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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

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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

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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

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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

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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

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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

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