Calcium in PDB 8bc0: Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed

The binding sites of Calcium atom in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed (pdb code 8bc0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed, PDB code: 8bc0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


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 CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:83.2 occ:1.00 OE2 A:GLU699 2.2 43.2 1.0 OD1 A:ASN621 2.4 68.1 1.0 ND2 A:ASN620 2.5 77.1 1.0 CD A:GLU699 3.1 47.1 1.0 CG A:ASN620 3.2 77.7 1.0 CG A:ASN621 3.3 73.4 1.0 OE2 A:GLU624 3.5 57.3 1.0 OE1 A:GLU699 3.5 54.1 1.0 CB A:ASN620 3.7 80.4 1.0 OE1 A:GLU624 3.7 63.9 1.0 CD A:GLU624 3.8 66.1 1.0 ND2 A:ASN621 3.9 79.4 1.0 O A:LYS616 3.9 83.4 1.0 OE1 A:GLU670 4.0 57.8 1.0 OD1 A:ASN620 4.1 73.3 1.0 N A:ASN621 4.1 69.8 1.0 C A:ASN620 4.3 83.1 1.0 CA A:CA1002 4.4 55.7 1.0 CG A:GLU699 4.4 53.3 1.0 CA A:ASN621 4.5 75.4 1.0 CD A:GLU670 4.5 60.0 1.0 CB A:ASN621 4.5 74.8 1.0 C A:LYS616 4.5 77.6 1.0 CA A:ASN620 4.6 81.0 1.0 O A:ALA617 4.7 90.8 1.0 O A:ASN620 4.8 88.5 1.0 CG A:LYS616 4.8 82.0 1.0 NZ A:LYS616 4.8 87.7 1.0 CA A:ALA617 4.8 81.5 1.0 OE2 A:GLU670 4.8 53.0 1.0 N A:ALA617 5.0 79.0 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


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 CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:55.7 occ:1.00 OE2 A:GLU667 2.1 56.0 1.0 OD1 A:ASP703 2.2 69.2 1.0 OE2 A:GLU624 2.3 57.3 1.0 OE1 A:GLU667 2.3 56.4 1.0 CD A:GLU667 2.4 61.5 1.0 OE1 A:GLU624 2.5 63.9 1.0 CD A:GLU624 2.6 66.1 1.0 CG A:ASP703 3.0 66.7 1.0 OD2 A:ASP703 3.1 73.0 1.0 OE1 A:GLU670 3.3 57.8 1.0 CG A:GLU699 3.7 53.3 1.0 CG A:GLU624 3.8 74.0 1.0 OE2 A:GLU699 3.9 43.2 1.0 CG A:GLU667 3.9 59.8 1.0 CD A:GLU699 4.0 47.1 1.0 OD1 A:ASN621 4.2 68.1 1.0 CD A:GLU670 4.3 60.0 1.0 CA A:CA1001 4.4 83.2 1.0 CB A:ASP703 4.4 57.8 1.0 CB A:GLU624 4.4 75.7 1.0 OE2 A:GLU670 4.5 53.0 1.0 CG1 A:VAL702 4.6 63.8 1.0 CG2 A:VAL702 4.7 70.2 1.0 O A:GLU699 4.7 47.5 1.0 N A:ASP703 4.7 69.4 1.0 CB A:GLU699 4.8 53.3 1.0 OE1 A:GLU699 4.8 54.1 1.0 CA A:GLU699 4.8 57.2 1.0 CB A:GLU667 4.9 49.2 1.0 CA A:ASP703 4.9 66.5 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


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 CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:128.2 occ:1.00 OG A:SER854 2.3 88.4 1.0 OE2 A:GLU395 2.4 100.9 1.0 O A:SER854 2.4 98.1 1.0 CA A:SER854 2.9 84.2 1.0 C A:SER854 2.9 93.2 1.0 CG A:GLU395 3.0 106.4 1.0 CB A:SER854 3.0 88.7 1.0 CD A:GLU395 3.0 105.5 1.0 O A:ILE857 3.5 100.1 1.0 OD2 A:ASP859 3.7 122.3 1.0 OD1 A:ASP859 3.7 128.4 1.0 CG A:ASP859 4.0 122.9 1.0 N A:TYR855 4.2 113.1 1.0 OE1 A:GLU395 4.3 107.6 1.0 N A:SER854 4.3 81.7 1.0 CB A:GLU395 4.5 101.8 1.0 O A:ILE853 4.6 94.0 1.0 C A:ILE857 4.7 103.8 1.0 C A:ILE853 4.9 87.0 1.0 CA A:TYR855 5.0 117.0 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


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 CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:125.5 occ:1.00 OE2 B:GLU670 2.3 77.9 1.0 OE1 B:GLU699 2.3 72.5 1.0 OD1 B:ASN621 2.7 87.7 1.0 ND2 B:ASN620 3.0 92.6 1.0 O B:ALA617 3.0 101.6 1.0 CD B:GLU699 3.2 74.3 1.0 OE2 B:GLU699 3.3 84.2 1.0 CA B:ALA617 3.4 100.8 1.0 CD B:GLU670 3.5 77.0 1.0 CG B:ASN621 3.5 89.5 1.0 C B:ALA617 3.6 102.5 1.0 CB B:ASN620 3.6 96.0 1.0 OD1 B:ASN695 3.7 56.6 1.0 CG B:ASN620 3.7 95.6 1.0 CB B:ALA617 3.7 99.6 1.0 ND2 B:ASN621 4.0 89.9 1.0 N B:ASN621 4.2 92.1 1.0 CG B:GLU670 4.3 78.4 1.0 OE1 B:GLU670 4.4 67.5 1.0 CG B:ASN695 4.5 59.1 1.0 ND2 B:ASN695 4.5 60.3 1.0 C B:ASN620 4.6 98.0 1.0 OE1 B:GLU624 4.6 69.3 1.0 CG B:GLU699 4.6 59.2 1.0 CA B:ASN620 4.6 94.7 1.0 CB B:ASN621 4.7 91.6 1.0 O B:LYS616 4.7 93.8 1.0 N B:ALA617 4.7 95.9 1.0 OD1 B:ASN620 4.8 92.8 1.0 CA B:ASN621 4.8 92.6 1.0 N B:ILE618 4.9 101.7 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:52.4 occ:1.00 OE2 B:GLU624 2.2 76.2 1.0 OE2 B:GLU699 2.4 84.2 1.0 OE1 B:GLU670 2.5 67.5 1.0 OD1 B:ASP703 2.6 58.6 1.0 OD2 B:ASP703 2.8 63.2 1.0 CD B:GLU624 2.9 80.5 1.0 OE1 B:GLU624 3.0 69.3 1.0 CG B:ASP703 3.1 60.6 1.0 CG B:GLU667 3.2 71.7 1.0 CD B:GLU670 3.5 77.0 1.0 CD B:GLU699 3.5 74.3 1.0 OE2 B:GLU667 3.8 77.0 1.0 OE2 B:GLU670 3.8 77.9 1.0 OH B:TYR299 4.0 70.5 1.0 CD B:GLU667 4.0 68.7 1.0 CG B:GLU699 4.0 59.2 1.0 CB B:GLU667 4.1 68.9 1.0 ND2 B:ASN620 4.3 92.6 1.0 CA B:GLU667 4.4 72.0 1.0 CG B:GLU624 4.4 85.9 1.0 CB B:ASP703 4.6 60.9 1.0 OE1 B:GLU699 4.6 72.5 1.0 OD1 B:ASN621 4.6 87.7 1.0 CG B:GLU670 4.8 78.4 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of CA2+-Bound MTMEM16F F518A Q623A Mutant in Gdn Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:134.7 occ:1.00 OD1 B:ASP859 2.3 124.3 1.0 O B:ILE857 2.3 84.2 1.0 CA B:PRO858 2.6 120.4 1.0 N B:ASP859 2.7 126.8 1.0 C B:PRO858 2.9 121.0 1.0 C B:ILE857 3.2 89.5 1.0 O B:SER854 3.2 94.2 1.0 CG B:ASP859 3.3 126.6 1.0 N B:PRO858 3.3 119.3 1.0 OE1 B:GLU395 3.8 100.6 1.0 O B:PRO858 3.8 121.4 1.0 CA B:ASP859 3.9 127.9 1.0 CB B:PRO858 4.0 120.3 1.0 CB B:ASP859 4.1 128.3 1.0 OD2 B:ASP859 4.2 130.2 1.0 C B:SER854 4.4 86.2 1.0 OE2 B:GLU395 4.4 100.0 1.0 CD B:GLU395 4.5 100.9 1.0 CA B:ILE857 4.6 88.6 1.0 CD B:PRO858 4.7 120.4 1.0 O B:TYR855 4.9 97.3 1.0 N B:ILE857 5.0 88.0 1.0 OG B:SER854 5.0 71.5 1.0

M.Arndt, C.Alvadia, M.S.Straub, V.Clerico Mosina, C.Paulino, R.Dutzler. Structural Basis For the Activation of the Lipid Scramblase TMEM16F. Nat Commun V. 13 6692 2022.
ISSN: ESSN 2041-1723
PubMed: 36335104
DOI: 10.1038/S41467-022-34497-X