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
Go back to
Calcium Binding Sites List in 6qp6
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 Sites List in 6qp6
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 Sites List in 6qp6
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
Go back to
Calcium Binding Sites List in 6qp6
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
Go back to
Calcium Binding Sites List in 6qp6
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
Go back to
Calcium Binding Sites List in 6qp6
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
|