Calcium in PDB 8b8q: Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ (pdb code 8b8q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+, PDB code: 8b8q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8b8q

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Calcium binding site 1 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:107.0
occ:1.00
 OE2 A:GLU670 2.3 104.7 1.0
OD1 A:ASN621 2.3 101.6 1.0
OE2 A:GLU699 2.3 93.0 1.0
OE1 A:GLU624 2.3 105.4 1.0
OE1 A:GLU699 2.5 99.3 1.0
CD A:GLU699 2.7 95.7 1.0
CD A:GLU670 3.3 106.3 1.0
CD A:GLU624 3.4 107.0 1.0
CG A:ASN621 3.5 101.9 1.0
OE1 A:GLU670 3.6 106.5 1.0
OE2 A:GLU624 3.9 104.4 1.0
CG A:ASN620 4.0 114.8 1.0
N A:ASN621 4.1 101.4 1.0
CA A:CA1002 4.1 95.9 1.0
CB A:ASN620 4.1 110.3 1.0
CG A:GLU699 4.2 92.1 1.0
ND2 A:ASN620 4.2 115.1 1.0
CA A:ASN621 4.2 97.8 1.0
OD1 A:ASN620 4.2 119.5 1.0
ND2 A:ASN621 4.3 106.4 1.0
C A:ASN620 4.3 113.9 1.0
OD1 A:ASN695 4.4 96.2 1.0
CB A:ASN621 4.5 99.1 1.0
O A:ASN620 4.5 122.0 1.0
CG A:GLU670 4.6 98.3 1.0
CG A:GLU624 4.6 108.9 1.0
O A:ALA617 4.8 128.1 1.0
CA A:ASN620 4.9 110.2 1.0
CG1 A:VAL702 5.0 84.5 1.0

Calcium binding site 2 out of 6 in 8b8q

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Calcium binding site 2 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:95.9
occ:1.00
 OE1 A:GLU667 2.2 98.6 1.0
OE2 A:GLU699 2.3 93.0 1.0
OD1 A:ASP703 2.4 89.3 1.0
OD2 A:ASP703 2.6 97.1 1.0
OE2 A:GLU624 2.7 104.4 1.0
CG A:ASP703 2.8 87.3 1.0
OE1 A:GLU670 2.9 106.5 1.0
CD A:GLU699 3.3 95.7 1.0
CD A:GLU667 3.4 106.9 1.0
CD A:GLU624 3.6 107.0 1.0
CG A:GLU699 3.6 92.1 1.0
OE1 A:GLU624 3.8 105.4 1.0
CD A:GLU670 3.9 106.3 1.0
OE2 A:GLU667 4.1 109.3 1.0
CA A:CA1001 4.1 107.0 1.0
OH A:TYR299 4.3 85.2 1.0
OE2 A:GLU670 4.3 104.7 1.0
CB A:ASP703 4.3 80.0 1.0
OE1 A:GLU699 4.4 99.3 1.0
NZ A:LYS706 4.4 95.7 1.0
CG A:GLU667 4.4 101.7 1.0
CB A:GLU667 4.5 95.9 1.0
CA A:GLU667 4.8 95.6 1.0
CE A:LYS706 4.8 93.2 1.0
CG1 A:VAL702 4.8 84.5 1.0
O A:GLU699 5.0 101.4 1.0
CG A:GLU624 5.0 108.9 1.0

Calcium binding site 3 out of 6 in 8b8q

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Calcium binding site 3 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:159.0
occ:1.00
 O A:ILE857 2.3 138.3 1.0
OD1 A:ASP859 2.3 174.1 1.0
O A:SER854 2.3 129.3 1.0
CG A:ASP859 3.3 173.8 1.0
C A:ILE857 3.5 138.6 1.0
C A:SER854 3.6 126.2 1.0
OD2 A:ASP859 3.7 173.8 1.0
N A:ASP859 3.9 168.7 1.0
OG A:SER854 4.0 123.5 1.0
OE2 A:GLU395 4.0 129.3 1.0
C A:PRO858 4.2 160.2 1.0
CA A:PRO858 4.2 160.3 1.0
N A:PRO858 4.3 159.9 1.0
CA A:SER854 4.3 117.6 1.0
CB A:ASP859 4.4 170.7 1.0
CA A:ASP859 4.4 170.2 1.0
CA A:ILE857 4.5 137.2 1.0
N A:TYR855 4.6 137.6 1.0
CG A:GLU395 4.6 127.1 1.0
O A:TYR855 4.6 140.2 1.0
N A:ILE857 4.6 133.6 1.0
CA A:TYR855 4.7 139.0 1.0
C A:TYR855 4.8 139.4 1.0
CD A:GLU395 4.8 128.9 1.0
CB A:SER854 4.8 121.2 1.0
CB A:ILE857 4.8 136.3 1.0
O A:PRO858 4.9 160.6 1.0

Calcium binding site 4 out of 6 in 8b8q

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Calcium binding site 4 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:98.0
occ:1.00
 OE2 B:GLU670 2.2 104.2 1.0
OE1 B:GLU699 2.2 98.3 1.0
OD1 B:ASN621 2.3 96.4 1.0
OE2 B:GLU699 2.4 89.6 1.0
CD B:GLU699 2.6 90.4 1.0
OE1 B:GLU624 2.9 96.2 1.0
CD B:GLU670 3.3 107.1 1.0
CG B:ASN621 3.5 93.5 1.0
OE1 B:GLU670 3.7 100.5 1.0
CD B:GLU624 3.8 100.6 1.0
CG B:ASN620 4.0 109.7 1.0
N B:ASN621 4.0 87.8 1.0
OD1 B:ASN620 4.1 111.9 1.0
CB B:ASN620 4.1 105.9 1.0
CG B:GLU699 4.2 82.9 1.0
CA B:CA1002 4.2 83.8 1.0
CA B:ASN621 4.2 90.3 1.0
C B:ASN620 4.2 102.7 1.0
OE2 B:GLU624 4.4 96.5 1.0
ND2 B:ASN620 4.4 110.0 1.0
ND2 B:ASN621 4.4 91.1 1.0
O B:ASN620 4.5 112.4 1.0
CB B:ASN621 4.5 94.3 1.0
OD1 B:ASN695 4.5 92.3 1.0
CG B:GLU670 4.6 100.1 1.0
O B:ALA617 4.7 127.1 1.0
CA B:ASN620 4.9 101.6 1.0
CG B:GLU624 4.9 102.6 1.0
CB B:GLU699 4.9 83.7 1.0
CG1 B:VAL702 4.9 77.9 1.0

Calcium binding site 5 out of 6 in 8b8q

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Calcium binding site 5 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:83.8
occ:1.00
 OE1 B:GLU667 2.3 108.8 1.0
OE2 B:GLU699 2.4 89.6 1.0
OE2 B:GLU624 2.4 96.5 1.0
OD1 B:ASP703 2.4 97.3 1.0
OD2 B:ASP703 2.7 98.6 1.0
OE1 B:GLU670 2.7 100.5 1.0
CG B:ASP703 2.9 93.4 1.0
CD B:GLU624 3.2 100.6 1.0
OE1 B:GLU624 3.3 96.2 1.0
CD B:GLU699 3.5 90.4 1.0
CD B:GLU667 3.5 106.2 1.0
CD B:GLU670 3.7 107.1 1.0
CG B:GLU699 4.0 82.9 1.0
OE2 B:GLU670 4.1 104.2 1.0
OH B:TYR299 4.1 90.6 1.0
CA B:CA1001 4.2 98.0 1.0
OE2 B:GLU667 4.3 108.8 1.0
CB B:ASP703 4.4 83.7 1.0
CB B:GLU667 4.4 92.7 1.0
CG B:GLU667 4.5 99.5 1.0
OE1 B:GLU699 4.5 98.3 1.0
CA B:GLU667 4.6 95.9 1.0
NZ B:LYS706 4.6 92.3 1.0
CG B:GLU624 4.6 102.6 1.0
CG B:GLU670 4.9 100.1 1.0
CE B:LYS706 5.0 83.2 1.0

Calcium binding site 6 out of 6 in 8b8q

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Calcium binding site 6 out of 6 in the Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of MTMEM16F in Lipid Nanodiscs in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:160.1
occ:1.00
 O B:SER854 2.3 122.9 1.0
OD1 B:ASP859 2.3 162.1 1.0
O B:ILE857 2.4 131.9 1.0
CG B:ASP859 3.1 163.7 1.0
C B:SER854 3.5 119.8 1.0
OD2 B:ASP859 3.5 164.9 1.0
C B:ILE857 3.6 130.8 1.0
N B:ASP859 3.8 160.0 1.0
OG B:SER854 3.9 115.3 1.0
CA B:SER854 4.2 113.2 1.0
OE2 B:GLU395 4.3 121.9 1.0
CA B:PRO858 4.3 156.8 1.0
C B:PRO858 4.3 156.6 1.0
CB B:ASP859 4.4 162.7 1.0
N B:PRO858 4.4 154.2 1.0
CA B:ASP859 4.5 160.8 1.0
N B:TYR855 4.5 126.0 1.0
CA B:ILE857 4.6 132.5 1.0
N B:ILE857 4.7 131.4 1.0
CA B:TYR855 4.7 127.6 1.0
CB B:SER854 4.7 117.7 1.0
CG B:GLU395 4.7 119.2 1.0
O B:TYR855 4.7 128.8 1.0
CB B:ILE857 4.8 133.2 1.0
C B:TYR855 4.8 128.4 1.0
CD B:GLU395 5.0 120.5 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: Tue Apr 4 19:27:47 2023

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