Calcium in PDB 6qpc: Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc

The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc (pdb code 6qpc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc, PDB code: 6qpc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:65.0 occ:1.00 OE2 A:GLU699 2.5 67.6 1.0 OE1 A:GLU670 2.5 68.7 1.0 OE1 A:GLU699 2.5 67.6 1.0 CD A:GLU699 2.8 67.6 1.0 OD1 A:ASN621 3.0 73.7 1.0 OE2 A:GLU670 3.0 68.7 1.0 CD A:GLU670 3.1 68.7 1.0 OE1 A:GLU624 3.7 73.4 1.0 CB A:ASN620 3.7 70.3 1.0 CG A:ASN621 3.8 73.7 1.0 O A:ALA617 3.9 70.6 1.0 N A:ASN621 4.2 73.7 1.0 ND2 A:ASN621 4.2 73.7 1.0 CG A:ASN620 4.3 70.3 1.0 CG A:GLU699 4.3 67.6 1.0 CA A:ALA617 4.3 70.6 1.0 C A:ASN620 4.4 70.3 1.0 CE A:MET671 4.4 61.4 1.0 CG A:GLU670 4.4 68.7 1.0 CA A:CA1002 4.5 73.7 1.0 O A:LYS616 4.5 71.4 1.0 ND2 A:ASN695 4.5 67.6 1.0 OD1 A:ASN695 4.5 67.6 1.0 CD A:GLU624 4.6 73.4 1.0 C A:ALA617 4.6 70.6 1.0 ND2 A:ASN620 4.6 70.3 1.0 NZ A:LYS616 4.6 71.4 1.0 CA A:ASN620 4.6 70.3 1.0 CA A:ASN621 4.7 73.7 1.0 CB A:ASN621 4.8 73.7 1.0 OE2 A:GLU624 4.9 73.4 1.0 O A:ASN620 4.9 70.3 1.0 OD1 A:ASN620 4.9 70.3 1.0 CG A:ASN695 5.0 67.6 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:73.7 occ:1.00 OE2 A:GLU670 2.5 68.7 1.0 OD1 A:ASP703 2.5 71.8 1.0 OD2 A:ASP703 2.5 71.8 1.0 OE2 A:GLU624 2.5 73.4 1.0 OE2 A:GLU699 2.6 67.6 1.0 CG A:ASP703 2.8 71.8 1.0 OE1 A:GLU667 2.9 71.3 1.0 CD A:GLU624 3.4 73.4 1.0 OE1 A:GLU624 3.5 73.4 1.0 CD A:GLU699 3.5 67.6 1.0 OH A:TYR299 3.6 64.3 1.0 CD A:GLU670 3.6 68.7 1.0 CG A:GLU699 3.8 67.6 1.0 CD A:GLU667 4.0 71.3 1.0 CG A:GLU670 4.2 68.7 1.0 CB A:ASP703 4.3 71.8 1.0 CA A:CA1001 4.5 65.0 1.0 CB A:GLU667 4.5 71.3 1.0 OE1 A:GLU670 4.6 68.7 1.0 CA A:GLU667 4.6 71.3 1.0 OE1 A:GLU699 4.7 67.6 1.0 O A:GLU667 4.8 71.3 1.0 OE2 A:GLU667 4.8 71.3 1.0 CG A:GLU624 4.8 73.4 1.0 O A:GLU699 4.8 67.6 1.0 CZ A:TYR299 4.8 64.3 1.0 CG A:GLU667 4.9 71.3 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:65.0 occ:1.00 OE2 B:GLU699 2.5 67.6 1.0 OE1 B:GLU670 2.5 68.7 1.0 OE1 B:GLU699 2.5 67.6 1.0 CD B:GLU699 2.8 67.6 1.0 OD1 B:ASN621 3.0 73.7 1.0 OE2 B:GLU670 3.0 68.7 1.0 CD B:GLU670 3.1 68.7 1.0 OE1 B:GLU624 3.7 73.4 1.0 CB B:ASN620 3.7 70.3 1.0 CG B:ASN621 3.8 73.7 1.0 O B:ALA617 3.9 70.6 1.0 N B:ASN621 4.2 73.7 1.0 ND2 B:ASN621 4.2 73.7 1.0 CG B:ASN620 4.3 70.3 1.0 CG B:GLU699 4.3 67.6 1.0 CA B:ALA617 4.3 70.6 1.0 C B:ASN620 4.4 70.3 1.0 CE B:MET671 4.4 61.4 1.0 CG B:GLU670 4.4 68.7 1.0 CA B:CA1002 4.5 73.7 1.0 O B:LYS616 4.5 71.4 1.0 ND2 B:ASN695 4.5 67.6 1.0 OD1 B:ASN695 4.5 67.6 1.0 CD B:GLU624 4.6 73.4 1.0 C B:ALA617 4.6 70.6 1.0 ND2 B:ASN620 4.6 70.3 1.0 NZ B:LYS616 4.6 71.4 1.0 CA B:ASN620 4.6 70.3 1.0 CA B:ASN621 4.7 73.7 1.0 CB B:ASN621 4.8 73.7 1.0 OE2 B:GLU624 4.9 73.4 1.0 O B:ASN620 4.9 70.3 1.0 OD1 B:ASN620 4.9 70.3 1.0 CG B:ASN695 5.0 67.6 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:73.7 occ:1.00 OE2 B:GLU670 2.5 68.7 1.0 OD1 B:ASP703 2.5 71.8 1.0 OD2 B:ASP703 2.5 71.8 1.0 OE2 B:GLU624 2.5 73.4 1.0 OE2 B:GLU699 2.6 67.6 1.0 CG B:ASP703 2.8 71.8 1.0 OE1 B:GLU667 2.9 71.3 1.0 CD B:GLU624 3.4 73.4 1.0 OE1 B:GLU624 3.5 73.4 1.0 CD B:GLU699 3.5 67.6 1.0 OH B:TYR299 3.6 64.3 1.0 CD B:GLU670 3.6 68.7 1.0 CG B:GLU699 3.8 67.6 1.0 CD B:GLU667 4.0 71.3 1.0 CG B:GLU670 4.2 68.7 1.0 CB B:ASP703 4.3 71.8 1.0 CA B:CA1001 4.5 65.0 1.0 CB B:GLU667 4.5 71.3 1.0 OE1 B:GLU670 4.6 68.7 1.0 CA B:GLU667 4.6 71.3 1.0 OE1 B:GLU699 4.7 67.6 1.0 O B:GLU667 4.8 71.3 1.0 OE2 B:GLU667 4.8 71.3 1.0 CG B:GLU624 4.8 73.4 1.0 O B:GLU699 4.8 67.6 1.0 CZ B:TYR299 4.8 64.3 1.0 CG B:GLU667 4.9 71.3 1.0

C.Alvadia, N.K.Lim, V.Clerico Mosina, G.T.Oostergetel, R.Dutzler, C.Paulino. Cryo-Em Structures and Functional Characterization of the Murine Lipid Scramblase TMEM16F. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30785399
DOI: 10.7554/ELIFE.44365