Calcium in PDB 8tol: NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State)

The binding sites of Calcium atom in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State) (pdb code 8tol). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State), PDB code: 8tol:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:76.6 occ:1.00 OD1 A:ASP503 2.3 79.7 1.0 OE2 A:GLU535 2.3 87.1 1.0 OE2 A:GLU452 2.3 100.9 1.0 OD1 A:ASP539 2.5 79.8 1.0 OE1 A:GLU506 2.9 77.7 1.0 OD2 A:ASP539 2.9 89.8 1.0 CG A:ASP539 3.1 77.4 1.0 CD A:GLU452 3.2 99.3 1.0 CD A:GLU535 3.2 86.1 1.0 CG A:ASP503 3.4 75.2 1.0 OE1 A:GLU452 3.4 97.6 1.0 CG A:GLU535 3.5 73.8 1.0 CD A:GLU506 3.8 87.3 1.0 CB A:ASP503 4.0 65.6 1.0 OH A:TYR188 4.1 70.1 1.0 CA A:ASP503 4.2 65.0 1.0 OE2 A:GLU506 4.2 86.8 1.0 CA A:CA802 4.3 96.8 1.0 NZ A:LYS542 4.3 78.5 1.0 OE1 A:GLU535 4.4 88.2 1.0 OD2 A:ASP503 4.4 77.5 1.0 CB A:ASP539 4.6 62.5 1.0 CG A:GLU452 4.6 95.2 1.0 CG A:GLU506 4.8 78.3 1.0 CB A:GLU506 4.9 66.2 1.0 CB A:GLU535 5.0 64.0 1.0 CE A:MET507 5.0 68.4 1.0

Calcium binding site 2 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:96.8 occ:1.00 OE2 A:GLU535 2.3 87.1 1.0 OD1 A:ASN448 2.3 86.9 1.0 OE1 A:GLU535 2.3 88.2 1.0 OE2 A:GLU506 2.5 86.8 1.0 OE1 A:GLU452 2.6 97.6 1.0 CD A:GLU535 2.6 86.1 1.0 CD A:GLU506 3.4 87.3 1.0 CG A:ASN448 3.5 89.8 1.0 OE1 A:GLU506 3.6 77.7 1.0 CD A:GLU452 3.8 99.3 1.0 CG A:GLU535 4.1 73.8 1.0 OD1 A:ASN531 4.2 76.8 1.0 CA A:CA801 4.3 76.6 1.0 N A:PHE449 4.3 79.3 1.0 CA A:PHE449 4.3 83.8 1.0 OE2 A:GLU452 4.3 100.9 1.0 ND2 A:ASN448 4.4 93.6 1.0 C A:ASN448 4.4 85.8 1.0 CB A:ASN448 4.5 81.1 1.0 O A:ASN448 4.5 98.4 1.0 CB A:PHE449 4.8 83.7 1.0 CG A:GLU506 4.8 78.3 1.0 CB A:GLU452 4.8 88.9 1.0 CG A:GLU452 4.9 95.2 1.0 ND2 A:ASN531 4.9 74.0 1.0 CB A:GLU535 4.9 64.0 1.0

Calcium binding site 3 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:76.6 occ:1.00 OD1 B:ASP503 2.3 79.7 1.0 OE2 B:GLU535 2.3 87.1 1.0 OE2 B:GLU452 2.3 100.9 1.0 OD1 B:ASP539 2.5 79.8 1.0 OE1 B:GLU506 2.9 77.7 1.0 OD2 B:ASP539 2.9 89.8 1.0 CG B:ASP539 3.1 77.4 1.0 CD B:GLU452 3.2 99.3 1.0 CD B:GLU535 3.2 86.1 1.0 CG B:ASP503 3.4 75.2 1.0 OE1 B:GLU452 3.4 97.6 1.0 CG B:GLU535 3.5 73.8 1.0 CD B:GLU506 3.8 87.3 1.0 CB B:ASP503 4.0 65.6 1.0 OH B:TYR188 4.1 70.1 1.0 CA B:ASP503 4.2 65.0 1.0 OE2 B:GLU506 4.2 86.8 1.0 CA B:CA802 4.3 96.8 1.0 NZ B:LYS542 4.3 78.5 1.0 OE1 B:GLU535 4.4 88.2 1.0 OD2 B:ASP503 4.4 77.5 1.0 CB B:ASP539 4.6 62.5 1.0 CG B:GLU452 4.6 95.2 1.0 CG B:GLU506 4.8 78.3 1.0 CB B:GLU506 4.9 66.2 1.0 CB B:GLU535 5.0 64.0 1.0 CE B:MET507 5.0 68.4 1.0

Calcium binding site 4 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:96.8 occ:1.00 OE2 B:GLU535 2.3 87.1 1.0 OD1 B:ASN448 2.3 86.9 1.0 OE1 B:GLU535 2.3 88.2 1.0 OE2 B:GLU506 2.5 86.8 1.0 OE1 B:GLU452 2.6 97.6 1.0 CD B:GLU535 2.6 86.1 1.0 CD B:GLU506 3.4 87.3 1.0 CG B:ASN448 3.5 89.8 1.0 OE1 B:GLU506 3.6 77.7 1.0 CD B:GLU452 3.8 99.3 1.0 CG B:GLU535 4.1 73.8 1.0 OD1 B:ASN531 4.2 76.8 1.0 CA B:CA801 4.3 76.6 1.0 N B:PHE449 4.3 79.3 1.0 CA B:PHE449 4.3 83.8 1.0 OE2 B:GLU452 4.3 100.9 1.0 ND2 B:ASN448 4.4 93.6 1.0 C B:ASN448 4.4 85.8 1.0 CB B:ASN448 4.5 81.1 1.0 O B:ASN448 4.5 98.4 1.0 CB B:PHE449 4.8 83.7 1.0 CG B:GLU506 4.8 78.3 1.0 CB B:GLU452 4.8 88.9 1.0 CG B:GLU452 4.9 95.2 1.0 ND2 B:ASN531 4.9 74.0 1.0 CB B:GLU535 4.9 64.0 1.0

Z.Feng, O.E.Alvarenga, A.Accardi. Structural Basis of Closed Groove Scrambling By A TMEM16 Protein. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 38684930
DOI: 10.1038/S41594-024-01284-9