Calcium in PDB 8sgj: Cryo-Em Structure of Human NCX1 in Apo Inactivated State

Other elements in 8sgj:

The structure of Cryo-Em Structure of Human NCX1 in Apo Inactivated State also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 8sgj

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Calcium binding site 1 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:59.1
occ:1.00
 O A:ILE190 2.4 62.0 1.0
O A:VAL194 2.4 64.4 1.0
O A:ILE186 2.4 57.9 1.0
OE2 A:GLU199 2.5 61.6 1.0
OE1 A:GLU199 2.5 61.6 1.0
OG A:SER191 2.6 64.4 1.0
CD A:GLU199 2.8 61.6 1.0
O A:SER191 3.1 64.4 1.0
C A:ILE190 3.6 62.0 1.0
C A:ILE186 3.6 57.9 1.0
C A:VAL194 3.6 64.4 1.0
CB A:SER191 3.9 64.4 1.0
C A:SER191 3.9 64.4 1.0
CA A:ILE186 4.1 57.9 1.0
CA A:SER191 4.2 64.4 1.0
CG A:GLU199 4.3 61.6 1.0
N A:SER191 4.3 64.4 1.0
CA A:VAL195 4.3 59.8 1.0
N A:VAL195 4.4 59.8 1.0
OE1 A:GLU196 4.5 65.1 1.0
CB A:ILE186 4.6 57.9 1.0
CB A:ILE190 4.6 62.0 1.0
CA A:VAL194 4.6 64.4 1.0
CA A:ILE190 4.6 62.0 1.0
CG2 A:ILE190 4.6 62.0 1.0
N A:VAL194 4.7 64.4 1.0
N A:LEU187 4.7 62.0 1.0
N A:GLU196 4.7 65.1 1.0
CB A:VAL194 4.9 64.4 1.0
CA A:LEU187 4.9 62.0 1.0
CD A:GLU196 5.0 65.1 1.0
N A:PRO192 5.0 68.4 1.0

Calcium binding site 2 out of 6 in 8sgj

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Calcium binding site 2 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:64.7
occ:1.00
 OE2 A:GLU579 2.5 62.1 1.0
OE2 A:GLU242 2.5 54.8 1.0
OE1 A:GLU242 2.7 54.8 1.0
CD A:GLU242 3.0 54.8 1.0
OD2 A:ASP577 3.1 62.1 1.0
CD A:GLU579 3.6 62.1 1.0
OD1 A:ASN96 3.8 50.8 1.0
CG A:ASP577 4.0 62.1 1.0
OE1 A:GLU579 4.0 62.1 1.0
CB A:ASP577 4.2 62.1 1.0
CG A:GLU242 4.5 54.8 1.0
CE A:LYS229 4.6 55.0 1.0
O A:ASP577 4.6 62.1 1.0
CG A:ASN96 4.8 50.8 1.0
CG A:GLU579 4.8 62.1 1.0
OH A:TYR231 4.9 53.6 1.0
ND2 A:ASN96 5.0 50.8 1.0
CD A:LYS229 5.0 55.0 1.0

Calcium binding site 3 out of 6 in 8sgj

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Calcium binding site 3 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:71.4
occ:1.00
 OE2 A:GLU451 2.0 62.6 1.0
OD2 A:ASP421 2.1 76.5 1.0
OD1 A:ASP421 2.2 76.5 1.0
CG A:ASP421 2.4 76.5 1.0
OE1 A:GLU454 2.7 76.1 1.0
OE2 A:GLU454 2.8 76.1 1.0
CD A:GLU451 3.0 62.6 1.0
CD A:GLU454 3.1 76.1 1.0
OE1 A:GLU451 3.6 62.6 1.0
CB A:ASP421 3.9 76.5 1.0
CG A:GLU451 4.2 62.6 1.0
CA A:CA1004 4.3 65.7 1.0
CG A:GLU454 4.6 76.1 1.0
OG A:SER420 4.7 75.8 1.0
CB A:GLU451 4.8 62.6 1.0
CA A:ASP421 4.9 76.5 1.0
CA A:ALA416 4.9 81.8 1.0

Calcium binding site 4 out of 6 in 8sgj

Go back to Calcium Binding Sites List in 8sgj
Calcium binding site 4 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:65.7
occ:1.00
 OE2 A:GLU385 2.4 65.8 1.0
OE1 A:GLU451 2.4 62.6 1.0
OD2 A:ASP421 2.4 76.5 1.0
CG A:ASP421 3.4 76.5 1.0
CD A:GLU385 3.4 65.8 1.0
CD A:GLU451 3.5 62.6 1.0
CB A:ASP421 3.7 76.5 1.0
CG A:GLU385 3.8 65.8 1.0
OE2 A:GLU451 3.9 62.6 1.0
CA A:ASP421 4.0 76.5 1.0
CA A:CA1006 4.1 62.7 1.0
OD2 A:ASP447 4.1 63.0 1.0
CA A:CA1003 4.3 71.4 1.0
O A:ILE445 4.4 70.7 1.0
O A:ASP421 4.4 76.5 1.0
OE1 A:GLU454 4.5 76.1 1.0
OD1 A:ASP421 4.5 76.5 1.0
OE1 A:GLU385 4.6 65.8 1.0
C A:ASP421 4.7 76.5 1.0
CG2 A:ILE496 4.7 72.9 1.0
CG A:GLU451 4.7 62.6 1.0
CG A:ASP447 4.8 63.0 1.0
OD1 A:ASP447 4.9 63.0 1.0
O A:SER420 4.9 75.8 1.0

Calcium binding site 5 out of 6 in 8sgj

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Calcium binding site 5 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated 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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:57.9
occ:1.00
 OE1 A:GLU385 2.4 65.8 1.0
OD1 A:ASP446 2.5 65.3 1.0
OD1 A:ASP500 2.5 57.6 1.0
OD1 A:ASP499 2.5 61.4 1.0
OD2 A:ASP500 3.1 57.6 1.0
CG A:ASP500 3.1 57.6 1.0
O A:ASP447 3.4 63.0 1.0
CG A:ASP499 3.5 61.4 1.0
CG A:ASP446 3.5 65.3 1.0
CD A:GLU385 3.5 65.8 1.0
CB A:GLU385 3.8 65.8 1.0
OD2 A:ASP446 3.9 65.3 1.0
OD2 A:ASP499 3.9 61.4 1.0
CG A:GLU385 4.1 65.8 1.0
OD1 A:ASP498 4.3 62.6 1.0
N A:ASP447 4.4 63.0 1.0
N A:ASP499 4.5 61.4 1.0
C A:ASP447 4.5 63.0 1.0
CB A:ASP500 4.6 57.6 1.0
OE2 A:GLU385 4.6 65.8 1.0
C A:ASP499 4.6 61.4 1.0
CA A:CA1006 4.6 62.7 1.0
N A:ASP500 4.6 57.6 1.0
NH2 A:ARG532 4.6 48.5 1.0
N A:ASN386 4.7 67.8 1.0
NE A:ARG532 4.7 48.5 1.0
C A:GLU385 4.7 65.8 1.0
CB A:ASP499 4.7 61.4 1.0
CB A:ASN386 4.8 67.8 1.0
CB A:ASP446 4.8 65.3 1.0
CA A:ASP499 4.8 61.4 1.0
CA A:GLU385 4.9 65.8 1.0
CZ A:PHE621 4.9 65.8 1.0
O A:ASP499 4.9 61.4 1.0
OD1 A:ASP447 4.9 63.0 1.0
CA A:ASP500 5.0 57.6 1.0

Calcium binding site 6 out of 6 in 8sgj

Go back to Calcium Binding Sites List in 8sgj
Calcium binding site 6 out of 6 in the Cryo-Em Structure of Human NCX1 in Apo Inactivated State


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 Apo Inactivated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:62.7
occ:1.00
 OE2 A:GLU385 2.4 65.8 1.0
OD2 A:ASP498 2.4 62.6 1.0
O A:ILE449 2.4 56.3 1.0
OD1 A:ASP447 2.5 63.0 1.0
OD2 A:ASP500 2.5 57.6 1.0
OE1 A:GLU385 2.8 65.8 1.0
CD A:GLU385 2.9 65.8 1.0
CG A:ASP498 3.0 62.6 1.0
OE1 A:GLU451 3.1 62.6 1.0
OD1 A:ASP498 3.2 62.6 1.0
CG A:ASP447 3.5 63.0 1.0
C A:ILE449 3.7 56.3 1.0
CG A:ASP500 3.7 57.6 1.0
OD2 A:ASP447 3.8 63.0 1.0
CD A:GLU451 4.0 62.6 1.0
CA A:CA1004 4.1 65.7 1.0
CG A:GLU451 4.1 62.6 1.0
CB A:ASP498 4.1 62.6 1.0
N A:GLU451 4.3 62.6 1.0
CG A:GLU385 4.4 65.8 1.0
CB A:GLU451 4.4 62.6 1.0
CB A:ASP500 4.4 57.6 1.0
N A:ILE449 4.4 56.3 1.0
C A:PHE450 4.6 55.8 1.0
CA A:ILE449 4.6 56.3 1.0
CA A:PHE450 4.6 55.8 1.0
N A:PHE450 4.6 55.8 1.0
CA A:CA1005 4.6 57.9 1.0
OD1 A:ASP500 4.6 57.6 1.0
O A:ASP447 4.7 63.0 1.0
C A:ASP447 4.8 63.0 1.0
CA A:ASP498 4.8 62.6 1.0
CB A:ASP447 4.8 63.0 1.0
C A:ASP448 5.0 60.5 1.0
CA A:GLU451 5.0 62.6 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: Fri Jul 19 11:26:54 2024

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