Calcium in PDB 8b8j: Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant in Digitonin

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant in Digitonin (pdb code 8b8j). 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 F518H Mutant in Digitonin, PDB code: 8b8j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8b8j

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Calcium binding site 1 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:133.0
occ:1.00
 OD1 A:ASN621 2.3 116.8 1.0
OE2 A:GLU670 2.3 108.2 1.0
OE2 A:GLU699 2.3 112.4 1.0
OE1 A:GLU699 2.4 106.5 1.0
OE1 A:GLU624 2.5 107.1 1.0
CD A:GLU699 2.7 106.8 1.0
CD A:GLU670 3.2 110.8 1.0
OE1 A:GLU670 3.3 107.5 1.0
CG A:ASN621 3.4 118.9 1.0
CD A:GLU624 3.8 113.2 1.0
CA A:ASN621 3.9 111.0 1.0
N A:ASN621 4.0 112.3 1.0
CA A:CA1002 4.0 88.0 1.0
OD1 A:ASN620 4.1 124.5 1.0
CG A:ASN620 4.1 125.3 1.0
CG A:GLU699 4.2 96.0 1.0
C A:ASN620 4.2 116.4 1.0
CB A:ASN621 4.2 115.7 1.0
ND2 A:ASN621 4.3 120.9 1.0
O A:ASN620 4.4 122.2 1.0
OE2 A:GLU624 4.4 115.8 1.0
CB A:ASN620 4.5 120.1 1.0
ND2 A:ASN620 4.6 121.4 1.0
CG A:GLU670 4.6 106.2 1.0
CB A:GLU624 4.7 115.1 1.0
ND2 A:ASN695 4.8 99.9 1.0
CG A:GLU624 4.8 119.1 1.0
O A:ALA617 4.9 118.9 1.0
CG1 A:VAL702 4.9 102.8 1.0
CB A:GLU699 4.9 99.2 1.0

Calcium binding site 2 out of 6 in 8b8j

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Calcium binding site 2 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:88.0
occ:1.00
 OE1 A:GLU667 2.3 121.6 1.0
OE2 A:GLU624 2.3 115.8 1.0
OE2 A:GLU699 2.3 112.4 1.0
OD1 A:ASP703 2.5 109.0 1.0
OD2 A:ASP703 2.8 105.2 1.0
OE1 A:GLU670 2.9 107.5 1.0
CG A:ASP703 3.1 104.0 1.0
CD A:GLU624 3.1 113.2 1.0
OE1 A:GLU624 3.1 107.1 1.0
CD A:GLU699 3.4 106.8 1.0
CD A:GLU667 3.5 121.9 1.0
CG A:GLU699 3.8 96.0 1.0
CD A:GLU670 3.9 110.8 1.0
CA A:CA1001 4.0 133.0 1.0
OE2 A:GLU667 4.2 125.0 1.0
OH A:TYR299 4.3 100.0 1.0
OE2 A:GLU670 4.4 108.2 1.0
OE1 A:GLU699 4.5 106.5 1.0
CG A:GLU624 4.5 119.1 1.0
CA A:GLU667 4.6 107.4 1.0
CB A:ASP703 4.6 92.7 1.0
CB A:GLU667 4.6 110.3 1.0
CG A:GLU667 4.6 114.6 1.0

Calcium binding site 3 out of 6 in 8b8j

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Calcium binding site 3 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:153.6
occ:1.00
 O A:ILE857 2.3 127.4 1.0
OD1 A:ASP859 2.4 154.4 1.0
OE1 A:GLU395 2.7 134.3 1.0
O A:SER854 2.9 122.2 1.0
C A:ILE857 3.5 127.2 1.0
CG A:ASP859 3.6 152.8 1.0
CD A:GLU395 3.6 133.8 1.0
N A:ASP859 3.9 146.5 1.0
C A:SER854 4.0 123.8 1.0
C A:PRO858 4.0 143.7 1.0
OE2 A:GLU395 4.0 130.9 1.0
CA A:ASP859 4.2 147.8 1.0
CB A:ILE857 4.3 124.5 1.0
OG A:SER854 4.3 120.2 1.0
CA A:ILE857 4.3 123.7 1.0
CG2 A:ILE857 4.4 124.5 1.0
O A:PRO858 4.4 146.8 1.0
OD2 A:ASP859 4.4 151.5 1.0
N A:PRO858 4.4 146.4 1.0
CA A:PRO858 4.5 145.2 1.0
CB A:ASP859 4.5 150.4 1.0
CA A:SER854 4.5 118.3 1.0
N A:ILE857 4.5 123.6 1.0
CG A:GLU395 4.7 131.7 1.0

Calcium binding site 4 out of 6 in 8b8j

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Calcium binding site 4 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:133.0
occ:1.00
 OD1 B:ASN621 2.3 116.8 1.0
OE2 B:GLU670 2.3 108.2 1.0
OE2 B:GLU699 2.3 112.4 1.0
OE1 B:GLU699 2.4 106.5 1.0
OE1 B:GLU624 2.5 107.1 1.0
CD B:GLU699 2.7 106.8 1.0
CD B:GLU670 3.2 110.8 1.0
OE1 B:GLU670 3.3 107.5 1.0
CG B:ASN621 3.4 118.9 1.0
CD B:GLU624 3.8 113.2 1.0
CA B:ASN621 3.9 111.0 1.0
N B:ASN621 4.0 112.3 1.0
CA B:CA1002 4.0 88.0 1.0
OD1 B:ASN620 4.1 124.5 1.0
CG B:ASN620 4.1 125.3 1.0
CG B:GLU699 4.2 96.0 1.0
C B:ASN620 4.2 116.4 1.0
CB B:ASN621 4.2 115.7 1.0
ND2 B:ASN621 4.3 120.9 1.0
O B:ASN620 4.4 122.2 1.0
OE2 B:GLU624 4.4 115.8 1.0
CB B:ASN620 4.5 120.1 1.0
ND2 B:ASN620 4.6 121.4 1.0
CG B:GLU670 4.6 106.2 1.0
CB B:GLU624 4.7 115.1 1.0
ND2 B:ASN695 4.8 99.9 1.0
CG B:GLU624 4.8 119.1 1.0
O B:ALA617 4.9 118.9 1.0
CG1 B:VAL702 4.9 102.8 1.0
CB B:GLU699 4.9 99.2 1.0

Calcium binding site 5 out of 6 in 8b8j

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Calcium binding site 5 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:88.0
occ:1.00
 OE1 B:GLU667 2.3 121.6 1.0
OE2 B:GLU624 2.3 115.8 1.0
OE2 B:GLU699 2.3 112.4 1.0
OD1 B:ASP703 2.5 109.0 1.0
OD2 B:ASP703 2.8 105.2 1.0
OE1 B:GLU670 2.9 107.5 1.0
CG B:ASP703 3.1 104.0 1.0
CD B:GLU624 3.1 113.2 1.0
OE1 B:GLU624 3.1 107.1 1.0
CD B:GLU699 3.4 106.8 1.0
CD B:GLU667 3.5 121.9 1.0
CG B:GLU699 3.8 96.0 1.0
CD B:GLU670 3.9 110.8 1.0
CA B:CA1001 4.0 133.0 1.0
OE2 B:GLU667 4.2 125.0 1.0
OH B:TYR299 4.3 100.0 1.0
OE2 B:GLU670 4.4 108.2 1.0
OE1 B:GLU699 4.5 106.5 1.0
CG B:GLU624 4.5 119.1 1.0
CA B:GLU667 4.6 107.4 1.0
CB B:ASP703 4.6 92.7 1.0
CB B:GLU667 4.6 110.3 1.0
CG B:GLU667 4.6 114.6 1.0

Calcium binding site 6 out of 6 in 8b8j

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Calcium binding site 6 out of 6 in the Cryo-Em Structure of CA2+-Bound MTMEM16F F518H Mutant 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 CA2+-Bound MTMEM16F F518H Mutant in Digitonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:153.6
occ:1.00
 O B:ILE857 2.3 127.4 1.0
OD1 B:ASP859 2.4 154.4 1.0
OE1 B:GLU395 2.7 134.3 1.0
O B:SER854 2.9 122.2 1.0
C B:ILE857 3.5 127.2 1.0
CG B:ASP859 3.6 152.8 1.0
CD B:GLU395 3.6 133.8 1.0
N B:ASP859 3.9 146.5 1.0
C B:SER854 4.0 123.8 1.0
C B:PRO858 4.0 143.7 1.0
OE2 B:GLU395 4.0 130.9 1.0
CA B:ASP859 4.2 147.8 1.0
CB B:ILE857 4.3 124.5 1.0
OG B:SER854 4.3 120.2 1.0
CA B:ILE857 4.3 123.7 1.0
CG2 B:ILE857 4.4 124.5 1.0
O B:PRO858 4.4 146.8 1.0
OD2 B:ASP859 4.4 151.5 1.0
N B:PRO858 4.4 146.4 1.0
CA B:PRO858 4.5 145.2 1.0
CB B:ASP859 4.5 150.4 1.0
CA B:SER854 4.5 118.3 1.0
N B:ILE857 4.5 123.6 1.0
CG B:GLU395 4.7 131.7 1.0

Reference:

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
Page generated: Fri Jul 19 07:13:35 2024

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