Calcium in PDB 8b8m: Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Open/Closed

The binding sites of Calcium atom in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Open/Closed (pdb code 8b8m). 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 N562A Mutant in Digitonin Open/Closed, PDB code: 8b8m:
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 N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:100.8 occ:1.00 OE2 A:GLU699 2.3 69.9 1.0 OE2 A:GLU670 2.3 71.8 1.0 OE1 A:GLU699 2.4 73.5 1.0 CD A:GLU699 2.5 68.5 1.0 OD1 A:ASN695 3.2 75.4 1.0 CD A:GLU670 3.3 78.3 1.0 ND2 A:ASN695 3.5 74.2 1.0 OD1 A:ASN621 3.6 78.2 1.0 CG A:ASN695 3.7 75.7 1.0 CA A:ALA617 3.8 86.0 1.0 CG A:GLU699 3.9 59.9 1.0 O A:ALA617 3.9 86.8 1.0 ND2 A:ASN621 4.0 87.9 1.0 CG A:ASN621 4.0 85.4 1.0 OE1 A:GLU670 4.0 80.7 1.0 CB A:ALA617 4.2 89.3 1.0 CG A:GLU670 4.2 71.8 1.0 C A:ALA617 4.3 87.2 1.0 CE A:MET671 4.4 64.7 1.0 CB A:ASN620 4.4 81.1 1.0 NZ A:LYS616 4.6 81.5 1.0 CB A:GLU699 4.8 69.1 1.0 CA A:CA1002 4.8 45.0 1.0 N A:ASN621 4.9 86.1 1.0 O A:LYS616 4.9 78.9 1.0 N A:ALA617 4.9 82.7 1.0 OE1 A:GLN674 5.0 56.1 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:45.0 occ:1.00 OE1 A:GLU667 2.2 57.6 1.0 OE2 A:GLU667 2.2 69.0 1.0 OE1 A:GLU624 2.2 72.3 1.0 OE2 A:GLU624 2.3 83.5 1.0 CD A:GLU624 2.5 79.9 1.0 CD A:GLU667 2.5 66.1 1.0 OD1 A:ASP703 2.7 75.1 1.0 OE2 A:GLU699 2.8 69.9 1.0 OE1 A:GLU670 2.8 80.7 1.0 OD2 A:ASP703 3.4 85.6 1.0 CG A:ASP703 3.4 77.4 1.0 CD A:GLU699 3.7 68.5 1.0 CD A:GLU670 3.8 78.3 1.0 CG A:GLU624 3.9 77.7 1.0 CG A:GLU699 4.0 59.9 1.0 OE2 A:GLU670 4.1 71.8 1.0 CG A:GLU667 4.1 66.7 1.0 OD1 A:ASN621 4.2 78.2 1.0 CB A:GLU624 4.7 82.7 1.0 OE1 A:GLU699 4.8 73.5 1.0 CA A:CA1001 4.8 100.8 1.0 CB A:GLU667 4.9 63.4 1.0 CB A:ASP703 4.9 67.4 1.0 CG1 A:VAL702 5.0 79.0 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:136.7 occ:1.00 OD1 A:ASP859 2.3 123.2 1.0 O A:SER854 2.4 99.7 1.0 OE2 A:GLU395 2.4 109.8 1.0 OE1 A:GLU395 2.8 107.0 1.0 OG A:SER854 2.9 98.6 1.0 CD A:GLU395 2.9 106.9 1.0 O A:ILE857 3.2 93.7 1.0 CG A:ASP859 3.3 123.2 1.0 C A:SER854 3.3 96.5 1.0 OD2 A:ASP859 3.5 125.4 1.0 CA A:SER854 3.6 91.5 1.0 NZ A:LYS398 3.6 98.7 1.0 CB A:SER854 3.8 96.3 1.0 CG A:GLU395 4.3 100.3 1.0 C A:ILE857 4.4 96.3 1.0 N A:TYR855 4.5 115.3 1.0 N A:ASP859 4.6 121.6 1.0 CE A:LYS398 4.6 96.1 1.0 CB A:ASP859 4.6 122.5 1.0 CA A:ASP859 5.0 123.3 1.0 CA A:TYR855 5.0 120.5 1.0 C A:PRO858 5.0 108.3 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:142.5 occ:1.00 OE1 B:GLU699 2.3 78.2 1.0 OD1 B:ASN621 2.3 104.1 1.0 OE2 B:GLU670 2.3 83.6 1.0 CD B:GLU699 2.9 75.5 1.0 OE2 B:GLU699 2.9 71.8 1.0 CD B:GLU670 3.0 80.5 1.0 CG B:ASN621 3.4 99.6 1.0 OE1 B:GLU670 3.7 80.3 1.0 ND2 B:ASN621 3.7 97.3 1.0 CG B:GLU670 3.8 75.3 1.0 ND2 B:ASN695 3.8 93.5 1.0 O B:ALA617 3.9 94.4 1.0 OD1 B:ASN695 4.2 95.7 1.0 CG B:GLU699 4.3 69.1 1.0 CG B:ASN695 4.4 95.2 1.0 CB B:ALA617 4.5 91.7 1.0 CE B:MET671 4.6 73.8 1.0 CB B:ASN620 4.6 99.0 1.0 C B:ALA617 4.6 94.6 1.0 N B:ASN621 4.6 99.2 1.0 CA B:ALA617 4.7 90.2 1.0 CG B:ASN620 4.7 98.1 1.0 CB B:ASN621 4.7 98.7 1.0 CA B:CA1002 4.7 39.3 1.0 OD1 B:ASN620 4.9 92.9 1.0 CA B:ASN621 4.9 98.5 1.0 CB B:GLU699 5.0 68.6 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:39.3 occ:1.00 OE2 B:GLU699 2.4 71.8 1.0 OE1 B:GLU624 2.4 90.1 1.0 OE1 B:GLU670 2.5 80.3 1.0 OE2 B:GLU624 2.6 94.1 1.0 OD1 B:ASP703 2.6 79.5 1.0 OE1 B:GLU667 2.7 83.5 1.0 CD B:GLU624 2.8 93.5 1.0 OD2 B:ASP703 3.3 82.4 1.0 CG B:ASP703 3.3 79.2 1.0 CD B:GLU699 3.5 75.5 1.0 CD B:GLU670 3.6 80.5 1.0 CD B:GLU667 3.9 84.4 1.0 OE2 B:GLU670 4.0 83.6 1.0 CG B:GLU699 4.2 69.1 1.0 CG B:GLU624 4.3 88.7 1.0 OE2 B:GLU667 4.4 83.3 1.0 OE1 B:GLU699 4.5 78.2 1.0 CA B:CA1001 4.7 142.5 1.0 CB B:ASP703 4.8 71.8 1.0 CG B:GLU670 4.8 75.3 1.0 CB B:GLU667 4.9 77.0 1.0 CA B:GLU667 4.9 76.9 1.0 CG B:GLU667 5.0 82.6 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin 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 N562A Mutant in Digitonin Open/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:129.9 occ:1.00 O B:ILE857 2.3 88.2 1.0 OD1 B:ASP859 2.3 131.0 1.0 O B:SER854 2.4 85.4 1.0 OE2 B:GLU395 2.9 89.8 1.0 CG B:ASP859 3.3 130.7 1.0 C B:ILE857 3.5 91.7 1.0 N B:ASP859 3.7 127.5 1.0 C B:SER854 3.7 80.1 1.0 OD2 B:ASP859 3.8 132.3 1.0 C B:PRO858 3.9 128.5 1.0 CA B:PRO858 4.0 128.8 1.0 CD B:GLU395 4.1 94.1 1.0 N B:PRO858 4.2 125.8 1.0 CA B:ASP859 4.3 126.6 1.0 CB B:ASP859 4.4 128.6 1.0 O B:TYR855 4.4 102.1 1.0 OG B:SER854 4.5 80.0 1.0 CA B:TYR855 4.5 103.0 1.0 C B:TYR855 4.5 103.5 1.0 N B:ILE857 4.5 89.7 1.0 CA B:ILE857 4.6 90.8 1.0 N B:TYR855 4.6 99.3 1.0 CA B:SER854 4.6 74.3 1.0 O B:PRO858 4.6 128.5 1.0 OE1 B:GLU395 4.9 93.9 1.0 CG B:GLU395 4.9 93.1 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