Calcium in PDB 9iv8: Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound State
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound State
(pdb code 9iv8). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound State, PDB code: 9iv8:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 9iv8
Go back to
Calcium Binding Sites List in 9iv8
Calcium binding site 1 out
of 5 in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound 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 Human NCX1 in PIP2 DIC8 Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1001
b:48.7
occ:1.00
|
OE1
|
A:GLU199
|
2.3
|
48.9
|
1.0
|
O
|
A:SER191
|
2.4
|
47.9
|
1.0
|
O
|
A:ILE190
|
2.5
|
43.9
|
1.0
|
OE2
|
A:GLU199
|
2.6
|
48.9
|
1.0
|
CB
|
A:SER191
|
2.7
|
47.9
|
1.0
|
CD
|
A:GLU199
|
2.8
|
48.9
|
1.0
|
O
|
A:ILE186
|
3.0
|
34.9
|
1.0
|
O
|
A:VAL194
|
3.0
|
48.7
|
1.0
|
C
|
A:SER191
|
3.1
|
47.9
|
1.0
|
OG
|
A:SER191
|
3.3
|
47.9
|
1.0
|
CA
|
A:SER191
|
3.3
|
47.9
|
1.0
|
C
|
A:ILE190
|
3.4
|
43.9
|
1.0
|
N
|
A:SER191
|
3.7
|
47.9
|
1.0
|
C
|
A:ILE186
|
4.0
|
34.9
|
1.0
|
C
|
A:VAL194
|
4.1
|
48.7
|
1.0
|
CG
|
A:GLU199
|
4.2
|
48.9
|
1.0
|
CG2
|
A:VAL194
|
4.3
|
48.7
|
1.0
|
N
|
A:PRO192
|
4.4
|
48.3
|
1.0
|
CA
|
A:ILE186
|
4.4
|
34.9
|
1.0
|
CA
|
A:ILE190
|
4.7
|
43.9
|
1.0
|
CA
|
A:VAL195
|
4.8
|
43.5
|
1.0
|
CB
|
A:ILE186
|
4.8
|
34.9
|
1.0
|
N
|
A:VAL195
|
4.8
|
43.5
|
1.0
|
N
|
A:VAL194
|
4.8
|
48.7
|
1.0
|
CA
|
A:PRO192
|
4.9
|
48.3
|
1.0
|
N
|
A:GLU196
|
5.0
|
48.3
|
1.0
|
CA
|
A:VAL194
|
5.0
|
48.7
|
1.0
|
CB
|
A:ILE190
|
5.0
|
43.9
|
1.0
|
|
Calcium binding site 2 out
of 5 in 9iv8
Go back to
Calcium Binding Sites List in 9iv8
Calcium binding site 2 out
of 5 in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound 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 Human NCX1 in PIP2 DIC8 Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1003
b:40.8
occ:1.00
|
OE1
|
A:GLU451
|
2.4
|
36.3
|
1.0
|
OD2
|
A:ASP421
|
2.7
|
43.7
|
1.0
|
OE1
|
A:GLU454
|
2.8
|
47.4
|
1.0
|
OE2
|
A:GLU454
|
2.9
|
47.4
|
1.0
|
CD
|
A:GLU454
|
3.3
|
47.4
|
1.0
|
CD
|
A:GLU451
|
3.5
|
36.3
|
1.0
|
CG
|
A:ASP421
|
3.7
|
43.7
|
1.0
|
CB
|
A:ASP421
|
3.9
|
43.7
|
1.0
|
OE2
|
A:GLU451
|
4.2
|
36.3
|
1.0
|
CA
|
A:CA1004
|
4.4
|
19.4
|
1.0
|
CG
|
A:GLU451
|
4.6
|
36.3
|
1.0
|
OG
|
A:SER420
|
4.6
|
48.1
|
1.0
|
N
|
A:ASN417
|
4.8
|
59.9
|
1.0
|
CA
|
A:ALA416
|
4.8
|
57.5
|
1.0
|
CG
|
A:GLU454
|
4.8
|
47.4
|
1.0
|
OD1
|
A:ASP421
|
4.9
|
43.7
|
1.0
|
ND2
|
A:ASN417
|
4.9
|
59.9
|
1.0
|
|
Calcium binding site 3 out
of 5 in 9iv8
Go back to
Calcium Binding Sites List in 9iv8
Calcium binding site 3 out
of 5 in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound 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 Human NCX1 in PIP2 DIC8 Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1004
b:19.4
occ:1.00
|
OE2
|
A:GLU385
|
2.3
|
31.2
|
1.0
|
OD2
|
A:ASP421
|
2.3
|
43.7
|
1.0
|
OE2
|
A:GLU451
|
2.4
|
36.3
|
1.0
|
OD1
|
A:ASP421
|
2.5
|
43.7
|
1.0
|
CG
|
A:ASP421
|
2.6
|
43.7
|
1.0
|
CD
|
A:GLU451
|
3.0
|
36.3
|
1.0
|
OE1
|
A:GLU451
|
3.1
|
36.3
|
1.0
|
CD
|
A:GLU385
|
3.5
|
31.2
|
1.0
|
CA
|
A:CA1006
|
3.7
|
27.2
|
1.0
|
CB
|
A:ASP421
|
4.1
|
43.7
|
1.0
|
OD1
|
A:ASP447
|
4.1
|
31.2
|
1.0
|
OD2
|
A:ASP498
|
4.1
|
32.2
|
1.0
|
CG
|
A:GLU385
|
4.1
|
31.2
|
1.0
|
CG
|
A:GLU451
|
4.3
|
36.3
|
1.0
|
CA
|
A:CA1003
|
4.4
|
40.8
|
1.0
|
O
|
A:ILE445
|
4.4
|
39.2
|
1.0
|
OE1
|
A:GLU385
|
4.4
|
31.2
|
1.0
|
OE1
|
A:GLU454
|
4.6
|
47.4
|
1.0
|
CA
|
A:ASP421
|
4.7
|
43.7
|
1.0
|
CB
|
A:GLU451
|
4.8
|
36.3
|
1.0
|
OD2
|
A:ASP447
|
4.9
|
31.2
|
1.0
|
CG
|
A:ASP447
|
4.9
|
31.2
|
1.0
|
CG
|
A:ASP498
|
4.9
|
32.2
|
1.0
|
|
Calcium binding site 4 out
of 5 in 9iv8
Go back to
Calcium Binding Sites List in 9iv8
Calcium binding site 4 out
of 5 in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound 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 Human NCX1 in PIP2 DIC8 Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1005
b:27.6
occ:1.00
|
OE1
|
A:GLU385
|
2.4
|
31.2
|
1.0
|
OD1
|
A:ASP500
|
2.4
|
28.0
|
1.0
|
OD1
|
A:ASP446
|
2.5
|
29.4
|
1.0
|
OD2
|
A:ASP500
|
3.0
|
28.0
|
1.0
|
CG
|
A:ASP500
|
3.0
|
28.0
|
1.0
|
O
|
A:ASP447
|
3.2
|
31.2
|
1.0
|
OD1
|
A:ASP499
|
3.3
|
32.2
|
1.0
|
CD
|
A:GLU385
|
3.5
|
31.2
|
1.0
|
CG
|
A:ASP446
|
3.5
|
29.4
|
1.0
|
NH1
|
A:ARG532
|
3.8
|
22.8
|
1.0
|
OD2
|
A:ASP446
|
4.0
|
29.4
|
1.0
|
CG
|
A:GLU385
|
4.0
|
31.2
|
1.0
|
CB
|
A:GLU385
|
4.0
|
31.2
|
1.0
|
CA
|
A:CA1006
|
4.1
|
27.2
|
1.0
|
CG
|
A:ASP499
|
4.4
|
32.2
|
1.0
|
C
|
A:ASP447
|
4.4
|
31.2
|
1.0
|
CB
|
A:ASP500
|
4.5
|
28.0
|
1.0
|
OD1
|
A:ASP498
|
4.5
|
32.2
|
1.0
|
OE2
|
A:GLU385
|
4.5
|
31.2
|
1.0
|
N
|
A:ASP447
|
4.6
|
31.2
|
1.0
|
CB
|
A:ASP446
|
4.7
|
29.4
|
1.0
|
OD2
|
A:ASP499
|
4.8
|
32.2
|
1.0
|
N
|
A:ASP499
|
4.9
|
32.2
|
1.0
|
N
|
A:ASN386
|
4.9
|
32.7
|
1.0
|
C
|
A:ASP499
|
4.9
|
32.2
|
1.0
|
CB
|
A:ASN386
|
4.9
|
32.7
|
1.0
|
N
|
A:ASP500
|
5.0
|
28.0
|
1.0
|
|
Calcium binding site 5 out
of 5 in 9iv8
Go back to
Calcium Binding Sites List in 9iv8
Calcium binding site 5 out
of 5 in the Cryo-Em Structure of Human NCX1 in PIP2 DIC8 Bound State
 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 Human NCX1 in PIP2 DIC8 Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1006
b:27.2
occ:1.00
|
OE2
|
A:GLU385
|
2.3
|
31.2
|
1.0
|
OD2
|
A:ASP498
|
2.3
|
32.2
|
1.0
|
OE1
|
A:GLU385
|
2.4
|
31.2
|
1.0
|
OD2
|
A:ASP500
|
2.4
|
28.0
|
1.0
|
O
|
A:ILE449
|
2.7
|
29.8
|
1.0
|
CD
|
A:GLU385
|
2.7
|
31.2
|
1.0
|
OD1
|
A:ASP447
|
2.7
|
31.2
|
1.0
|
OE2
|
A:GLU451
|
3.0
|
36.3
|
1.0
|
CG
|
A:ASP498
|
3.1
|
32.2
|
1.0
|
OD1
|
A:ASP498
|
3.3
|
32.2
|
1.0
|
O
|
A:ASP447
|
3.4
|
31.2
|
1.0
|
CG
|
A:ASP500
|
3.6
|
28.0
|
1.0
|
CA
|
A:CA1004
|
3.7
|
19.4
|
1.0
|
C
|
A:ILE449
|
3.8
|
29.8
|
1.0
|
CD
|
A:GLU451
|
4.0
|
36.3
|
1.0
|
CG
|
A:ASP447
|
4.0
|
31.2
|
1.0
|
C
|
A:ASP447
|
4.1
|
31.2
|
1.0
|
CA
|
A:CA1005
|
4.1
|
27.6
|
1.0
|
CG
|
A:GLU385
|
4.2
|
31.2
|
1.0
|
N
|
A:ILE449
|
4.3
|
29.8
|
1.0
|
CG
|
A:GLU451
|
4.3
|
36.3
|
1.0
|
CB
|
A:ASP498
|
4.3
|
32.2
|
1.0
|
N
|
A:ASP447
|
4.4
|
31.2
|
1.0
|
OD1
|
A:ASP500
|
4.4
|
28.0
|
1.0
|
CB
|
A:ASP500
|
4.5
|
28.0
|
1.0
|
CA
|
A:ILE449
|
4.6
|
29.8
|
1.0
|
CA
|
A:ASP447
|
4.7
|
31.2
|
1.0
|
C
|
A:ASP448
|
4.7
|
28.4
|
1.0
|
OD2
|
A:ASP447
|
4.8
|
31.2
|
1.0
|
OD1
|
A:ASP446
|
4.8
|
29.4
|
1.0
|
N
|
A:ASP448
|
4.9
|
28.4
|
1.0
|
N
|
A:PHE450
|
4.9
|
30.3
|
1.0
|
N
|
A:GLU451
|
4.9
|
36.3
|
1.0
|
CB
|
A:ASP447
|
4.9
|
31.2
|
1.0
|
|
Reference:
J.Xue,
Y.Jiang.
Structural Mechanisms of Human Cardiac Sodium Calcium Exchanger NCX1 To Be Published.
Page generated: Thu Jul 10 09:55:37 2025
|