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Calcium in PDB 8v2g: Cryo-Em Structure of the KCA2.2 Channel in Apo State

Other elements in 8v2g:

The structure of Cryo-Em Structure of the KCA2.2 Channel in Apo State also contains other interesting chemical elements:

Potassium (K) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the KCA2.2 Channel in Apo State (pdb code 8v2g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cryo-Em Structure of the KCA2.2 Channel in Apo State, PDB code: 8v2g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 1 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:103.5
occ:1.00
OE2 E:GLU31 2.3 107.5 1.0
O E:THR26 2.4 103.0 1.0
OE1 E:GLU31 2.4 105.3 1.0
CD E:GLU31 2.7 105.9 1.0
OD1 E:ASP20 2.7 113.2 1.0
CB E:ASP24 2.8 120.0 1.0
OD2 E:ASP24 3.3 120.4 1.0
CG E:ASP24 3.5 120.0 1.0
C E:THR26 3.6 101.0 1.0
O E:LYS21 3.6 124.6 1.0
CG E:ASP20 3.8 109.9 1.0
CG2 E:THR28 4.0 102.2 1.0
CA E:ASP24 4.0 120.3 1.0
OD1 E:ASP22 4.1 123.4 1.0
CG E:GLU31 4.1 97.7 1.0
N E:THR26 4.2 104.7 1.0
N E:ASP24 4.2 121.1 1.0
OG1 E:THR26 4.4 116.1 1.0
N E:LYS21 4.5 111.2 1.0
N E:ILE27 4.5 96.5 1.0
CA E:ILE27 4.5 95.6 1.0
CA E:THR26 4.5 103.8 1.0
N E:THR28 4.5 102.9 1.0
CA E:ASP20 4.5 100.0 1.0
N E:GLY25 4.6 115.8 1.0
OD2 E:ASP20 4.6 112.9 1.0
OD2 E:ASP22 4.6 123.0 1.0
C E:ASP24 4.6 118.1 1.0
CB E:ASP20 4.6 100.8 1.0
OD1 E:ASP24 4.7 120.3 1.0
CG E:ASP22 4.7 126.3 1.0
C E:LYS21 4.7 123.2 1.0
C E:ASP20 4.8 108.0 1.0
C E:ILE27 4.9 101.9 1.0

Calcium binding site 2 out of 8 in 8v2g

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:120.5
occ:1.00
O E:THR62 2.4 114.0 1.0
OE2 E:GLU67 2.6 112.9 1.0
OD1 E:ASP56 2.9 125.6 1.0
OD1 E:ASN60 2.9 128.8 1.0
OE1 E:GLU67 3.0 113.1 1.0
CD E:GLU67 3.2 111.8 1.0
C E:THR62 3.2 113.1 1.0
ND2 E:ASN60 3.4 120.2 1.0
CG2 E:THR62 3.4 113.8 1.0
CG E:ASN60 3.5 124.6 1.0
CB E:ASP58 3.7 131.7 1.0
CG E:ASP56 3.9 126.0 1.0
N E:ILE63 3.9 105.5 1.0
CA E:ILE63 4.0 98.1 1.0
N E:ASP64 4.1 98.5 1.0
OD1 E:ASP64 4.1 100.9 1.0
CA E:THR62 4.2 112.3 1.0
CG E:ASP64 4.3 99.8 1.0
C E:ILE63 4.3 97.8 1.0
N E:THR62 4.4 113.4 1.0
CB E:THR62 4.4 110.7 1.0
CG E:ASP58 4.4 132.5 1.0
OD2 E:ASP56 4.6 125.2 1.0
OD2 E:ASP64 4.6 99.3 1.0
CG E:GLU67 4.7 107.1 1.0
OD2 E:ASP58 4.7 130.9 1.0
CB E:ASP56 4.7 126.5 1.0
CB E:ASP64 4.7 93.1 1.0
CA E:ASP58 5.0 134.8 1.0

Calcium binding site 3 out of 8 in 8v2g

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:109.7
occ:1.00
OE2 F:GLU31 2.3 108.5 1.0
O F:THR26 2.4 106.4 1.0
OE1 F:GLU31 2.5 104.2 1.0
OD1 F:ASP20 2.7 116.5 1.0
CD F:GLU31 2.7 105.0 1.0
CB F:ASP24 2.9 123.2 1.0
O F:LYS21 3.6 129.1 1.0
C F:THR26 3.6 102.5 1.0
CG F:ASP24 3.6 127.0 1.0
OD2 F:ASP22 3.9 125.9 1.0
CG F:ASP20 3.9 113.4 1.0
OD1 F:ASP24 4.1 123.5 1.0
CA F:ASP24 4.1 124.1 1.0
CG F:GLU31 4.2 96.9 1.0
OD2 F:ASP24 4.2 130.2 1.0
N F:THR26 4.2 108.5 1.0
N F:LYS21 4.3 115.5 1.0
N F:ASP24 4.3 126.3 1.0
CG2 F:THR28 4.4 102.1 1.0
OG1 F:THR26 4.4 116.5 1.0
CA F:ASP20 4.5 103.7 1.0
CA F:THR26 4.5 104.7 1.0
N F:ILE27 4.5 97.4 1.0
OD1 F:ASP22 4.5 132.6 1.0
CG F:ASP22 4.6 132.3 1.0
CA F:ILE27 4.6 94.7 1.0
CB F:ASP20 4.6 103.9 1.0
C F:LYS21 4.6 127.7 1.0
N F:GLY25 4.6 119.2 1.0
C F:ASP24 4.6 121.2 1.0
N F:THR28 4.7 101.7 1.0
C F:ASP20 4.7 109.9 1.0
OD2 F:ASP20 4.9 114.8 1.0

Calcium binding site 4 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 4 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:123.6
occ:1.00
O F:THR62 2.4 117.5 1.0
OE1 F:GLU67 2.4 110.5 1.0
OE2 F:GLU67 2.7 120.0 1.0
OD1 F:ASN60 2.7 133.2 1.0
CD F:GLU67 2.9 115.3 1.0
ND2 F:ASN60 3.0 127.5 1.0
OD1 F:ASP56 3.1 128.8 1.0
CG F:ASN60 3.2 130.7 1.0
CB F:ASP58 3.5 135.3 1.0
C F:THR62 3.6 115.5 1.0
OD2 F:ASP56 3.6 123.6 1.0
CG F:ASP56 3.6 126.9 1.0
OD1 F:ASP64 4.0 101.2 1.0
CG F:ASP64 4.2 102.8 1.0
CA F:ILE63 4.2 98.9 1.0
N F:ASP64 4.3 96.8 1.0
N F:ILE63 4.3 107.1 1.0
OD2 F:ASP64 4.4 101.0 1.0
CG F:GLU67 4.4 108.7 1.0
CG F:ASP58 4.4 138.7 1.0
CG2 F:THR62 4.5 112.0 1.0
N F:ASP58 4.6 136.8 1.0
C F:ILE63 4.6 97.8 1.0
N F:THR62 4.6 118.6 1.0
CA F:ASP58 4.6 138.6 1.0
CA F:THR62 4.7 114.5 1.0
CB F:ASN60 4.7 125.7 1.0
CB F:ASP56 4.9 127.0 1.0
CB F:ASP64 4.9 97.8 1.0
OD2 F:ASP58 4.9 140.3 1.0

Calcium binding site 5 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 5 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:98.5
occ:1.00
OD1 G:ASP20 2.4 113.6 1.0
O G:THR26 2.5 103.6 1.0
CB G:ASP22 3.0 115.0 1.0
OD1 G:ASP24 3.5 115.8 1.0
CG G:ASP20 3.6 108.5 1.0
C G:THR26 3.6 99.3 1.0
OE2 G:GLU31 3.8 112.5 1.0
CD G:GLU31 3.9 108.6 1.0
OD2 G:ASP22 4.0 121.8 1.0
CG G:ASP22 4.0 122.2 1.0
OE1 G:GLU31 4.1 108.6 1.0
N G:ASP22 4.1 113.9 1.0
CA G:ASP22 4.1 113.8 1.0
O G:ASP24 4.1 111.5 1.0
CG2 G:THR26 4.2 110.7 1.0
CB G:ASP20 4.3 95.5 1.0
CA G:ILE27 4.3 93.9 1.0
CG G:ASP24 4.4 116.9 1.0
N G:ILE27 4.4 95.5 1.0
CG G:GLU31 4.4 103.0 1.0
CA G:ASP20 4.5 96.9 1.0
OD2 G:ASP20 4.5 109.0 1.0
N G:THR28 4.5 103.0 1.0
CA G:THR26 4.7 101.3 1.0
CG2 G:THR28 4.7 100.6 1.0
OG1 G:THR28 4.7 110.9 1.0
C G:ASP22 4.7 113.3 1.0
N G:THR26 4.7 100.8 1.0
OD2 G:ASP24 4.8 116.3 1.0
C G:ILE27 4.9 101.4 1.0
N G:LYS21 4.9 102.6 1.0
C G:ASP20 5.0 101.7 1.0

Calcium binding site 6 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 6 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo 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 the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:126.3
occ:1.00
OE1 G:GLU67 2.4 109.9 1.0
O G:THR62 2.4 115.5 1.0
OE2 G:GLU67 2.7 121.6 1.0
OD1 G:ASN60 2.7 133.6 1.0
CD G:GLU67 2.9 116.2 1.0
ND2 G:ASN60 3.0 127.0 1.0
CG G:ASN60 3.2 130.4 1.0
OD1 G:ASP56 3.3 130.1 1.0
CB G:ASP58 3.4 136.9 1.0
C G:THR62 3.6 114.5 1.0
OD2 G:ASP56 3.8 126.0 1.0
CG G:ASP56 3.8 129.8 1.0
OD2 G:ASP58 4.0 138.4 1.0
OD1 G:ASP64 4.0 98.4 1.0
CG G:ASP58 4.2 140.2 1.0
CG G:ASP64 4.2 96.7 1.0
CA G:ILE63 4.3 97.9 1.0
N G:ASP64 4.3 97.9 1.0
N G:ILE63 4.3 105.4 1.0
CG G:GLU67 4.4 108.5 1.0
OD2 G:ASP64 4.5 93.5 1.0
OG1 G:THR62 4.6 122.5 1.0
CA G:ASP58 4.6 138.8 1.0
N G:THR62 4.6 118.8 1.0
CA G:THR62 4.6 115.8 1.0
N G:ASP58 4.6 137.2 1.0
C G:ILE63 4.6 98.0 1.0
CB G:ASN60 4.7 123.8 1.0
CB G:ASP64 4.9 91.4 1.0

Calcium binding site 7 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 7 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:105.9
occ:1.00
OE2 H:GLU31 2.3 110.0 1.0
O H:THR26 2.4 107.3 1.0
OE1 H:GLU31 2.6 108.9 1.0
OD1 H:ASP24 2.7 124.3 1.0
OD2 H:ASP24 2.7 126.9 1.0
CD H:GLU31 2.8 108.3 1.0
CG H:ASP24 3.0 123.4 1.0
OD1 H:ASP20 3.2 111.9 1.0
O H:LYS21 3.2 123.4 1.0
O H:GLY23 3.5 119.1 1.0
C H:THR26 3.6 104.3 1.0
OD2 H:ASP22 3.7 124.2 1.0
OD1 H:ASP22 4.0 124.7 1.0
OG1 H:THR26 4.1 120.6 1.0
CG H:ASP22 4.2 127.4 1.0
CG H:GLU31 4.2 99.8 1.0
N H:THR26 4.3 111.4 1.0
CG H:ASP20 4.3 107.9 1.0
C H:LYS21 4.3 120.8 1.0
CA H:THR26 4.4 106.7 1.0
CG2 H:THR28 4.5 106.4 1.0
CB H:ASP24 4.5 120.2 1.0
N H:LYS21 4.5 109.5 1.0
N H:ILE27 4.5 99.3 1.0
C H:GLY23 4.6 120.3 1.0
CA H:ILE27 4.6 97.1 1.0
N H:THR28 4.8 105.4 1.0
CA H:ASP20 4.8 99.6 1.0
CB H:THR26 4.8 113.4 1.0
C H:ASP20 4.8 105.5 1.0

Calcium binding site 8 out of 8 in 8v2g

Go back to Calcium Binding Sites List in 8v2g
Calcium binding site 8 out of 8 in the Cryo-Em Structure of the KCA2.2 Channel in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the KCA2.2 Channel in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:122.8
occ:1.00
O H:THR62 2.4 117.5 1.0
OE1 H:GLU67 2.6 110.2 1.0
OD1 H:ASN60 2.7 134.8 1.0
OD1 H:ASP56 2.9 127.7 1.0
OE2 H:GLU67 3.0 119.2 1.0
ND2 H:ASN60 3.1 129.1 1.0
CD H:GLU67 3.2 113.9 1.0
CG H:ASN60 3.3 131.2 1.0
C H:THR62 3.4 115.8 1.0
CB H:ASP58 3.6 133.7 1.0
CG H:ASP56 3.7 128.7 1.0
OD2 H:ASP56 3.8 127.5 1.0
CG2 H:THR62 3.9 112.9 1.0
CA H:ILE63 4.1 99.3 1.0
N H:ASP64 4.1 98.0 1.0
OD1 H:ASP64 4.1 100.0 1.0
N H:ILE63 4.1 108.8 1.0
CG H:ASP64 4.2 100.4 1.0
CG H:ASP58 4.3 136.0 1.0
C H:ILE63 4.4 98.6 1.0
CA H:THR62 4.4 114.3 1.0
N H:THR62 4.5 118.3 1.0
OD2 H:ASP64 4.5 100.5 1.0
OD2 H:ASP58 4.6 136.8 1.0
CG H:GLU67 4.7 108.2 1.0
CB H:ASP64 4.7 96.2 1.0
CB H:ASN60 4.8 127.1 1.0
CB H:THR62 4.9 111.1 1.0
CA H:ASP58 4.9 135.2 1.0
CB H:ASP56 4.9 128.8 1.0
OD1 H:ASP58 5.0 134.6 1.0

Reference:

Y.W.Nam, D.Im, A.Santa Cruz Garcia, M.L.Tringides, H.M.Nguyen, Y.Liu, R.Orfali, A.Ramanishka, G.Pintilie, C.C.Su, M.Cui, D.E.Logothetis, E.W.Yu, H.Wulff, K.G.Chandy, M.Zhang. Cryo-Em Structures of the Small-Conductance CA2+-Activated KCA2.2 Channel Nat Commun 2025.
ISSN: ESSN 2041-1723
Page generated: Thu Jul 10 07:54:38 2025

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