Calcium in PDB 6qmb: Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
(pdb code 6qmb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State), PDB code: 6qmb:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6qmb
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Calcium Binding Sites List in 6qmb
Calcium binding site 1 out
of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
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 NHTMEM16 Lipid Scramblase in Nanodisc (Closed State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:57.3
occ:1.00
|
OE2
|
A:GLU452
|
2.5
|
81.3
|
1.0
|
OD2
|
A:ASP539
|
2.5
|
55.7
|
1.0
|
OD1
|
A:ASP503
|
2.5
|
55.6
|
1.0
|
OE1
|
A:GLU506
|
2.5
|
57.3
|
1.0
|
OE2
|
A:GLU535
|
2.7
|
55.2
|
1.0
|
OD1
|
A:ASP539
|
2.8
|
55.7
|
1.0
|
CG
|
A:ASP539
|
3.0
|
55.7
|
1.0
|
CG
|
A:ASP503
|
3.1
|
55.6
|
1.0
|
CD
|
A:GLU506
|
3.4
|
57.3
|
1.0
|
CD
|
A:GLU452
|
3.6
|
81.3
|
1.0
|
CB
|
A:ASP503
|
3.7
|
55.6
|
1.0
|
OD2
|
A:ASP503
|
3.8
|
55.6
|
1.0
|
CD
|
A:GLU535
|
3.8
|
55.2
|
1.0
|
CA
|
A:ASP503
|
3.8
|
55.6
|
1.0
|
OE2
|
A:GLU506
|
3.9
|
57.3
|
1.0
|
OH
|
A:TYR188
|
4.0
|
49.3
|
1.0
|
NZ
|
A:LYS542
|
4.1
|
54.9
|
1.0
|
OE1
|
A:GLU452
|
4.1
|
81.3
|
1.0
|
CA
|
A:CA802
|
4.3
|
76.9
|
1.0
|
CB
|
A:GLU506
|
4.3
|
57.3
|
1.0
|
CG
|
A:GLU506
|
4.4
|
57.3
|
1.0
|
CG
|
A:GLU535
|
4.5
|
55.2
|
1.0
|
CB
|
A:ASP539
|
4.5
|
55.7
|
1.0
|
O
|
A:ASP503
|
4.6
|
55.6
|
1.0
|
CG
|
A:GLU452
|
4.8
|
81.3
|
1.0
|
N
|
A:ASP503
|
4.8
|
55.6
|
1.0
|
OE1
|
A:GLU535
|
4.8
|
55.2
|
1.0
|
C
|
A:ASP503
|
4.8
|
55.6
|
1.0
|
CE
|
A:MET507
|
4.9
|
50.5
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6qmb
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Calcium Binding Sites List in 6qmb
Calcium binding site 2 out
of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
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 NHTMEM16 Lipid Scramblase in Nanodisc (Closed State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:76.9
occ:1.00
|
OE1
|
A:GLU452
|
2.5
|
81.3
|
1.0
|
OE1
|
A:GLU535
|
2.5
|
55.2
|
1.0
|
OE2
|
A:GLU506
|
2.5
|
57.3
|
1.0
|
ND2
|
A:ASN448
|
2.6
|
81.3
|
1.0
|
OE2
|
A:GLU535
|
2.7
|
55.2
|
1.0
|
CD
|
A:GLU452
|
2.9
|
81.3
|
1.0
|
CD
|
A:GLU535
|
3.0
|
55.2
|
1.0
|
OE2
|
A:GLU452
|
3.0
|
81.3
|
1.0
|
CG
|
A:ASN448
|
3.2
|
81.3
|
1.0
|
OD1
|
A:ASN448
|
3.3
|
81.3
|
1.0
|
CD
|
A:GLU506
|
3.4
|
57.3
|
1.0
|
OE1
|
A:GLU506
|
3.6
|
57.3
|
1.0
|
CG
|
A:GLU452
|
4.1
|
81.3
|
1.0
|
CB
|
A:GLU452
|
4.1
|
81.3
|
1.0
|
O
|
A:ASN448
|
4.1
|
81.3
|
1.0
|
CA
|
A:CA801
|
4.3
|
57.3
|
1.0
|
C
|
A:ASN448
|
4.5
|
81.3
|
1.0
|
CG
|
A:GLU535
|
4.5
|
55.2
|
1.0
|
CB
|
A:ASN448
|
4.5
|
81.3
|
1.0
|
OD1
|
A:ASN531
|
4.8
|
53.6
|
1.0
|
CG
|
A:GLU506
|
4.8
|
57.3
|
1.0
|
N
|
A:PHE449
|
4.9
|
83.8
|
1.0
|
CA
|
A:PHE449
|
5.0
|
83.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6qmb
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Calcium Binding Sites List in 6qmb
Calcium binding site 3 out
of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
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 NHTMEM16 Lipid Scramblase in Nanodisc (Closed State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca801
b:57.3
occ:1.00
|
OE2
|
B:GLU452
|
2.5
|
81.3
|
1.0
|
OD2
|
B:ASP539
|
2.5
|
55.7
|
1.0
|
OD1
|
B:ASP503
|
2.5
|
55.6
|
1.0
|
OE1
|
B:GLU506
|
2.5
|
57.3
|
1.0
|
OE2
|
B:GLU535
|
2.7
|
55.2
|
1.0
|
OD1
|
B:ASP539
|
2.8
|
55.7
|
1.0
|
CG
|
B:ASP539
|
3.0
|
55.7
|
1.0
|
CG
|
B:ASP503
|
3.1
|
55.6
|
1.0
|
CD
|
B:GLU506
|
3.4
|
57.3
|
1.0
|
CD
|
B:GLU452
|
3.6
|
81.3
|
1.0
|
CB
|
B:ASP503
|
3.7
|
55.6
|
1.0
|
OD2
|
B:ASP503
|
3.8
|
55.6
|
1.0
|
CD
|
B:GLU535
|
3.8
|
55.2
|
1.0
|
CA
|
B:ASP503
|
3.8
|
55.6
|
1.0
|
OE2
|
B:GLU506
|
3.9
|
57.3
|
1.0
|
OH
|
B:TYR188
|
4.0
|
49.3
|
1.0
|
NZ
|
B:LYS542
|
4.1
|
54.9
|
1.0
|
OE1
|
B:GLU452
|
4.1
|
81.3
|
1.0
|
CA
|
B:CA802
|
4.3
|
76.9
|
1.0
|
CB
|
B:GLU506
|
4.3
|
57.3
|
1.0
|
CG
|
B:GLU506
|
4.4
|
57.3
|
1.0
|
CG
|
B:GLU535
|
4.5
|
55.2
|
1.0
|
CB
|
B:ASP539
|
4.5
|
55.7
|
1.0
|
O
|
B:ASP503
|
4.6
|
55.6
|
1.0
|
CG
|
B:GLU452
|
4.8
|
81.3
|
1.0
|
N
|
B:ASP503
|
4.8
|
55.6
|
1.0
|
OE1
|
B:GLU535
|
4.8
|
55.2
|
1.0
|
C
|
B:ASP503
|
4.8
|
55.6
|
1.0
|
CE
|
B:MET507
|
4.9
|
50.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6qmb
Go back to
Calcium Binding Sites List in 6qmb
Calcium binding site 4 out
of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Closed State)
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 NHTMEM16 Lipid Scramblase in Nanodisc (Closed State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca802
b:76.9
occ:1.00
|
OE1
|
B:GLU452
|
2.5
|
81.3
|
1.0
|
OE1
|
B:GLU535
|
2.5
|
55.2
|
1.0
|
OE2
|
B:GLU506
|
2.5
|
57.3
|
1.0
|
ND2
|
B:ASN448
|
2.6
|
81.3
|
1.0
|
OE2
|
B:GLU535
|
2.7
|
55.2
|
1.0
|
CD
|
B:GLU452
|
2.9
|
81.3
|
1.0
|
CD
|
B:GLU535
|
3.0
|
55.2
|
1.0
|
OE2
|
B:GLU452
|
3.0
|
81.3
|
1.0
|
CG
|
B:ASN448
|
3.2
|
81.3
|
1.0
|
OD1
|
B:ASN448
|
3.3
|
81.3
|
1.0
|
CD
|
B:GLU506
|
3.4
|
57.3
|
1.0
|
OE1
|
B:GLU506
|
3.6
|
57.3
|
1.0
|
CG
|
B:GLU452
|
4.1
|
81.3
|
1.0
|
CB
|
B:GLU452
|
4.1
|
81.3
|
1.0
|
O
|
B:ASN448
|
4.1
|
81.3
|
1.0
|
CA
|
B:CA801
|
4.3
|
57.3
|
1.0
|
C
|
B:ASN448
|
4.5
|
81.3
|
1.0
|
CG
|
B:GLU535
|
4.5
|
55.2
|
1.0
|
CB
|
B:ASN448
|
4.5
|
81.3
|
1.0
|
OD1
|
B:ASN531
|
4.8
|
53.6
|
1.0
|
CG
|
B:GLU506
|
4.8
|
57.3
|
1.0
|
N
|
B:PHE449
|
4.9
|
83.8
|
1.0
|
CA
|
B:PHE449
|
5.0
|
83.8
|
1.0
|
|
Reference:
V.Kalienkova,
V.Clerico Mosina,
L.Bryner,
G.T.Oostergetel,
R.Dutzler,
C.Paulino.
Stepwise Activation Mechanism of the Scramblase NHTMEM16 Revealed By Cryo-Em. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30785398
DOI: 10.7554/ELIFE.44364
Page generated: Tue Jul 16 13:55:24 2024
|