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Calcium in PDB 8sgi: Cryo-Em Structure of Human NCX1 in Complex with SEA0400

Other elements in 8sgi:

The structure of Cryo-Em Structure of Human NCX1 in Complex with SEA0400 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400 (pdb code 8sgi). 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 Human NCX1 in Complex with SEA0400, PDB code: 8sgi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8sgi

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Calcium binding site 1 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:28.1
occ:1.00
 O A:VAL194 2.4 32.0 1.0
O A:ILE190 2.4 30.0 1.0
O A:ILE186 2.4 26.6 1.0
OE1 A:GLU199 2.4 28.9 1.0
OG A:SER191 2.4 31.7 1.0
OE2 A:GLU199 2.5 28.9 1.0
CD A:GLU199 2.8 28.9 1.0
O A:SER191 2.8 31.7 1.0
C A:ILE186 3.5 26.6 1.0
C A:ILE190 3.5 30.0 1.0
C A:VAL194 3.5 32.0 1.0
CB A:SER191 3.7 31.7 1.0
C A:SER191 3.7 31.7 1.0
CA A:ILE186 4.0 26.6 1.0
CA A:SER191 4.1 31.7 1.0
N A:SER191 4.2 31.7 1.0
CA A:VAL195 4.2 30.5 1.0
CG A:GLU199 4.3 28.9 1.0
N A:VAL195 4.3 30.5 1.0
CB A:ILE186 4.4 26.6 1.0
N A:GLU196 4.5 33.5 1.0
CA A:VAL194 4.6 32.0 1.0
N A:VAL194 4.6 32.0 1.0
N A:LEU187 4.6 30.2 1.0
CA A:ILE190 4.7 30.0 1.0
CB A:ILE190 4.8 30.0 1.0
N A:PRO192 4.8 32.4 1.0
CG2 A:ILE190 4.8 30.0 1.0
CG A:GLU196 4.8 33.5 1.0
C A:VAL195 4.9 30.5 1.0
CA A:LEU187 4.9 30.2 1.0
CB A:VAL194 5.0 32.0 1.0
CB A:GLU199 5.0 28.9 1.0

Calcium binding site 2 out of 6 in 8sgi

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Calcium binding site 2 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:30.0
occ:1.00
 OE2 A:GLU579 2.4 47.0 1.0
OD2 A:ASP577 2.7 47.9 1.0
OE2 A:GLU242 2.8 40.1 1.0
OE1 A:GLU242 2.8 40.1 1.0
CD A:GLU242 3.2 40.1 1.0
CD A:GLU579 3.5 47.0 1.0
CG A:ASP577 3.8 47.9 1.0
OE1 A:GLU579 3.9 47.0 1.0
OD1 A:ASN96 3.9 36.6 1.0
CB A:ASP577 4.3 47.9 1.0
O A:ASP577 4.4 47.9 1.0
CG A:GLU242 4.7 40.1 1.0
CE A:LYS229 4.7 43.3 1.0
OD1 A:ASP577 4.8 47.9 1.0
CG A:GLU579 4.8 47.0 1.0
CG A:ASN96 4.8 36.6 1.0
OH A:TYR231 4.8 40.2 1.0
C A:ASP577 4.9 47.9 1.0
ND2 A:ASN96 5.0 36.6 1.0

Calcium binding site 3 out of 6 in 8sgi

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Calcium binding site 3 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:46.8
occ:1.00
 OD1 A:ASP421 2.2 49.3 1.0
OD2 A:ASP421 2.2 49.3 1.0
OE2 A:GLU451 2.3 41.9 1.0
CG A:ASP421 2.5 49.3 1.0
OE1 A:GLU454 2.5 50.5 1.0
OE2 A:GLU454 2.9 50.5 1.0
CD A:GLU454 3.1 50.5 1.0
CD A:GLU451 3.3 41.9 1.0
CB A:ASP421 4.0 49.3 1.0
OE1 A:GLU451 4.0 41.9 1.0
CG A:GLU451 4.3 41.9 1.0
CA A:CA1005 4.4 42.4 1.0
CG A:GLU454 4.6 50.5 1.0
OE2 A:GLU660 4.9 61.1 1.0
CA A:ASP421 4.9 49.3 1.0
CA A:ALA416 4.9 54.3 1.0

Calcium binding site 4 out of 6 in 8sgi

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Calcium binding site 4 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:42.4
occ:1.00
 OE2 A:GLU385 2.4 41.3 1.0
OD2 A:ASP421 2.4 49.3 1.0
OE1 A:GLU451 2.5 41.9 1.0
CG A:ASP421 3.4 49.3 1.0
CD A:GLU385 3.4 41.3 1.0
CD A:GLU451 3.5 41.9 1.0
CB A:ASP421 3.7 49.3 1.0
OE2 A:GLU451 3.7 41.9 1.0
CG A:GLU385 3.8 41.3 1.0
CA A:ASP421 3.9 49.3 1.0
CA A:CA1007 4.1 33.0 1.0
OD2 A:ASP447 4.2 38.7 1.0
O A:ILE445 4.2 44.1 1.0
O A:ASP421 4.3 49.3 1.0
CA A:CA1004 4.4 46.8 1.0
OD1 A:ASP421 4.5 49.3 1.0
OE1 A:GLU385 4.6 41.3 1.0
OE1 A:GLU454 4.6 50.5 1.0
C A:ASP421 4.6 49.3 1.0
O A:SER420 4.7 51.0 1.0
CG A:ASP447 4.8 38.7 1.0
CG A:GLU451 4.8 41.9 1.0
OD1 A:ASP447 4.9 38.7 1.0
N A:ASP421 5.0 49.3 1.0

Calcium binding site 5 out of 6 in 8sgi

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Calcium binding site 5 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:36.1
occ:1.00
 OE1 A:GLU385 2.3 41.3 1.0
OD1 A:ASP500 2.3 35.5 1.0
OD1 A:ASP446 2.4 41.1 1.0
OD1 A:ASP499 2.8 37.9 1.0
OD2 A:ASP500 2.9 35.5 1.0
CG A:ASP500 2.9 35.5 1.0
O A:ASP447 3.2 38.7 1.0
CD A:GLU385 3.5 41.3 1.0
CG A:ASP446 3.5 41.1 1.0
CG A:ASP499 3.8 37.9 1.0
OD2 A:ASP446 3.9 41.1 1.0
CB A:GLU385 4.0 41.3 1.0
OD1 A:ASP498 4.1 40.7 1.0
OD2 A:ASP499 4.1 37.9 1.0
CG A:GLU385 4.2 41.3 1.0
N A:ASP447 4.2 38.7 1.0
C A:ASP447 4.3 38.7 1.0
CB A:ASP500 4.4 35.5 1.0
CA A:CA1007 4.4 33.0 1.0
OE2 A:GLU385 4.4 41.3 1.0
N A:ASP499 4.6 37.9 1.0
N A:ASP500 4.6 35.5 1.0
C A:ASP499 4.7 37.9 1.0
NE A:ARG532 4.7 31.2 1.0
OD1 A:ASP447 4.8 38.7 1.0
CB A:ASP446 4.8 41.1 1.0
NH2 A:ARG532 4.9 31.2 1.0
CA A:ASP500 4.9 35.5 1.0
CA A:ASP447 4.9 38.7 1.0
N A:ASN386 4.9 42.6 1.0
CB A:ASP499 5.0 37.9 1.0
CA A:ASP446 5.0 41.1 1.0
CZ A:PHE621 5.0 42.0 1.0
CA A:ASP499 5.0 37.9 1.0
C A:GLU385 5.0 41.3 1.0

Calcium binding site 6 out of 6 in 8sgi

Go back to Calcium Binding Sites List in 8sgi
Calcium binding site 6 out of 6 in the Cryo-Em Structure of Human NCX1 in Complex with SEA0400


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 Human NCX1 in Complex with SEA0400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:33.0
occ:1.00
 OE2 A:GLU385 2.4 41.3 1.0
OD2 A:ASP500 2.4 35.5 1.0
O A:ILE449 2.5 36.3 1.0
OD1 A:ASP447 2.6 38.7 1.0
OE1 A:GLU451 2.8 41.9 1.0
OE1 A:GLU385 2.9 41.3 1.0
CD A:GLU385 2.9 41.3 1.0
OD1 A:ASP498 3.0 40.7 1.0
OD2 A:ASP498 3.0 40.7 1.0
CG A:ASP498 3.2 40.7 1.0
CG A:ASP447 3.6 38.7 1.0
CG A:ASP500 3.6 35.5 1.0
CD A:GLU451 3.7 41.9 1.0
C A:ILE449 3.7 36.3 1.0
OD2 A:ASP447 3.9 38.7 1.0
CG A:GLU451 4.0 41.9 1.0
CA A:CA1005 4.1 42.4 1.0
CB A:ASP498 4.3 40.7 1.0
CB A:ASP500 4.3 35.5 1.0
CB A:GLU451 4.3 41.9 1.0
N A:ILE449 4.4 36.3 1.0
CG A:GLU385 4.4 41.3 1.0
CA A:CA1006 4.4 36.1 1.0
N A:GLU451 4.5 41.9 1.0
OD1 A:ASP500 4.5 35.5 1.0
CA A:ILE449 4.6 36.3 1.0
N A:PHE450 4.7 36.0 1.0
C A:PHE450 4.7 36.0 1.0
CA A:PHE450 4.7 36.0 1.0
O A:ASP447 4.8 38.7 1.0
OE2 A:GLU451 4.8 41.9 1.0
C A:ASP447 4.8 38.7 1.0
CB A:ASP447 4.9 38.7 1.0
CA A:ASP498 4.9 40.7 1.0

Reference:

J.Xue, Y.Han, W.Zeng, Y.Jiang. Structural Mechanisms of Human Cardiac Sodium Calcium Exchanger NCX1 To Be Published.
Page generated: Thu Jul 10 07:02:03 2025

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