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Calcium in PDB 6qp6: Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin (pdb code 6qp6). 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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin, PDB code: 6qp6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6qp6

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Calcium binding site 1 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:32.9
occ:1.00
 OE2 A:GLU699 2.5 22.5 1.0
OE2 A:GLU670 2.5 24.6 1.0
OD1 A:ASN621 2.5 33.1 1.0
OE1 A:GLU624 2.5 35.1 1.0
OE1 A:GLU699 3.0 22.5 1.0
CD A:GLU624 3.1 35.1 1.0
CD A:GLU699 3.1 22.5 1.0
CD A:GLU670 3.2 24.6 1.0
OE1 A:GLU670 3.2 24.6 1.0
OE2 A:GLU624 3.4 35.1 1.0
CB A:ASN620 3.5 32.4 1.0
CG A:ASN620 3.5 32.4 1.0
C A:ASN620 3.5 32.4 1.0
N A:ASN621 3.6 33.1 1.0
ND2 A:ASN620 3.6 32.4 1.0
CG A:ASN621 3.7 33.1 1.0
O A:ASN620 3.7 32.4 1.0
CA A:ASN621 4.0 33.1 1.0
OD1 A:ASN620 4.1 32.4 1.0
CA A:ASN620 4.1 32.4 1.0
CA A:CA1002 4.1 23.3 1.0
CG A:GLU624 4.2 35.1 1.0
CB A:ASN621 4.4 33.1 1.0
CG A:GLU670 4.5 24.6 1.0
O A:ALA617 4.6 29.7 1.0
CG A:GLU699 4.6 22.5 1.0
ND2 A:ASN621 4.7 33.1 1.0
CB A:GLU624 4.8 35.1 1.0

Calcium binding site 2 out of 6 in 6qp6

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Calcium binding site 2 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:23.3
occ:1.00
 OD1 A:ASP703 2.5 20.8 1.0
OE2 A:GLU699 2.5 22.5 1.0
OE2 A:GLU624 2.5 35.1 1.0
OE1 A:GLU667 2.5 26.8 1.0
OD2 A:ASP703 2.6 20.8 1.0
OE1 A:GLU670 2.8 24.6 1.0
CG A:ASP703 2.9 20.8 1.0
CD A:GLU699 3.5 22.5 1.0
CD A:GLU624 3.5 35.1 1.0
OH A:TYR299 3.6 21.1 1.0
CD A:GLU667 3.7 26.8 1.0
OE1 A:GLU624 3.7 35.1 1.0
CD A:GLU670 3.8 24.6 1.0
CG A:GLU699 3.8 22.5 1.0
CA A:CA1001 4.1 32.9 1.0
CB A:GLU667 4.2 26.8 1.0
OE2 A:GLU670 4.2 24.6 1.0
CA A:GLU667 4.2 26.8 1.0
CB A:ASP703 4.4 20.8 1.0
CG A:GLU667 4.5 26.8 1.0
OE1 A:GLU699 4.6 22.5 1.0
OE2 A:GLU667 4.6 26.8 1.0
O A:GLU667 4.6 26.8 1.0
CZ A:TYR299 4.8 21.1 1.0
CG A:GLU624 4.8 35.1 1.0
C A:GLU667 4.9 26.8 1.0
CG A:GLU670 5.0 24.6 1.0

Calcium binding site 3 out of 6 in 6qp6

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Calcium binding site 3 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:42.3
occ:1.00
 O A:ILE857 2.5 39.4 1.0
OD1 A:ASP859 2.5 55.9 1.0
O A:SER854 2.5 31.6 1.0
OE1 A:GLU395 2.6 33.0 1.0
CD A:GLU395 3.4 33.0 1.0
CG A:ASP859 3.6 55.9 1.0
C A:SER854 3.7 31.6 1.0
OE2 A:GLU395 3.7 33.0 1.0
C A:ILE857 3.8 39.4 1.0
N A:ASP859 4.1 55.9 1.0
OG A:SER854 4.1 31.6 1.0
NZ A:LYS398 4.2 35.3 1.0
CA A:SER854 4.2 31.6 1.0
C A:PRO858 4.3 52.4 1.0
OD2 A:ASP859 4.3 55.9 1.0
CA A:PRO858 4.4 52.4 1.0
CA A:ASP859 4.4 55.9 1.0
CB A:ASP859 4.5 55.9 1.0
N A:PRO858 4.6 52.4 1.0
CG A:GLU395 4.6 33.0 1.0
CB A:SER854 4.7 31.6 1.0
CA A:ILE857 4.8 39.4 1.0
N A:TYR855 4.8 37.5 1.0
O A:PRO858 4.9 52.4 1.0
CE A:LYS398 4.9 35.3 1.0
CB A:ILE857 4.9 39.4 1.0
N A:ILE857 4.9 39.4 1.0

Calcium binding site 4 out of 6 in 6qp6

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Calcium binding site 4 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:32.9
occ:1.00
 OE2 B:GLU699 2.5 22.5 1.0
OE2 B:GLU670 2.5 24.6 1.0
OD1 B:ASN621 2.5 33.1 1.0
OE1 B:GLU624 2.5 35.1 1.0
OE1 B:GLU699 3.0 22.5 1.0
CD B:GLU624 3.1 35.1 1.0
CD B:GLU699 3.1 22.5 1.0
CD B:GLU670 3.2 24.6 1.0
OE1 B:GLU670 3.2 24.6 1.0
OE2 B:GLU624 3.4 35.1 1.0
CB B:ASN620 3.5 32.4 1.0
CG B:ASN620 3.5 32.4 1.0
C B:ASN620 3.5 32.4 1.0
N B:ASN621 3.6 33.1 1.0
ND2 B:ASN620 3.7 32.4 1.0
CG B:ASN621 3.7 33.1 1.0
O B:ASN620 3.7 32.4 1.0
CA B:ASN621 4.0 33.1 1.0
OD1 B:ASN620 4.1 32.4 1.0
CA B:ASN620 4.1 32.4 1.0
CA B:CA1002 4.1 23.3 1.0
CG B:GLU624 4.2 35.1 1.0
CB B:ASN621 4.4 33.1 1.0
CG B:GLU670 4.5 24.6 1.0
O B:ALA617 4.6 29.7 1.0
CG B:GLU699 4.6 22.5 1.0
ND2 B:ASN621 4.7 33.1 1.0
CB B:GLU624 4.8 35.1 1.0

Calcium binding site 5 out of 6 in 6qp6

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Calcium binding site 5 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:23.3
occ:1.00
 OD1 B:ASP703 2.5 20.8 1.0
OE2 B:GLU699 2.5 22.5 1.0
OE2 B:GLU624 2.5 35.1 1.0
OE1 B:GLU667 2.5 26.8 1.0
OD2 B:ASP703 2.6 20.8 1.0
OE1 B:GLU670 2.8 24.6 1.0
CG B:ASP703 2.9 20.8 1.0
CD B:GLU699 3.5 22.5 1.0
CD B:GLU624 3.5 35.1 1.0
OH B:TYR299 3.6 21.1 1.0
CD B:GLU667 3.7 26.8 1.0
OE1 B:GLU624 3.7 35.1 1.0
CD B:GLU670 3.8 24.6 1.0
CG B:GLU699 3.8 22.5 1.0
CA B:CA1001 4.1 32.9 1.0
CB B:GLU667 4.2 26.8 1.0
OE2 B:GLU670 4.2 24.6 1.0
CA B:GLU667 4.2 26.8 1.0
CB B:ASP703 4.4 20.8 1.0
CG B:GLU667 4.5 26.8 1.0
OE1 B:GLU699 4.6 22.5 1.0
OE2 B:GLU667 4.6 26.8 1.0
O B:GLU667 4.6 26.8 1.0
CZ B:TYR299 4.8 21.1 1.0
CG B:GLU624 4.8 35.1 1.0
C B:GLU667 4.9 26.8 1.0
CG B:GLU670 5.0 24.6 1.0

Calcium binding site 6 out of 6 in 6qp6

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Calcium binding site 6 out of 6 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin


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 Calcium-Bound MTMEM16F Lipid Scramblase in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:43.9
occ:1.00
 O B:ILE857 2.5 39.4 1.0
OD1 B:ASP859 2.5 55.9 1.0
OE1 B:GLU395 2.5 33.0 1.0
O B:SER854 2.5 31.6 1.0
CD B:GLU395 3.4 33.0 1.0
CG B:ASP859 3.6 55.9 1.0
C B:SER854 3.7 31.6 1.0
OE2 B:GLU395 3.7 33.0 1.0
C B:ILE857 3.8 39.4 1.0
N B:ASP859 4.1 55.9 1.0
OG B:SER854 4.1 31.6 1.0
NZ B:LYS398 4.2 35.3 1.0
CA B:SER854 4.2 31.6 1.0
C B:PRO858 4.3 52.4 1.0
OD2 B:ASP859 4.3 55.9 1.0
CA B:PRO858 4.4 52.4 1.0
CA B:ASP859 4.4 55.9 1.0
CB B:ASP859 4.5 55.9 1.0
N B:PRO858 4.6 52.4 1.0
CG B:GLU395 4.6 33.0 1.0
CB B:SER854 4.7 31.6 1.0
CA B:ILE857 4.7 39.4 1.0
N B:TYR855 4.8 37.5 1.0
O B:PRO858 4.9 52.4 1.0
CE B:LYS398 4.9 35.3 1.0
CB B:ILE857 4.9 39.4 1.0
N B:ILE857 4.9 39.4 1.0

Reference:

C.Alvadia, N.K.Lim, V.Clerico Mosina, G.T.Oostergetel, R.Dutzler, C.Paulino. Cryo-Em Structures and Functional Characterization of the Murine Lipid Scramblase TMEM16F. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30785399
DOI: 10.7554/ELIFE.44365
Page generated: Tue Jul 16 13:56:27 2024

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