93.1 1.0 F2 A:BFD409 4.0 78.7 1.0 N A:ASN819 4.2 87.2 1.0 O A:GLY817 4.2 0.5 1.0 CA A:GLY817 4.3 0.4 1.0 CA A:ASN819 4.3 90.8 1.0 C A:GLY817 4.4 0.0 1.0 CA A:ASP820 4.4 95.1 1.0 C A:ASN819 4.4 0.1 1.0 BE A:BFD409 4.4 83.3 1.0 C A:ASP816 4.4 0.5 1.0 CA A:ASP816 4.4 0.6 1.0 CA A:GLY815 4.5 0.9 1.0 C A:GLY815 4.6 0.3 1.0 CG A:ASN819 4.6 98.8 1.0 CB A:ASP816 4.6 95.3 1.0 ND2 A:ASN819 4.6 99.8 1.0 OD2 A:ASP820 4.7 0.4 1.0 CB A:BFD409 4.7 84.4 1.0 OD1 A:BFD409 4.7 74.4 1.0 O A:THR411 4.8 65.4 1.0 O A:SER177 4.8 1.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 E:Mg1203 b:91.2 occ:1.00 O E:HOH1302 2.2 79.9 1.0 O E:HOH1301 2.2 84.2 1.0 F3 E:BFD409 2.9 80.9 1.0 OD1 E:ASP816 3.0 92.9 1.0 OD2 E:BFD409 3.0 88.1 1.0 N E:GLY817 3.0 86.0 1.0 CA E:GLY817 3.5 93.7 1.0 CG E:ASP816 3.6 96.1 1.0 OD1 E:BFD409 3.6 73.8 1.0 CG E:BFD409 3.6 79.8 1.0 CB E:ASN819 3.8 1.0 1.0 OD2 E:ASP816 3.8 92.9 1.0 BE E:BFD409 3.8 78.5 1.0 F2 E:BFD409 3.9 74.8 1.0 N E:ASP816 4.0 0.7 1.0 C E:GLY817 4.0 0.4 1.0 O E:GLY817 4.1 0.4 1.0 OD1 E:ASN819 4.1 0.4 1.0 C E:ASP816 4.1 88.6 1.0 O E:ALA176 4.1 79.8 1.0 O E:SER177 4.4 88.7 1.0 CA E:ASP816 4.4 99.2 1.0 CG E:ASN819 4.4 0.4 1.0 N E:ASN819 4.6 90.6 1.0 CB E:ASP816 4.6 98.8 1.0 OG1 E:THR411 4.7 0.7 1.0 CA E:ASN819 4.8 98.5 1.0 C E:GLY815 4.8 0.2 1.0 N E:ASP820 4.9 95.1 1.0 C E:SER177 4.9 93.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of ATP11C-CDC50A in Ptdser-Bound E2P State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 I:Mg1203 b:0.7 occ:1.00 O I:HOH1302 2.2 0.8 1.0 O I:HOH1301 2.2 0.9 1.0 O I:THR411 2.8 0.9 1.0 F3 I:BFD409 2.9 0.5 1.0 OD1 I:ASP816 2.9 0.4 1.0 CB I:BFD409 3.2 1.0 1.0 CG2 I:THR413 3.3 0.1 1.0 OG1 I:THR413 3.3 0.5 1.0 CG I:BFD409 3.5 0.6 1.0 C I:THR411 3.6 0.8 1.0 OD1 I:BFD409 3.7 0.3 1.0 N I:ASP816 3.8 0.7 1.0 N I:THR413 3.8 1.0 1.0 CB I:THR413 3.9 0.8 1.0 CG I:ASP816 4.0 0.6 1.0 BE I:BFD409 4.1 0.3 1.0 N I:LYS410 4.1 0.4 1.0 N I:THR411 4.1 0.3 1.0 OD2 I:ASP820 4.1 0.9 1.0 C I:BFD409 4.2 0.3 1.0 OD2 I:BFD409 4.2 0.6 1.0 C I:LYS410 4.2 0.2 1.0 CA I:BFD409 4.3 0.6 1.0 N I:GLY817 4.4 0.9 1.0 CA I:GLY815 4.4 0.9 1.0 N I:GLY412 4.4 0.2 1.0 CA I:THR411 4.4 0.8 1.0 CA I:THR413 4.5 0.0 1.0 C I:GLY412 4.5 0.0 1.0 CA I:GLY412 4.6 0.6 1.0 F2 I:BFD409 4.6 0.2 1.0 O I:LYS410 4.6 0.7 1.0 OG1 I:THR411 4.6 0.5 1.0 CB I:ASP816 4.6 0.4 1.0 C I:GLY815 4.6 0.4 1.0 CA I:ASP816 4.7 0.2 1.0 CA I:LYS410 4.7 0.3 1.0 O I:BFD409 4.8 0.9 1.0 CG I:ASP820 4.9 0.7 1.0 OD2 I:ASP816 5.0 0.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 M:Mg1202 b:0.6 occ:1.00 O M:HOH1302 2.2 0.5 1.0 O M:HOH1301 2.2 0.1 1.0 OD2 M:ASP816 2.8 0.5 1.0 F3 M:BFD409 2.9 0.1 1.0 OG1 M:THR413 3.0 0.8 1.0 O M:THR411 3.1 1.0 1.0 CG M:BFD409 3.1 0.7 1.0 OD2 M:ASP820 3.3 0.5 1.0 CB M:BFD409 3.3 1.0 1.0 OD1 M:BFD409 3.4 0.7 1.0 CG M:ASP816 3.5 0.1 1.0 OD2 M:BFD409 3.5 0.2 1.0 OD1 M:ASP816 3.7 0.9 1.0 BE M:BFD409 3.8 0.8 1.0 F2 M:BFD409 3.9 0.3 1.0 N M:ASP816 4.0 0.9 1.0 N M:THR413 4.1 1.0 1.0 CB M:THR413 4.2 0.4 1.0 C M:THR411 4.3 0.7 1.0 CG M:ASP820 4.4 0.7 1.0 NH1 M:ARG237 4.4 0.2 1.0 N M:GLY817 4.5 0.6 1.0 CB M:ASP816 4.6 0.2 1.0 CA M:GLY815 4.7 0.5 1.0 CA M:ASP816 4.8 0.1 1.0 CA M:THR413 4.8 0.6 1.0 CA M:BFD409 4.8 0.2 1.0 C M:GLY815 4.8 0.1 1.0 OD1 M:ASP820 4.9 0.1 1.0 CA M:GLY412 5.0 0.7 1.0

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