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Calcium in PDB 4djc: 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex

Protein crystallography data

The structure of 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex, PDB code: 4djc was solved by M.F.Sarhan, C.-C.Tung, F.Van Petegem, C.A.Ahern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.380, 72.720, 97.010, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.6

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex (pdb code 4djc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex, PDB code: 4djc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4djc

Go back to Calcium Binding Sites List in 4djc
Calcium binding site 1 out of 4 in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:16.1
occ:1.00
 OD1 A:ASP21 2.2 18.8 1.0
O A:THR27 2.3 17.9 1.0
OD1 A:ASP23 2.4 20.3 1.0
OD2 A:ASP25 2.4 19.3 1.0
OE2 A:GLU32 2.5 19.1 1.0
OE1 A:GLU32 2.5 16.0 1.0
O A:HOH346 2.5 19.4 1.0
CD A:GLU32 2.8 16.5 1.0
CG A:ASP23 3.4 22.7 1.0
CG A:ASP25 3.4 20.1 1.0
CG A:ASP21 3.4 15.8 1.0
C A:THR27 3.5 15.1 1.0
OD2 A:ASP23 3.7 25.2 1.0
OD1 A:ASP25 4.0 25.7 1.0
OG1 A:THR27 4.1 26.0 1.0
CA A:ASP21 4.1 17.6 1.0
N A:THR27 4.1 15.9 1.0
CB A:ASP21 4.2 16.1 1.0
N A:ASP25 4.3 17.8 1.0
CG A:GLU32 4.3 14.4 1.0
OD2 A:ASP21 4.3 17.9 1.0
CA A:THR27 4.4 17.2 1.0
CB A:ASP25 4.4 19.1 1.0
C A:ASP21 4.4 17.4 1.0
N A:ILE28 4.5 13.9 1.0
N A:ASP23 4.5 22.6 1.0
CA A:ILE28 4.6 13.6 1.0
O A:HOH398 4.6 36.9 1.0
CB A:ASP23 4.7 22.5 1.0
O A:HOH314 4.7 19.8 1.0
N A:GLY24 4.7 19.6 1.0
CA A:ASP25 4.7 17.9 1.0
N A:LYS22 4.8 21.3 1.0
N A:GLY26 4.8 15.5 1.0
CB A:THR27 4.9 19.9 1.0
CA A:ASP23 4.9 21.8 1.0
CG2 A:THR29 4.9 14.9 1.0
N A:THR29 4.9 13.6 1.0
C A:ASP25 5.0 17.1 1.0
O A:ASP21 5.0 19.4 1.0
C A:ASP23 5.0 21.4 1.0

Calcium binding site 2 out of 4 in 4djc

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Calcium binding site 2 out of 4 in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:12.9
occ:1.00
 OD2 A:ASP57 2.2 13.7 1.0
O A:HOH344 2.3 18.9 1.0
O A:THR63 2.3 13.0 1.0
OD1 A:ASN61 2.4 13.0 1.0
OD1 A:ASP59 2.4 13.3 1.0
OE1 A:GLU68 2.5 14.6 1.0
OE2 A:GLU68 2.5 13.4 1.0
CD A:GLU68 2.8 12.8 1.0
CG A:ASP59 3.3 14.1 1.0
CG A:ASN61 3.4 11.8 1.0
CG A:ASP57 3.4 12.7 1.0
C A:THR63 3.5 12.0 1.0
OD2 A:ASP59 3.6 15.3 1.0
ND2 A:ASN61 4.0 14.4 1.0
N A:ASN61 4.2 13.2 1.0
N A:THR63 4.2 14.0 1.0
O A:HOH324 4.3 21.8 1.0
CA A:ASP57 4.3 16.2 1.0
OD1 A:ASP57 4.3 16.6 1.0
CG A:GLU68 4.3 13.4 1.0
CB A:ASP57 4.3 15.9 1.0
CA A:ILE64 4.4 11.9 0.3
N A:ILE64 4.4 11.1 1.0
CA A:ILE64 4.4 12.9 0.7
N A:ASP59 4.4 13.7 1.0
CB A:ASN61 4.4 13.5 1.0
CA A:THR63 4.5 13.4 1.0
N A:ASP65 4.5 11.5 1.0
CB A:ASP59 4.5 13.2 1.0
C A:ASP57 4.6 14.8 1.0
N A:GLY62 4.6 14.4 1.0
OG1 A:THR63 4.6 17.0 1.0
CA A:ASN61 4.6 12.9 1.0
N A:GLY60 4.7 13.7 1.0
CD1 A:ILE64 4.7 9.5 0.3
N A:ALA58 4.8 14.4 1.0
CA A:ASP59 4.8 13.2 1.0
C A:ASN61 4.9 14.1 1.0
C A:ASP59 4.9 13.4 1.0
OD1 A:ASP65 4.9 17.3 1.0
C A:ILE64 4.9 12.4 1.0
CG A:ASP65 5.0 14.5 1.0
O A:HOH327 5.0 18.3 1.0

Calcium binding site 3 out of 4 in 4djc

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Calcium binding site 3 out of 4 in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:10.8
occ:1.00
 O A:TYR100 2.3 14.4 1.0
OD1 A:ASP94 2.3 12.3 1.0
OD1 A:ASP96 2.3 11.4 1.0
OD1 A:ASN98 2.4 11.4 1.0
O A:HOH316 2.4 17.9 1.0
OE1 A:GLU105 2.4 13.3 1.0
OE2 A:GLU105 2.5 12.6 1.0
CD A:GLU105 2.8 11.3 1.0
CG A:ASP96 3.3 12.7 1.0
CG A:ASN98 3.3 11.7 1.0
C A:TYR100 3.5 12.6 1.0
CG A:ASP94 3.5 11.9 1.0
OD2 A:ASP96 3.8 17.1 1.0
ND2 A:ASN98 4.1 12.6 1.0
N A:ASN98 4.1 11.0 1.0
N A:TYR100 4.1 11.3 1.0
N A:ASP96 4.2 13.2 1.0
CA A:ASP94 4.2 12.3 1.0
CB A:ASN98 4.3 11.9 1.0
CG A:GLU105 4.3 12.9 1.0
CA A:TYR100 4.3 10.9 1.0
C A:ASP94 4.3 12.8 1.0
OD2 A:ASP94 4.3 12.4 1.0
CB A:ASP94 4.4 12.6 1.0
N A:LYS95 4.4 13.3 1.0
N A:ILE101 4.4 11.8 1.0
CB A:ASP96 4.5 12.6 1.0
N A:GLY97 4.5 12.5 1.0
CA A:ILE101 4.5 11.0 1.0
CA A:ASN98 4.6 12.0 1.0
N A:SER102 4.7 12.0 1.0
CA A:ASP96 4.7 12.2 1.0
CB A:TYR100 4.7 12.1 1.0
O A:HOH340 4.7 27.7 1.0
N A:GLY99 4.8 11.6 1.0
O A:ASP94 4.8 13.7 1.0
C A:ASP96 4.8 13.6 1.0
C A:ASN98 4.9 12.0 1.0

Calcium binding site 4 out of 4 in 4djc

Go back to Calcium Binding Sites List in 4djc
Calcium binding site 4 out of 4 in the 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.35 A Crystal Structure of the NAV1.5 Diii-IV-Ca/Cam Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:14.2
occ:1.00
 O A:GLN136 2.2 14.1 0.5
OD1 A:ASP130 2.3 15.3 1.0
OD1 A:ASP132 2.3 19.1 1.0
OD1 A:ASP134 2.4 17.2 1.0
O A:GLN136 2.4 13.7 0.5
O A:HOH348 2.4 16.7 1.0
OE1 A:GLU141 2.5 14.4 1.0
OE2 A:GLU141 2.5 17.2 1.0
CD A:GLU141 2.8 13.1 1.0
CG A:ASP132 3.2 21.2 1.0
CG A:ASP134 3.3 18.6 1.0
CG A:ASP130 3.4 14.9 1.0
C A:GLN136 3.5 13.2 0.5
C A:GLN136 3.5 12.4 0.5
OD2 A:ASP132 3.7 24.3 1.0
OD2 A:ASP134 3.7 19.2 1.0
CA A:ASP130 4.1 16.3 1.0
N A:ASP134 4.1 17.9 1.0
N A:GLN136 4.2 15.3 0.5
CB A:ASP130 4.2 15.8 1.0
N A:GLN136 4.2 14.4 0.5
N A:ASP132 4.3 18.5 1.0
OD2 A:ASP130 4.3 17.0 1.0
CG A:GLU141 4.3 14.0 1.0
N A:VAL137 4.3 12.1 1.0
CA A:VAL137 4.4 11.7 1.0
CB A:ASP134 4.4 18.9 1.0
CB A:ASP132 4.4 20.0 1.0
CA A:GLN136 4.4 14.4 0.5
N A:GLY133 4.4 19.1 1.0
N A:ASN138 4.5 11.9 1.0
C A:ASP130 4.5 17.6 1.0
CA A:GLN136 4.5 12.6 0.5
CA A:ASP132 4.6 20.1 1.0
N A:ILE131 4.6 17.4 1.0
CA A:ASP134 4.7 17.9 1.0
CG A:GLN136 4.7 11.3 0.5
C A:ASP132 4.8 20.2 1.0
N A:GLY135 4.8 16.9 1.0
C A:VAL137 4.9 11.9 1.0
C A:ASP134 4.9 16.8 1.0
O A:ASP130 4.9 20.3 1.0

Reference:

M.F.Sarhan, C.C.Tung, F.Van Petegem, C.A.Ahern. Crystallographic Basis For Calcium Regulation of Sodium Channels. Proc.Natl.Acad.Sci.Usa V. 109 3558 2012.
ISSN: ISSN 0027-8424
PubMed: 22331908
DOI: 10.1073/PNAS.1114748109
Page generated: Sat Jul 13 23:27:14 2024

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