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Calcium in PDB 4jpz: Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin

Protein crystallography data

The structure of Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin, PDB code: 4jpz 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) 48.23 / 3.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.133, 86.106, 109.399, 90.00, 100.90, 90.00
R / Rfree (%) 21.2 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin (pdb code 4jpz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin, PDB code: 4jpz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4jpz

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Calcium binding site 1 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U 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 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:97.3
occ:1.00
 OD1 C:ASP21 2.2 93.6 1.0
OD1 C:ASP25 2.3 0.4 1.0
OD1 C:ASP23 2.3 0.8 1.0
OE2 C:GLU32 2.4 0.2 1.0
O C:THR27 2.6 95.4 1.0
OE1 C:GLU32 2.6 92.7 1.0
CD C:GLU32 2.8 91.7 1.0
O C:HOH301 2.9 86.4 1.0
CG C:ASP25 3.2 0.5 1.0
CG C:ASP21 3.4 0.9 1.0
CG C:ASP23 3.4 0.9 1.0
OD2 C:ASP25 3.7 97.9 1.0
C C:THR27 3.8 0.7 1.0
OD2 C:ASP23 3.8 0.1 1.0
OD2 C:ASP21 4.0 0.4 1.0
N C:ASP25 4.1 0.9 1.0
CB C:ASP25 4.3 0.1 1.0
N C:ASP23 4.3 0.5 1.0
CG C:GLU32 4.4 84.7 1.0
CA C:ASP21 4.4 97.6 1.0
N C:GLY24 4.5 0.7 1.0
N C:LYS22 4.5 97.8 1.0
CB C:ASP21 4.5 97.5 1.0
N C:THR27 4.6 94.7 1.0
N C:ILE28 4.7 99.7 1.0
CA C:ILE28 4.7 89.6 1.0
CB C:ASP23 4.7 0.7 1.0
CA C:ASP25 4.7 0.7 1.0
C C:ASP21 4.7 99.1 1.0
CA C:THR27 4.8 97.5 1.0
CA C:ASP23 4.8 0.3 1.0
C C:ASP23 4.8 0.2 1.0
N C:THR29 5.0 88.2 1.0

Calcium binding site 2 out of 8 in 4jpz

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Calcium binding site 2 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U 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 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:90.4
occ:1.00
 OD1 C:ASN61 2.3 89.2 1.0
OD1 C:ASP57 2.4 94.6 1.0
O C:HOH302 2.5 85.0 1.0
O C:THR63 2.5 92.0 1.0
OE1 C:GLU68 2.6 97.0 1.0
OE2 C:GLU68 3.0 90.8 1.0
CG C:ASN61 3.0 88.7 1.0
CD C:GLU68 3.2 94.0 1.0
OD2 C:ASP59 3.2 82.9 1.0
ND2 C:ASN61 3.4 92.6 1.0
CG C:ASP57 3.4 96.3 1.0
CB C:ASP59 3.6 88.3 1.0
CG C:ASP59 3.6 90.7 1.0
C C:THR63 3.7 90.6 1.0
N C:ASN61 3.9 95.0 1.0
OD2 C:ASP57 3.9 92.4 1.0
N C:ASP59 4.1 97.7 1.0
N C:GLY60 4.2 95.8 1.0
N C:THR63 4.2 86.0 1.0
CB C:ASN61 4.2 88.4 1.0
CA C:ASP59 4.4 91.4 1.0
CA C:ASN61 4.4 94.7 1.0
OD1 C:ASP65 4.5 93.0 1.0
N C:GLY62 4.5 95.5 1.0
OG1 C:THR63 4.5 96.2 1.0
CA C:THR63 4.5 84.7 1.0
N C:ILE64 4.6 92.0 1.0
CB C:ASP57 4.6 95.3 1.0
C C:ASN61 4.6 95.5 1.0
CA C:ASP57 4.6 95.3 1.0
OD1 C:ASP59 4.6 96.8 1.0
N C:ALA58 4.6 97.0 1.0
CA C:ILE64 4.7 93.8 1.0
CG C:GLU68 4.7 88.9 1.0
C C:ASP59 4.7 94.5 1.0
C C:GLY60 4.9 92.8 1.0

Calcium binding site 3 out of 8 in 4jpz

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Calcium binding site 3 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U 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 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:71.4
occ:1.00
 OD1 C:ASN98 2.3 62.9 1.0
O C:HOH303 2.3 64.8 1.0
OD1 C:ASP94 2.4 59.9 1.0
OD1 C:ASP96 2.4 83.9 1.0
O C:TYR100 2.4 64.3 1.0
O C:HOH304 2.5 57.9 1.0
CG C:ASN98 3.2 67.3 1.0
CG C:ASP96 3.3 76.9 1.0
ND2 C:ASN98 3.5 68.7 1.0
CG C:ASP94 3.5 62.1 1.0
C C:TYR100 3.6 58.8 1.0
OD2 C:ASP96 3.6 74.8 1.0
OD2 C:ASP94 4.1 59.7 1.0
N C:TYR100 4.3 68.1 1.0
N C:ASP96 4.3 67.3 1.0
CA C:TYR100 4.4 60.7 1.0
N C:ASN98 4.4 65.5 1.0
CB C:ASN98 4.5 65.2 1.0
CB C:TYR100 4.6 65.4 1.0
N C:LYS95 4.6 62.8 1.0
CB C:ASP96 4.6 73.3 1.0
N C:ILE101 4.6 61.6 1.0
CA C:ASP94 4.7 59.1 1.0
CB C:ASP94 4.7 60.4 1.0
N C:GLY97 4.7 66.2 1.0
CA C:ILE101 4.7 61.6 1.0
C C:ASP94 4.8 61.8 1.0
CA C:ASP96 4.8 65.9 1.0
CA C:ASN98 4.9 65.7 1.0
N C:GLY99 5.0 58.4 1.0

Calcium binding site 4 out of 8 in 4jpz

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Calcium binding site 4 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U 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 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:88.5
occ:1.00
 O C:HOH305 2.3 76.3 1.0
OD1 C:ASP132 2.3 85.3 1.0
O C:HOH306 2.3 59.4 1.0
O C:GLN136 2.3 69.4 1.0
OD1 C:ASP134 2.5 80.5 1.0
OD1 C:ASP130 2.5 76.5 1.0
CG C:ASP132 3.3 86.2 1.0
C C:GLN136 3.5 67.7 1.0
CG C:ASP134 3.5 80.1 1.0
OD2 C:ASP132 3.7 88.9 1.0
CG C:ASP130 3.7 73.5 1.0
OD2 C:ASP134 4.0 76.4 1.0
CA C:ASP130 4.1 65.8 1.0
N C:ASP132 4.3 72.9 1.0
N C:ILE131 4.3 65.3 1.0
CA C:VAL137 4.3 67.3 1.0
N C:VAL137 4.3 66.2 1.0
N C:GLN136 4.4 70.8 1.0
N C:ASP134 4.4 76.7 1.0
C C:ASP130 4.4 65.3 1.0
CA C:GLN136 4.4 72.0 1.0
CB C:ASP130 4.5 69.7 1.0
N C:GLY133 4.5 73.1 1.0
OD2 C:ASP130 4.6 67.8 1.0
CB C:ASP132 4.6 82.0 1.0
O C:ALA129 4.7 69.0 1.0
CB C:ASP134 4.7 78.1 1.0
N C:ASN138 4.8 64.9 1.0
CA C:ASP132 4.8 75.2 1.0
CB C:GLN136 4.8 75.7 1.0
N C:GLY135 5.0 68.7 1.0

Calcium binding site 5 out of 8 in 4jpz

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Calcium binding site 5 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca201

b:0.5
occ:1.00
 OD1 I:ASP21 2.3 0.2 1.0
OD1 I:ASP23 2.3 0.0 1.0
OE2 I:GLU32 2.4 0.8 1.0
OD1 I:ASP25 2.4 0.9 1.0
O I:THR27 2.6 0.1 1.0
CD I:GLU32 3.0 0.9 1.0
OE1 I:GLU32 3.0 0.9 1.0
CG I:ASP25 3.3 0.0 1.0
CG I:ASP21 3.5 0.1 1.0
CG I:ASP23 3.5 0.4 1.0
OD2 I:ASP25 3.8 0.4 1.0
C I:THR27 3.8 0.8 1.0
N I:ASP23 3.9 0.9 1.0
N I:LYS22 4.0 0.4 1.0
CA I:ASP21 4.1 0.4 1.0
OD2 I:ASP23 4.1 0.7 1.0
N I:ASP25 4.2 0.1 1.0
N I:GLY24 4.2 0.5 1.0
OD2 I:ASP21 4.3 0.9 1.0
C I:ASP21 4.3 0.7 1.0
CB I:ASP21 4.4 0.8 1.0
CG I:GLU32 4.4 0.9 1.0
CA I:ILE28 4.5 0.6 1.0
CB I:ASP25 4.5 0.1 1.0
N I:ILE28 4.6 0.4 1.0
CA I:ASP23 4.6 0.8 1.0
CB I:ASP23 4.6 0.9 1.0
C I:ASP23 4.6 0.6 1.0
N I:THR27 4.7 0.4 1.0
CA I:THR27 4.8 0.5 1.0
N I:THR29 4.8 0.7 1.0
CA I:ASP25 4.8 0.7 1.0
CA I:LYS22 4.9 0.2 1.0
C I:LYS22 4.9 0.7 1.0

Calcium binding site 6 out of 8 in 4jpz

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Calcium binding site 6 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca202

b:0.8
occ:1.00
 OD1 I:ASN61 2.3 0.6 1.0
OD1 I:ASP57 2.3 0.0 1.0
OE1 I:GLU68 2.4 0.3 1.0
OE2 I:GLU68 2.4 0.2 1.0
O I:THR63 2.5 0.5 1.0
CD I:GLU68 2.8 0.8 1.0
CG I:ASN61 3.2 0.6 1.0
OD2 I:ASP59 3.4 0.7 1.0
ND2 I:ASN61 3.6 0.2 1.0
CG I:ASP57 3.6 0.5 1.0
C I:THR63 3.7 0.3 1.0
CG I:ASP59 3.9 0.5 1.0
CB I:ASP59 4.0 0.6 1.0
N I:ASN61 4.1 0.5 1.0
CG I:GLU68 4.3 1.0 1.0
N I:ASP59 4.3 0.8 1.0
CA I:ASP57 4.3 0.5 1.0
N I:THR63 4.4 0.1 1.0
OD2 I:ASP57 4.4 1.0 1.0
N I:GLY60 4.4 0.3 1.0
CB I:ASN61 4.4 0.5 1.0
N I:ALA58 4.5 0.2 1.0
CA I:ILE64 4.5 0.0 1.0
N I:ILE64 4.5 0.9 1.0
OD1 I:ASP65 4.5 0.0 1.0
CB I:ASP57 4.6 0.3 1.0
CA I:ASN61 4.6 0.7 1.0
CA I:THR63 4.6 0.3 1.0
N I:GLY62 4.7 0.3 1.0
CA I:ASP59 4.7 0.4 1.0
C I:ASN61 4.8 0.4 1.0
OG1 I:THR63 4.8 0.5 1.0
OD1 I:ASP59 4.9 0.4 1.0
C I:ASP57 4.9 0.2 1.0

Calcium binding site 7 out of 8 in 4jpz

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Calcium binding site 7 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca203

b:78.6
occ:1.00
 O I:TYR100 2.2 84.4 1.0
OD1 I:ASP96 2.3 85.2 1.0
OD1 I:ASN98 2.4 86.1 1.0
OD1 I:ASP94 2.6 72.6 1.0
CG I:ASN98 3.2 77.7 1.0
CG I:ASP96 3.3 80.0 1.0
C I:TYR100 3.4 82.5 1.0
ND2 I:ASN98 3.5 80.6 1.0
OD2 I:ASP96 3.6 80.9 1.0
CG I:ASP94 3.8 73.1 1.0
N I:TYR100 4.2 77.8 1.0
CA I:TYR100 4.2 79.5 1.0
N I:ASP96 4.3 73.8 1.0
N I:ILE101 4.4 77.6 1.0
CB I:TYR100 4.5 87.0 1.0
N I:LYS95 4.5 67.9 1.0
OD2 I:ASP94 4.5 76.1 1.0
CB I:ASN98 4.5 74.0 1.0
CA I:ILE101 4.6 70.0 1.0
CB I:ASP96 4.6 76.7 1.0
N I:ASN98 4.6 72.8 1.0
CA I:ASP94 4.6 71.9 1.0
C I:ASP94 4.8 74.4 1.0
NE2 I:GLN136 4.8 90.5 1.0
CB I:ASP94 4.8 69.2 1.0
N I:GLY97 4.9 78.1 1.0
CA I:ASP96 4.9 74.3 1.0

Calcium binding site 8 out of 8 in 4jpz

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Calcium binding site 8 out of 8 in the Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Voltage-Gated Sodium Channel 1.2 C-Terminal Domain in Complex with FGF13U and CA2+/Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca204

b:76.5
occ:1.00
 OD1 I:ASP132 2.3 77.3 1.0
O I:GLN136 2.4 82.3 1.0
OD1 I:ASP134 2.4 84.0 1.0
OD1 I:ASP130 2.5 81.6 1.0
OD2 I:ASP132 2.5 87.1 1.0
CG I:ASP132 2.8 82.2 1.0
CG I:ASP134 3.4 79.9 1.0
C I:GLN136 3.6 80.4 1.0
CG I:ASP130 3.8 82.1 1.0
OD2 I:ASP134 3.8 76.4 1.0
CB I:ASP132 4.3 79.2 1.0
N I:GLN136 4.4 85.0 1.0
CA I:GLN136 4.4 84.6 1.0
N I:VAL137 4.5 78.6 1.0
OD2 I:ASP130 4.5 82.2 1.0
CA I:ASP130 4.5 76.1 1.0
CB I:GLN136 4.6 90.4 1.0
N I:ASP134 4.6 80.9 1.0
CA I:VAL137 4.6 81.0 1.0
CB I:ASP134 4.7 83.9 1.0
N I:ASP132 4.7 76.5 1.0
CB I:ASP130 4.7 81.6 1.0
O I:ALA129 4.9 80.8 1.0
N I:GLY133 4.9 76.2 1.0
N I:ILE131 5.0 85.4 1.0
CA I:ASP132 5.0 76.7 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: Sun Jul 14 08:34:43 2024

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