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Calcium in PDB 4jq0: Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin

Protein crystallography data

The structure of Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin, PDB code: 4jq0 was solved by B.C.Chung, C.Wang, J.A.Hennessey, S.-Y.Lee, G.S.Pitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.57 / 3.84
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.200, 115.200, 120.110, 90.00, 90.00, 120.00
R / Rfree (%) 25.3 / 32

Calcium Binding Sites:

The binding sites of Calcium atom in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin (pdb code 4jq0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin, PDB code: 4jq0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4jq0

Go back to Calcium Binding Sites List in 4jq0
Calcium binding site 1 out of 4 in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:0.8
occ:1.00
ND2 C:ASN61 2.2 0.4 1.0
OD1 C:ASN61 2.4 0.8 1.0
OE1 C:GLU68 2.5 0.9 1.0
CG C:ASN61 2.6 0.0 1.0
OD2 C:ASP59 2.6 0.2 1.0
O C:THR63 2.9 0.1 1.0
OE2 C:GLU68 3.1 1.0 1.0
CD C:GLU68 3.1 0.8 1.0
CG C:ASP59 3.3 0.3 1.0
CB C:ASP59 3.6 0.1 1.0
C C:THR63 3.7 0.5 1.0
OD1 C:ASP65 3.9 0.3 1.0
OD1 C:ASP57 4.0 0.9 1.0
CB C:ASN61 4.0 0.3 1.0
N C:ASP65 4.3 0.0 1.0
OD1 C:ASP59 4.3 0.4 1.0
N C:ILE64 4.3 0.6 1.0
CG C:ASP65 4.4 0.8 1.0
CA C:ILE64 4.4 0.6 1.0
CA C:THR63 4.5 0.4 1.0
N C:ASN61 4.6 0.3 1.0
CG C:GLU68 4.6 0.1 1.0
CB C:THR63 4.6 0.1 1.0
N C:ASP59 4.6 0.2 1.0
CA C:ASP59 4.7 0.4 1.0
N C:THR63 4.7 0.7 1.0
C C:ILE64 4.7 0.3 1.0
CA C:ASN61 4.8 0.5 1.0
CB C:ASP65 4.9 0.6 1.0
OD2 C:ASP65 4.9 0.5 1.0
N C:GLY60 5.0 0.4 1.0

Calcium binding site 2 out of 4 in 4jq0

Go back to Calcium Binding Sites List in 4jq0
Calcium binding site 2 out of 4 in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:0.8
occ:1.00
OE2 C:GLU32 2.4 0.8 1.0
O C:THR27 2.4 1.0 1.0
OD1 C:ASP25 2.5 0.2 1.0
OE1 C:GLU32 2.6 0.3 1.0
OD1 C:ASP23 2.7 0.0 1.0
CD C:GLU32 2.8 0.5 1.0
OD1 C:ASP21 3.1 0.1 1.0
CG C:ASP25 3.2 0.7 1.0
OD2 C:ASP23 3.4 1.0 1.0
OD2 C:ASP25 3.4 0.1 1.0
CG C:ASP23 3.4 0.4 1.0
C C:THR27 3.7 0.1 1.0
CG C:ASP21 4.1 0.2 1.0
CG C:GLU32 4.3 0.6 1.0
N C:ILE28 4.5 0.1 1.0
CA C:ILE28 4.6 0.4 1.0
CB C:ASP25 4.6 0.3 1.0
CA C:THR27 4.6 0.3 1.0
N C:ASP25 4.7 0.8 1.0
OD2 C:ASP21 4.7 0.9 1.0
N C:THR27 4.7 0.7 1.0
N C:THR29 4.8 0.8 1.0
CA C:ASP21 4.9 0.5 1.0
CB C:ASP23 4.9 0.3 1.0

Calcium binding site 3 out of 4 in 4jq0

Go back to Calcium Binding Sites List in 4jq0
Calcium binding site 3 out of 4 in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:93.2
occ:1.00
O C:TYR100 2.4 0.5 1.0
OD1 C:ASP96 2.4 90.7 1.0
OD1 C:ASP94 2.6 0.0 1.0
OD1 C:ASN98 3.1 0.6 1.0
C C:TYR100 3.6 0.5 1.0
CG C:ASP96 3.6 94.5 1.0
CG C:ASP94 3.8 1.0 1.0
CG C:ASN98 4.0 0.5 1.0
N C:LYS95 4.0 0.5 1.0
N C:ASP96 4.1 1.0 1.0
CA C:ILE101 4.2 0.5 1.0
OD2 C:ASP96 4.2 86.5 1.0
CA C:ASP94 4.3 0.2 1.0
N C:ILE101 4.3 0.2 1.0
ND2 C:ASN98 4.3 0.8 1.0
C C:ASP94 4.4 0.9 1.0
OD2 C:ASP94 4.6 0.3 1.0
CB C:ASP94 4.6 0.5 1.0
CG1 C:ILE101 4.7 0.2 1.0
CA C:TYR100 4.7 0.2 1.0
CB C:ASP96 4.7 0.3 1.0
N C:TYR100 4.8 0.5 1.0
N C:GLY97 4.8 0.1 1.0
CA C:ASP96 4.8 0.5 1.0
N C:ASN98 4.9 0.4 1.0
CA C:LYS95 4.9 0.5 1.0
CB C:ILE101 5.0 0.6 1.0

Calcium binding site 4 out of 4 in 4jq0

Go back to Calcium Binding Sites List in 4jq0
Calcium binding site 4 out of 4 in the Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Voltage-Gated Sodium Channel 1.5 C-Terminal Domain in Complex with FGF12B and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:30.0
occ:1.00
OD1 C:ASP130 1.9 0.1 1.0
OD1 C:ASP134 2.0 0.7 1.0
OD1 C:ASP132 2.1 0.5 1.0
O C:GLN136 2.3 0.7 1.0
CG C:ASP134 3.0 0.8 1.0
CG C:ASP130 3.1 0.9 1.0
CG C:ASP132 3.3 0.3 1.0
C C:GLN136 3.4 0.6 1.0
N C:ASP134 3.5 1.0 1.0
OD2 C:ASP134 3.6 0.4 1.0
OD2 C:ASP132 3.8 0.4 1.0
N C:GLN136 3.8 0.4 1.0
OD2 C:ASP130 3.8 0.2 1.0
N C:GLY133 4.0 0.5 1.0
CB C:ASP134 4.1 0.3 1.0
CA C:ASP130 4.1 0.5 1.0
N C:GLY135 4.1 0.3 1.0
CA C:GLN136 4.1 0.8 1.0
CB C:ASP130 4.2 0.2 1.0
CA C:ASP134 4.2 0.5 1.0
N C:ASP132 4.2 0.8 1.0
C C:ASP130 4.4 0.5 1.0
N C:ILE131 4.5 0.9 1.0
N C:VAL137 4.5 0.7 1.0
C C:ASP132 4.5 0.4 1.0
CB C:ASP132 4.5 0.0 1.0
C C:ASP134 4.5 0.7 1.0
C C:GLY133 4.5 0.9 1.0
CA C:GLY133 4.6 0.3 1.0
CA C:ASP132 4.6 0.7 1.0
CB C:GLN136 4.6 0.2 1.0
CA C:VAL137 4.7 0.7 1.0
C C:GLY135 4.8 0.9 1.0

Reference:

C.Wang, B.C.Chung, H.Yan, H.G.Wang, S.Y.Lee, G.S.Pitt. Structural Analyses of Ca(2+)/Cam Interaction with Nav Channel C-Termini Reveal Mechanisms of Calcium-Dependent Regulation. Nat Commun V. 5 4896 2014.
ISSN: ESSN 2041-1723
PubMed: 25232683
DOI: 10.1038/NCOMMS5896
Page generated: Sat Dec 12 04:53:25 2020

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