Calcium in PDB 8b8k: Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/Closed

The binding sites of Calcium atom in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/Closed (pdb code 8b8k). 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 Closed/Closed, PDB code: 8b8k:
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 Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:117.2 occ:1.00 OE1 A:GLU699 2.3 93.7 1.0 OE2 A:GLU699 2.3 91.0 1.0 OD1 A:ASN621 2.4 96.9 1.0 OE2 A:GLU670 2.4 97.5 1.0 OE1 A:GLU624 2.6 92.5 1.0 CD A:GLU699 2.6 94.0 1.0 CD A:GLU624 3.2 101.5 1.0 OE1 A:GLU670 3.2 93.0 1.0 CD A:GLU670 3.2 101.6 1.0 OE2 A:GLU624 3.4 104.7 1.0 CG A:ASN621 3.5 101.0 1.0 N A:ASN621 3.7 97.2 1.0 C A:ASN620 3.8 104.1 1.0 CB A:ASN620 3.8 100.5 1.0 CA A:ASN621 3.8 95.6 1.0 CA A:CA1002 4.0 83.7 1.0 O A:ASN620 4.0 109.9 1.0 CG A:GLU699 4.1 86.5 1.0 CB A:ASN621 4.3 97.3 1.0 CG A:GLU624 4.3 99.5 1.0 CA A:ASN620 4.5 101.0 1.0 ND2 A:ASN621 4.5 100.2 1.0 CG A:GLU670 4.6 99.1 1.0 O A:ALA617 4.6 99.4 1.0 CG1 A:VAL702 4.7 77.6 1.0 CG A:ASN620 4.7 102.5 1.0 OD1 A:ASP703 4.9 97.8 1.0 CB A:GLU699 4.9 83.3 1.0 CB A:GLU624 4.9 98.1 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:83.7 occ:1.00 OE2 A:GLU699 2.3 91.0 1.0 OE1 A:GLU667 2.3 100.5 1.0 OD2 A:ASP703 2.4 101.7 1.0 OD1 A:ASP703 2.4 97.8 1.0 OE2 A:GLU624 2.4 104.7 1.0 CG A:ASP703 2.7 96.1 1.0 OE1 A:GLU670 3.1 93.0 1.0 CD A:GLU624 3.2 101.5 1.0 OE1 A:GLU624 3.4 92.5 1.0 CD A:GLU699 3.4 94.0 1.0 CD A:GLU667 3.5 100.7 1.0 CG A:GLU699 3.9 86.5 1.0 CB A:GLU667 3.9 90.9 1.0 OH A:TYR299 4.0 85.9 1.0 CA A:CA1001 4.0 117.2 1.0 CD A:GLU670 4.1 101.6 1.0 CA A:GLU667 4.1 95.3 1.0 CB A:ASP703 4.2 79.4 1.0 CG A:GLU667 4.3 95.3 1.0 OE1 A:GLU699 4.4 93.7 1.0 OE2 A:GLU667 4.5 103.9 1.0 OE2 A:GLU670 4.5 97.5 1.0 CG A:GLU624 4.6 99.5 1.0 NZ A:LYS706 5.0 85.3 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:122.6 occ:1.00 O A:SER854 2.3 113.2 1.0 OD1 A:ASP859 2.3 130.3 1.0 O A:ILE857 2.4 102.4 1.0 OE1 A:GLU395 2.5 113.5 1.0 CD A:GLU395 3.4 110.8 1.0 C A:SER854 3.4 105.8 1.0 CG A:ASP859 3.5 129.4 1.0 C A:ILE857 3.6 109.0 1.0 OE2 A:GLU395 3.7 112.0 1.0 OG A:SER854 3.7 113.6 1.0 CA A:SER854 3.9 97.8 1.0 OD2 A:ASP859 4.0 131.5 1.0 NZ A:LYS398 4.1 102.8 1.0 N A:ASP859 4.2 124.2 1.0 CA A:ILE857 4.4 104.8 1.0 CB A:SER854 4.5 107.1 1.0 CB A:ILE857 4.5 103.6 1.0 CG A:GLU395 4.5 101.1 1.0 C A:PRO858 4.5 121.3 1.0 N A:PRO858 4.5 123.9 1.0 N A:ILE857 4.5 104.8 1.0 CA A:PRO858 4.6 120.4 1.0 N A:TYR855 4.6 115.1 1.0 CB A:ASP859 4.7 123.1 1.0 CA A:ASP859 4.7 123.7 1.0 CE A:LYS398 4.8 103.0 1.0 CA A:TYR855 4.9 118.2 1.0 CG2 A:ILE857 4.9 106.8 1.0 O A:ILE853 5.0 109.0 1.0 C A:TYR855 5.0 117.9 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:117.3 occ:1.00 OE1 B:GLU699 2.3 93.3 1.0 OE2 B:GLU699 2.3 91.4 1.0 OD1 B:ASN621 2.4 99.6 1.0 OE2 B:GLU670 2.4 97.9 1.0 CD B:GLU699 2.6 93.5 1.0 OE1 B:GLU624 2.7 92.2 1.0 CD B:GLU670 3.2 102.3 1.0 OE1 B:GLU670 3.2 93.4 1.0 CD B:GLU624 3.2 101.5 1.0 OE2 B:GLU624 3.4 104.6 1.0 CG B:ASN621 3.5 103.2 1.0 N B:ASN621 3.7 98.9 1.0 CB B:ASN620 3.8 101.0 1.0 C B:ASN620 3.8 105.3 1.0 CA B:ASN621 3.8 97.7 1.0 O B:ASN620 4.0 111.4 1.0 CA B:CA1002 4.0 81.1 1.0 CG B:GLU699 4.1 85.2 1.0 CB B:ASN621 4.3 99.4 1.0 CG B:GLU624 4.3 100.3 1.0 CA B:ASN620 4.4 101.5 1.0 ND2 B:ASN621 4.5 102.4 1.0 O B:ALA617 4.6 99.2 1.0 CG B:GLU670 4.6 99.8 1.0 CG1 B:VAL702 4.7 77.5 1.0 CG B:ASN620 4.7 103.5 1.0 CB B:GLU699 4.9 82.3 1.0 OD1 B:ASP703 4.9 97.6 1.0 CB B:GLU624 4.9 98.3 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:81.1 occ:1.00 OE2 B:GLU699 2.3 91.4 1.0 OE1 B:GLU667 2.3 101.1 1.0 OD2 B:ASP703 2.4 100.9 1.0 OD1 B:ASP703 2.4 97.6 1.0 OE2 B:GLU624 2.5 104.6 1.0 CG B:ASP703 2.7 95.8 1.0 OE1 B:GLU670 3.1 93.4 1.0 CD B:GLU624 3.2 101.5 1.0 OE1 B:GLU624 3.3 92.2 1.0 CD B:GLU699 3.4 93.5 1.0 CD B:GLU667 3.6 101.7 1.0 CG B:GLU699 3.9 85.2 1.0 CB B:GLU667 3.9 92.0 1.0 CA B:CA1001 4.0 117.3 1.0 OH B:TYR299 4.0 85.4 1.0 CD B:GLU670 4.1 102.3 1.0 CA B:GLU667 4.1 95.7 1.0 CB B:ASP703 4.2 79.5 1.0 CG B:GLU667 4.3 96.7 1.0 OE1 B:GLU699 4.5 93.3 1.0 OE2 B:GLU667 4.5 104.7 1.0 OE2 B:GLU670 4.5 97.9 1.0 CG B:GLU624 4.6 100.3 1.0 NZ B:LYS706 5.0 83.9 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F N562A Mutant in Digitonin Closed/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 Closed/Closed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:119.4 occ:1.00 OD1 B:ASP859 2.4 128.2 1.0 O B:SER854 2.4 113.4 1.0 O B:ILE857 2.4 103.5 1.0 OE1 B:GLU395 2.5 113.4 1.0 CD B:GLU395 3.4 110.8 1.0 C B:SER854 3.5 106.2 1.0 CG B:ASP859 3.5 126.4 1.0 C B:ILE857 3.6 110.0 1.0 OE2 B:GLU395 3.8 112.5 1.0 OG B:SER854 3.8 113.3 1.0 OD2 B:ASP859 3.9 128.8 1.0 CA B:SER854 4.0 98.2 1.0 NZ B:LYS398 4.0 102.0 1.0 N B:ASP859 4.3 121.8 1.0 CA B:ILE857 4.4 105.4 1.0 CB B:ILE857 4.4 104.4 1.0 CG B:GLU395 4.5 101.1 1.0 CB B:SER854 4.5 106.8 1.0 N B:ILE857 4.5 105.2 1.0 N B:PRO858 4.5 124.3 1.0 C B:PRO858 4.6 120.5 1.0 CA B:PRO858 4.6 119.5 1.0 N B:TYR855 4.6 114.1 1.0 CB B:ASP859 4.7 120.0 1.0 CA B:ASP859 4.8 121.6 1.0 CE B:LYS398 4.8 101.9 1.0 CG2 B:ILE857 4.9 107.3 1.0 CA B:TYR855 4.9 116.6 1.0 O B:ILE853 5.0 108.3 1.0 C B:TYR855 5.0 116.3 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