Calcium in PDB 8bc1: Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn

The binding sites of Calcium atom in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn (pdb code 8bc1). 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, PDB code: 8bc1:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:84.7 occ:1.00 OE2 A:GLU699 2.4 70.3 1.0 ND2 A:ASN620 2.7 80.7 1.0 OD1 A:ASN621 3.4 78.2 1.0 CD A:GLU699 3.4 61.1 1.0 CG A:ASN620 3.4 81.7 1.0 CB A:ASN620 3.6 81.5 1.0 OE1 A:GLU699 3.6 65.5 1.0 OE2 A:GLU624 3.7 68.6 1.0 CA A:CA1002 4.0 57.6 1.0 OE1 A:GLU670 4.0 64.6 1.0 O A:LYS616 4.0 95.1 1.0 CG A:ASN621 4.1 84.8 1.0 OE1 A:GLU624 4.3 62.5 1.0 CD A:GLU624 4.3 73.0 1.0 N A:ASN621 4.4 77.0 1.0 OD1 A:ASN620 4.4 71.4 1.0 CD A:GLU670 4.5 64.0 1.0 C A:ASN620 4.5 90.2 1.0 CG A:LYS616 4.5 90.7 1.0 ND2 A:ASN621 4.5 80.0 1.0 NZ A:LYS616 4.6 91.1 1.0 C A:LYS616 4.6 91.2 1.0 O A:ALA617 4.6 98.1 1.0 CA A:ALA617 4.6 83.2 1.0 CA A:ASN620 4.6 78.5 1.0 CG A:GLU699 4.8 60.4 1.0 OE2 A:GLU670 4.9 64.1 1.0 N A:ALA617 4.9 83.7 1.0 CA A:ASN621 5.0 73.9 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:57.6 occ:1.00 OE1 A:GLU667 2.3 58.0 1.0 OE2 A:GLU624 2.4 68.6 1.0 OE1 A:GLU624 2.4 62.5 1.0 OE2 A:GLU667 2.5 60.5 1.0 CD A:GLU624 2.6 73.0 1.0 OE1 A:GLU670 2.6 64.6 1.0 OE2 A:GLU699 2.7 70.3 1.0 CD A:GLU667 2.7 69.6 1.0 OD1 A:ASP703 3.1 65.1 1.0 CD A:GLU699 3.5 61.1 1.0 CG A:GLU699 3.6 60.4 1.0 CD A:GLU670 3.7 64.0 1.0 CG A:ASP703 3.9 65.3 1.0 CA A:CA1001 4.0 84.7 1.0 CG A:GLU624 4.0 79.1 1.0 OD2 A:ASP703 4.0 75.5 1.0 OE2 A:GLU670 4.2 64.1 1.0 CG A:GLU667 4.2 70.7 1.0 OD1 A:ASN621 4.3 78.2 1.0 OE1 A:GLU699 4.6 65.5 1.0 ND2 A:ASN620 4.6 80.7 1.0 CB A:GLU624 4.8 73.6 1.0 CG1 A:VAL702 4.8 77.3 1.0 CB A:GLU667 5.0 65.8 1.0 CG A:GLU670 5.0 60.6 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:112.0 occ:1.00 OG A:SER854 2.4 78.2 1.0 OE2 A:GLU395 2.4 94.1 1.0 O A:SER854 2.5 84.3 1.0 CA A:SER854 2.8 77.5 1.0 C A:SER854 3.0 82.1 1.0 CB A:SER854 3.0 82.7 1.0 CD A:GLU395 3.1 98.0 1.0 CG A:GLU395 3.1 97.7 1.0 O A:ILE857 3.4 81.4 1.0 OD2 A:ASP859 3.8 114.3 1.0 OD1 A:ASP859 4.0 114.7 1.0 CG A:ASP859 4.2 115.5 1.0 N A:SER854 4.2 61.1 1.0 OE1 A:GLU395 4.3 100.4 1.0 N A:TYR855 4.3 92.3 1.0 O A:ILE853 4.5 79.5 1.0 CB A:GLU395 4.6 96.6 1.0 C A:ILE857 4.7 84.2 1.0 C A:ILE853 4.8 65.0 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:84.7 occ:1.00 OE2 B:GLU699 2.4 70.3 1.0 ND2 B:ASN620 2.7 80.7 1.0 OD1 B:ASN621 3.4 78.2 1.0 CD B:GLU699 3.4 61.1 1.0 CG B:ASN620 3.4 81.7 1.0 CB B:ASN620 3.6 81.5 1.0 OE1 B:GLU699 3.6 65.5 1.0 OE2 B:GLU624 3.7 68.6 1.0 CA B:CA1002 4.0 57.6 1.0 OE1 B:GLU670 4.0 64.6 1.0 O B:LYS616 4.0 95.1 1.0 CG B:ASN621 4.1 84.8 1.0 OE1 B:GLU624 4.3 62.5 1.0 CD B:GLU624 4.3 73.0 1.0 N B:ASN621 4.4 77.0 1.0 OD1 B:ASN620 4.4 71.4 1.0 CD B:GLU670 4.5 64.0 1.0 C B:ASN620 4.5 90.2 1.0 CG B:LYS616 4.5 90.7 1.0 ND2 B:ASN621 4.5 80.0 1.0 NZ B:LYS616 4.6 91.1 1.0 C B:LYS616 4.6 91.2 1.0 O B:ALA617 4.6 98.1 1.0 CA B:ALA617 4.6 83.2 1.0 CA B:ASN620 4.6 78.5 1.0 CG B:GLU699 4.8 60.4 1.0 N B:ALA617 4.9 83.7 1.0 OE2 B:GLU670 4.9 64.1 1.0 CA B:ASN621 5.0 73.9 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:57.6 occ:1.00 OE1 B:GLU667 2.3 58.0 1.0 OE2 B:GLU624 2.4 68.6 1.0 OE1 B:GLU624 2.4 62.5 1.0 OE2 B:GLU667 2.5 60.5 1.0 CD B:GLU624 2.6 73.0 1.0 OE1 B:GLU670 2.6 64.6 1.0 OE2 B:GLU699 2.7 70.3 1.0 CD B:GLU667 2.7 69.6 1.0 OD1 B:ASP703 3.1 65.1 1.0 CD B:GLU699 3.5 61.1 1.0 CG B:GLU699 3.6 60.4 1.0 CD B:GLU670 3.7 64.0 1.0 CG B:ASP703 3.9 65.3 1.0 CA B:CA1001 4.0 84.7 1.0 CG B:GLU624 4.0 79.1 1.0 OD2 B:ASP703 4.0 75.5 1.0 OE2 B:GLU670 4.2 64.1 1.0 CG B:GLU667 4.2 70.7 1.0 OD1 B:ASN621 4.3 78.2 1.0 OE1 B:GLU699 4.6 65.5 1.0 ND2 B:ASN620 4.6 80.7 1.0 CB B:GLU624 4.8 73.6 1.0 CG1 B:VAL702 4.8 77.3 1.0 CB B:GLU667 5.0 65.8 1.0 CG B:GLU670 5.0 60.6 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518A_Q623A Mutant in Gdn


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:112.0 occ:1.00 OG B:SER854 2.4 78.2 1.0 OE2 B:GLU395 2.4 94.1 1.0 O B:SER854 2.5 84.3 1.0 CA B:SER854 2.8 77.5 1.0 C B:SER854 3.0 82.1 1.0 CB B:SER854 3.0 82.7 1.0 CD B:GLU395 3.1 98.0 1.0 CG B:GLU395 3.1 97.7 1.0 O B:ILE857 3.4 81.4 1.0 OD2 B:ASP859 3.8 114.3 1.0 OD1 B:ASP859 4.0 114.7 1.0 CG B:ASP859 4.2 115.5 1.0 N B:SER854 4.2 61.1 1.0 OE1 B:GLU395 4.3 100.4 1.0 N B:TYR855 4.3 92.3 1.0 O B:ILE853 4.5 79.5 1.0 CB B:GLU395 4.6 96.6 1.0 C B:ILE857 4.7 84.2 1.0 C B:ILE853 4.8 65.0 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