Calcium in PDB 6qpc: Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
(pdb code 6qpc). 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 MTMEM16F Lipid Scramblase in Nanodisc, PDB code: 6qpc:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6qpc
Go back to
Calcium Binding Sites List in 6qpc
Calcium binding site 1 out
of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
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 Nanodisc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1001
b:65.0
occ:1.00
|
OE2
|
A:GLU699
|
2.5
|
67.6
|
1.0
|
OE1
|
A:GLU670
|
2.5
|
68.7
|
1.0
|
OE1
|
A:GLU699
|
2.5
|
67.6
|
1.0
|
CD
|
A:GLU699
|
2.8
|
67.6
|
1.0
|
OD1
|
A:ASN621
|
3.0
|
73.7
|
1.0
|
OE2
|
A:GLU670
|
3.0
|
68.7
|
1.0
|
CD
|
A:GLU670
|
3.1
|
68.7
|
1.0
|
OE1
|
A:GLU624
|
3.7
|
73.4
|
1.0
|
CB
|
A:ASN620
|
3.7
|
70.3
|
1.0
|
CG
|
A:ASN621
|
3.8
|
73.7
|
1.0
|
O
|
A:ALA617
|
3.9
|
70.6
|
1.0
|
N
|
A:ASN621
|
4.2
|
73.7
|
1.0
|
ND2
|
A:ASN621
|
4.2
|
73.7
|
1.0
|
CG
|
A:ASN620
|
4.3
|
70.3
|
1.0
|
CG
|
A:GLU699
|
4.3
|
67.6
|
1.0
|
CA
|
A:ALA617
|
4.3
|
70.6
|
1.0
|
C
|
A:ASN620
|
4.4
|
70.3
|
1.0
|
CE
|
A:MET671
|
4.4
|
61.4
|
1.0
|
CG
|
A:GLU670
|
4.4
|
68.7
|
1.0
|
CA
|
A:CA1002
|
4.5
|
73.7
|
1.0
|
O
|
A:LYS616
|
4.5
|
71.4
|
1.0
|
ND2
|
A:ASN695
|
4.5
|
67.6
|
1.0
|
OD1
|
A:ASN695
|
4.5
|
67.6
|
1.0
|
CD
|
A:GLU624
|
4.6
|
73.4
|
1.0
|
C
|
A:ALA617
|
4.6
|
70.6
|
1.0
|
ND2
|
A:ASN620
|
4.6
|
70.3
|
1.0
|
NZ
|
A:LYS616
|
4.6
|
71.4
|
1.0
|
CA
|
A:ASN620
|
4.6
|
70.3
|
1.0
|
CA
|
A:ASN621
|
4.7
|
73.7
|
1.0
|
CB
|
A:ASN621
|
4.8
|
73.7
|
1.0
|
OE2
|
A:GLU624
|
4.9
|
73.4
|
1.0
|
O
|
A:ASN620
|
4.9
|
70.3
|
1.0
|
OD1
|
A:ASN620
|
4.9
|
70.3
|
1.0
|
CG
|
A:ASN695
|
5.0
|
67.6
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6qpc
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Calcium Binding Sites List in 6qpc
Calcium binding site 2 out
of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
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 Nanodisc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1002
b:73.7
occ:1.00
|
OE2
|
A:GLU670
|
2.5
|
68.7
|
1.0
|
OD1
|
A:ASP703
|
2.5
|
71.8
|
1.0
|
OD2
|
A:ASP703
|
2.5
|
71.8
|
1.0
|
OE2
|
A:GLU624
|
2.5
|
73.4
|
1.0
|
OE2
|
A:GLU699
|
2.6
|
67.6
|
1.0
|
CG
|
A:ASP703
|
2.8
|
71.8
|
1.0
|
OE1
|
A:GLU667
|
2.9
|
71.3
|
1.0
|
CD
|
A:GLU624
|
3.4
|
73.4
|
1.0
|
OE1
|
A:GLU624
|
3.5
|
73.4
|
1.0
|
CD
|
A:GLU699
|
3.5
|
67.6
|
1.0
|
OH
|
A:TYR299
|
3.6
|
64.3
|
1.0
|
CD
|
A:GLU670
|
3.6
|
68.7
|
1.0
|
CG
|
A:GLU699
|
3.8
|
67.6
|
1.0
|
CD
|
A:GLU667
|
4.0
|
71.3
|
1.0
|
CG
|
A:GLU670
|
4.2
|
68.7
|
1.0
|
CB
|
A:ASP703
|
4.3
|
71.8
|
1.0
|
CA
|
A:CA1001
|
4.5
|
65.0
|
1.0
|
CB
|
A:GLU667
|
4.5
|
71.3
|
1.0
|
OE1
|
A:GLU670
|
4.6
|
68.7
|
1.0
|
CA
|
A:GLU667
|
4.6
|
71.3
|
1.0
|
OE1
|
A:GLU699
|
4.7
|
67.6
|
1.0
|
O
|
A:GLU667
|
4.8
|
71.3
|
1.0
|
OE2
|
A:GLU667
|
4.8
|
71.3
|
1.0
|
CG
|
A:GLU624
|
4.8
|
73.4
|
1.0
|
O
|
A:GLU699
|
4.8
|
67.6
|
1.0
|
CZ
|
A:TYR299
|
4.8
|
64.3
|
1.0
|
CG
|
A:GLU667
|
4.9
|
71.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6qpc
Go back to
Calcium Binding Sites List in 6qpc
Calcium binding site 3 out
of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
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 Nanodisc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1001
b:65.0
occ:1.00
|
OE2
|
B:GLU699
|
2.5
|
67.6
|
1.0
|
OE1
|
B:GLU670
|
2.5
|
68.7
|
1.0
|
OE1
|
B:GLU699
|
2.5
|
67.6
|
1.0
|
CD
|
B:GLU699
|
2.8
|
67.6
|
1.0
|
OD1
|
B:ASN621
|
3.0
|
73.7
|
1.0
|
OE2
|
B:GLU670
|
3.0
|
68.7
|
1.0
|
CD
|
B:GLU670
|
3.1
|
68.7
|
1.0
|
OE1
|
B:GLU624
|
3.7
|
73.4
|
1.0
|
CB
|
B:ASN620
|
3.7
|
70.3
|
1.0
|
CG
|
B:ASN621
|
3.8
|
73.7
|
1.0
|
O
|
B:ALA617
|
3.9
|
70.6
|
1.0
|
N
|
B:ASN621
|
4.2
|
73.7
|
1.0
|
ND2
|
B:ASN621
|
4.2
|
73.7
|
1.0
|
CG
|
B:ASN620
|
4.3
|
70.3
|
1.0
|
CG
|
B:GLU699
|
4.3
|
67.6
|
1.0
|
CA
|
B:ALA617
|
4.3
|
70.6
|
1.0
|
C
|
B:ASN620
|
4.4
|
70.3
|
1.0
|
CE
|
B:MET671
|
4.4
|
61.4
|
1.0
|
CG
|
B:GLU670
|
4.4
|
68.7
|
1.0
|
CA
|
B:CA1002
|
4.5
|
73.7
|
1.0
|
O
|
B:LYS616
|
4.5
|
71.4
|
1.0
|
ND2
|
B:ASN695
|
4.5
|
67.6
|
1.0
|
OD1
|
B:ASN695
|
4.5
|
67.6
|
1.0
|
CD
|
B:GLU624
|
4.6
|
73.4
|
1.0
|
C
|
B:ALA617
|
4.6
|
70.6
|
1.0
|
ND2
|
B:ASN620
|
4.6
|
70.3
|
1.0
|
NZ
|
B:LYS616
|
4.6
|
71.4
|
1.0
|
CA
|
B:ASN620
|
4.6
|
70.3
|
1.0
|
CA
|
B:ASN621
|
4.7
|
73.7
|
1.0
|
CB
|
B:ASN621
|
4.8
|
73.7
|
1.0
|
OE2
|
B:GLU624
|
4.9
|
73.4
|
1.0
|
O
|
B:ASN620
|
4.9
|
70.3
|
1.0
|
OD1
|
B:ASN620
|
4.9
|
70.3
|
1.0
|
CG
|
B:ASN695
|
5.0
|
67.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6qpc
Go back to
Calcium Binding Sites List in 6qpc
Calcium binding site 4 out
of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc
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 Nanodisc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1002
b:73.7
occ:1.00
|
OE2
|
B:GLU670
|
2.5
|
68.7
|
1.0
|
OD1
|
B:ASP703
|
2.5
|
71.8
|
1.0
|
OD2
|
B:ASP703
|
2.5
|
71.8
|
1.0
|
OE2
|
B:GLU624
|
2.5
|
73.4
|
1.0
|
OE2
|
B:GLU699
|
2.6
|
67.6
|
1.0
|
CG
|
B:ASP703
|
2.8
|
71.8
|
1.0
|
OE1
|
B:GLU667
|
2.9
|
71.3
|
1.0
|
CD
|
B:GLU624
|
3.4
|
73.4
|
1.0
|
OE1
|
B:GLU624
|
3.5
|
73.4
|
1.0
|
CD
|
B:GLU699
|
3.5
|
67.6
|
1.0
|
OH
|
B:TYR299
|
3.6
|
64.3
|
1.0
|
CD
|
B:GLU670
|
3.6
|
68.7
|
1.0
|
CG
|
B:GLU699
|
3.8
|
67.6
|
1.0
|
CD
|
B:GLU667
|
4.0
|
71.3
|
1.0
|
CG
|
B:GLU670
|
4.2
|
68.7
|
1.0
|
CB
|
B:ASP703
|
4.3
|
71.8
|
1.0
|
CA
|
B:CA1001
|
4.5
|
65.0
|
1.0
|
CB
|
B:GLU667
|
4.5
|
71.3
|
1.0
|
OE1
|
B:GLU670
|
4.6
|
68.7
|
1.0
|
CA
|
B:GLU667
|
4.6
|
71.3
|
1.0
|
OE1
|
B:GLU699
|
4.7
|
67.6
|
1.0
|
O
|
B:GLU667
|
4.8
|
71.3
|
1.0
|
OE2
|
B:GLU667
|
4.8
|
71.3
|
1.0
|
CG
|
B:GLU624
|
4.8
|
73.4
|
1.0
|
O
|
B:GLU699
|
4.8
|
67.6
|
1.0
|
CZ
|
B:TYR299
|
4.8
|
64.3
|
1.0
|
CG
|
B:GLU667
|
4.9
|
71.3
|
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 13:56:49 2024
|