Sodium in PDB 4wee: High-Resolution Structure of Synaptotagmin 1 C2A

The structure of High-Resolution Structure of Synaptotagmin 1 C2A, PDB code: 4wee was solved by R.B.Sutton, K.L.Fuson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 0.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.738, 38.547, 44.295, 90.00, 97.94, 90.00
R / Rfree (%)	14.9 / 16.4

The binding sites of Sodium atom in the High-Resolution Structure of Synaptotagmin 1 C2A (pdb code 4wee). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the High-Resolution Structure of Synaptotagmin 1 C2A, PDB code: 4wee:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:14.5 occ:1.00 NA A:NA303 2.8 14.3 1.0 O A:LEU135 2.8 10.2 1.0 O A:MET138 2.8 8.5 1.0 O A:HOH501 2.9 13.2 0.5 HB2 A:MET138 3.1 10.9 0.6 HA A:ASP136 3.2 9.9 1.0 HG3 A:GLU140 3.3 0.6 0.0 O A:ASP136 3.3 10.6 1.0 H A:MET138 3.4 5.5 0.4 HG2 A:GLU140 3.4 0.4 0.0 H A:MET138 3.4 36.2 0.6 HB2 A:MET138 3.5 87.0 0.4 O A:HOH564 3.5 31.0 0.3 C A:ASP136 3.6 9.0 1.0 C A:MET138 3.6 7.5 1.0 N A:MET138 3.7 8.1 1.0 CG A:GLU140 3.8 10.2 1.0 CA A:ASP136 3.8 9.7 1.0 CB A:MET138 3.9 8.9 0.6 C A:LEU135 3.9 10.1 1.0 O A:HOH578 3.9 28.1 0.9 CA A:MET138 3.9 8.3 0.6 CA A:MET138 4.0 8.4 0.4 HA A:GLU140 4.1 8.6 0.0 O A:HOH401 4.1 11.6 0.5 CB A:MET138 4.2 9.2 0.4 N A:ASP136 4.4 10.1 1.0 N A:SER137 4.4 8.2 1.0 HB3 A:MET138 4.4 11.0 0.6 N A:GLU140 4.5 7.6 1.0 C A:SER137 4.5 8.0 1.0 O A:HOH488 4.5 35.5 0.8 HB3 A:MET138 4.6 7.4 0.4 C A:VAL139 4.6 7.2 1.0 CA A:GLU140 4.6 7.4 1.0 H A:GLU140 4.7 0.0 0.0 N A:VAL139 4.7 7.0 1.0 OD1 A:ASP136 4.7 10.3 1.0 CD A:GLU140 4.8 10.0 1.0 OE2 A:GLU140 4.8 9.7 1.0 HG2 A:MET138 4.8 0.9 0.6 CB A:GLU140 4.8 8.2 1.0 O A:VAL139 4.9 8.2 1.0 H A:SER137 4.9 6.7 0.9 HA A:MET138 4.9 0.5 0.6 CG A:MET138 4.9 12.0 0.6 HA A:MET138 5.0 0.5 0.4 CA A:SER137 5.0 8.5 1.0

Sodium binding site 2 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:30.0 occ:1.00 O A:HOH476 2.5 17.2 0.7 OE1 A:GLN164 2.7 10.8 1.0 O A:ALA165 2.7 6.5 1.0 HB2 A:GLN164 3.0 5.0 0.8 HB3 A:ASN203 3.2 8.1 1.0 HB3 A:ALA166 3.4 11.5 1.0 CD A:GLN164 3.6 7.9 1.0 HH2 A:TRP259 3.6 11.0 0.9 C A:ALA165 3.6 6.0 1.0 HG3 A:GLN164 3.7 9.5 0.9 HA A:ALA166 3.8 7.9 0.8 CB A:GLN164 3.9 6.2 1.0 O A:ASN203 3.9 8.2 1.0 HA A:ASN203 3.9 3.4 0.6 CG A:GLN164 3.9 7.0 1.0 HG21 A:VAL205 4.0 32.7 0.8 O A:PRO204 4.0 7.0 1.0 C A:ASN203 4.1 7.1 1.0 CB A:ASN203 4.1 7.8 1.0 H A:ALA165 4.1 6.5 0.8 HG23 A:VAL205 4.1 53.5 1.0 CB A:ALA166 4.2 10.0 1.0 CA A:ASN203 4.3 7.1 1.0 CA A:ALA166 4.3 7.2 1.0 N A:ALA165 4.3 5.9 1.0 N A:ALA166 4.3 6.4 1.0 HB3 A:GLN164 4.4 11.9 1.0 HB2 A:ALA166 4.4 22.1 0.0 OD1 A:ASN203 4.5 9.3 1.0 CG2 A:VAL205 4.5 9.4 1.0 CH2 A:TRP259 4.6 9.3 1.0 CA A:ALA165 4.6 6.0 1.0 C A:PRO204 4.6 6.7 1.0 N A:PRO204 4.7 6.7 1.0 NE2 A:GLN164 4.7 7.7 1.0 HB2 A:ASN203 4.7 0.0 0.3 C A:GLN164 4.8 5.5 1.0 CG A:ASN203 4.8 7.9 1.0 HG2 A:GLN164 4.9 6.0 1.0 CA A:GLN164 4.9 5.6 1.0 HB1 A:ALA166 5.0 0.0 0.6 HE22 A:GLN164 5.0 2.6 0.3 HZ3 A:TRP259 5.0 10.0 1.0 HA A:ALA165 5.0 4.7 0.8

Sodium binding site 3 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:14.3 occ:1.00 O A:HOH401 2.0 11.6 0.5 OD1 A:ASP136 2.7 10.3 1.0 NA A:NA301 2.8 14.5 1.0 HA A:ASP136 3.0 9.9 1.0 O A:HOH488 3.1 35.5 0.8 OE2 A:GLU140 3.2 9.7 1.0 O A:ASP136 3.3 10.6 1.0 HG2 A:GLU140 3.4 0.4 0.0 HG3 A:GLU140 3.7 0.6 0.0 CG A:ASP136 3.8 10.3 1.0 CA A:ASP136 3.8 9.7 1.0 CG A:GLU140 3.8 10.2 1.0 NA A:NA304 3.9 15.1 1.0 CD A:GLU140 3.9 10.0 1.0 C A:ASP136 4.0 9.0 1.0 O A:HOH450 4.0 16.8 0.4 O A:HOH578 4.2 28.1 0.9 CB A:ASP136 4.4 10.5 1.0 O A:LEU135 4.6 10.2 1.0 OD2 A:ASP136 4.8 12.6 1.0 O A:HOH501 4.8 13.2 0.5 HB2 A:ASP136 4.9 12.4 1.0 O A:MET138 4.9 8.5 1.0 N A:ASP136 5.0 10.1 1.0 OE1 A:GLU140 5.0 12.8 1.0

Sodium binding site 4 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:15.1 occ:1.00 OD1 A:ASP136 2.7 10.3 1.0 O A:HOH417 3.3 18.9 0.9 CG A:ASP136 3.6 10.3 1.0 OD2 A:ASP136 3.8 12.6 1.0 NA A:NA303 3.9 14.3 1.0 O A:HOH401 4.1 11.6 0.5 O A:HOH450 4.5 16.8 0.4 CB A:ASP136 4.9 10.5 1.0 O A:HOH488 4.9 35.5 0.8

Sodium binding site 5 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:12.8 occ:1.00 HA A:GLN263 2.6 0.8 0.3 O A:HOH575 2.7 32.4 1.0 O A:GLU140 2.8 7.5 1.0 HG2 A:GLN263 2.8 62.4 0.3 O A:LEU262 2.8 10.2 1.0 HG13 A:VAL139 2.8 0.9 0.5 HD13 A:LEU142 2.8 20.2 1.0 H A:GLU140 3.0 0.0 0.0 HB2 A:GLU140 3.0 6.2 0.8 HA A:GLN263 3.0 0.2 0.7 HG A:LEU142 3.1 11.4 1.0 HG12 A:VAL139 3.3 56.4 1.0 N A:GLU140 3.4 7.6 1.0 HB2 A:LEU142 3.5 9.0 1.0 CG1 A:VAL139 3.5 9.1 1.0 CD1 A:LEU142 3.5 12.8 1.0 CA A:GLN263 3.5 11.5 0.3 H A:SER264 3.5 71.5 1.0 C A:GLU140 3.6 7.2 1.0 CG A:GLN263 3.6 13.2 0.3 CG A:LEU142 3.7 11.6 1.0 NA A:NA306 3.7 11.1 1.0 HD12 A:LEU142 3.7 15.5 1.0 CA A:GLU140 3.8 7.4 1.0 CB A:GLU140 3.8 8.2 1.0 C A:LEU262 3.8 8.8 1.0 CA A:GLN263 3.8 11.3 0.7 H A:LEU142 3.9 8.5 0.9 N A:SER264 3.9 15.1 1.0 HB3 A:GLN263 3.9 25.5 0.3 CB A:GLN263 4.0 11.2 0.3 HG11 A:VAL139 4.0 1.6 0.5 HG3 A:GLN263 4.0 15.2 0.3 CB A:LEU142 4.1 9.3 1.0 HA A:VAL139 4.1 5.7 1.0 C A:VAL139 4.2 7.2 1.0 C A:GLN263 4.2 10.9 1.0 N A:GLN263 4.2 10.9 1.0 HB3 A:SER264 4.3 23.3 0.0 HB3 A:GLU140 4.3 13.3 1.0 HD11 A:LEU142 4.4 24.2 0.9 N A:LEU142 4.5 7.8 1.0 HB2 A:SER264 4.5 0.0 0.1 CA A:VAL139 4.5 7.0 1.0 CB A:VAL139 4.6 8.0 1.0 OE1 A:GLU140 4.6 12.8 1.0 CB A:SER264 4.7 21.4 1.0 CA A:SER264 4.7 17.5 1.0 CD A:GLN263 4.7 16.6 0.3 HA A:SER264 4.7 0.7 0.2 HA A:GLU140 4.7 8.6 0.0 N A:LYS141 4.8 7.9 1.0 HG3 A:GLU140 4.8 0.6 0.0 HB3 A:LEU142 4.8 13.2 1.0 CG A:GLU140 4.8 10.2 1.0 HB2 A:GLN263 4.9 0.5 0.3 CA A:LEU142 4.9 8.9 1.0 HB3 A:ASP261 5.0 6.8 0.7

Sodium binding site 6 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:11.1 occ:1.00 H A:LEU142 2.2 8.5 0.9 NA A:NA307 2.7 14.5 1.0 O A:LEU262 2.8 10.2 1.0 O A:GLY143 2.8 6.6 1.0 HB2 A:LEU142 2.9 9.0 1.0 N A:LEU142 3.0 7.8 1.0 H A:LEU262 3.1 6.9 0.8 HB3 A:ASP261 3.1 18.7 0.3 HB3 A:ASP261 3.1 6.8 0.7 H A:GLY143 3.1 0.5 0.8 O A:GLU140 3.1 7.5 1.0 N A:GLY143 3.3 8.8 1.0 N A:LEU262 3.4 6.5 1.0 C A:LEU142 3.5 9.1 1.0 CA A:LEU142 3.5 8.9 1.0 HB2 A:LEU262 3.5 9.0 1.0 O A:HOH579 3.5 15.5 0.7 CB A:LEU142 3.6 9.3 1.0 NA A:NA305 3.7 12.8 1.0 HA A:LYS141 3.7 0.7 0.0 C A:LEU262 3.7 8.8 1.0 C A:GLY143 3.7 6.8 1.0 HA A:ASP261 3.8 5.5 0.7 HA A:ASP261 3.8 4.6 0.3 CB A:ASP261 3.9 7.5 0.3 CB A:ASP261 3.9 7.8 0.7 CA A:LEU262 4.0 7.0 1.0 HG12 A:VAL139 4.0 56.4 1.0 C A:ASP261 4.0 7.1 1.0 C A:LYS141 4.1 8.9 1.0 CA A:GLY143 4.1 9.0 1.0 CA A:ASP261 4.1 7.0 0.7 CA A:ASP261 4.1 6.7 0.3 HG A:LEU142 4.1 11.4 1.0 CB A:LEU262 4.2 7.0 1.0 O A:LEU142 4.2 11.1 1.0 OD1 A:ASP261 4.3 10.2 0.3 C A:GLU140 4.3 7.2 1.0 CA A:LYS141 4.3 9.8 1.0 HB3 A:LEU142 4.3 13.2 1.0 OD2 A:ASP261 4.4 10.0 0.7 HA A:LEU142 4.4 56.5 1.0 CG A:LEU142 4.5 11.6 1.0 HG11 A:VAL139 4.5 1.6 0.5 CG1 A:VAL139 4.5 9.1 1.0 HG13 A:VAL139 4.6 0.9 0.5 HB2 A:ASP261 4.6 10.9 0.3 HB2 A:ASP261 4.6 9.8 0.7 HA2 A:GLY143 4.6 15.8 1.0 CG A:ASP261 4.6 9.0 0.7 CG A:ASP261 4.7 9.0 0.3 HG2 A:GLN263 4.7 62.4 0.3 HA A:GLN263 4.7 0.8 0.3 HD13 A:LEU142 4.7 20.2 1.0 HG A:LEU262 4.7 6.9 1.0 N A:LYS141 4.8 7.9 1.0 HA3 A:GLY143 4.8 2.3 0.3 O A:ASP261 4.8 8.7 1.0 HG3 A:LYS144 4.8 18.7 0.7 HB3 A:LEU262 4.8 8.6 1.0 HZ2 A:LYS144 4.9 0.0 0.7 HA A:LEU262 4.9 6.0 1.0 HG2 A:LYS144 4.9 0.1 0.7 O A:HOH455 4.9 16.3 0.9 HG3 A:GLN263 4.9 15.2 0.3 HA A:LYS144 5.0 7.7 0.3 N A:GLN263 5.0 10.9 1.0 N A:LYS144 5.0 6.8 1.0 HA A:LYS144 5.0 5.7 0.7

Sodium binding site 7 out of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:14.5 occ:1.00 O A:HOH455 2.7 16.3 0.9 OD2 A:ASP261 2.7 10.0 0.7 O A:HOH579 2.7 15.5 0.7 NA A:NA306 2.7 11.1 1.0 OD1 A:ASP261 2.8 10.2 0.3 HA A:LYS141 2.9 0.7 0.0 HB3 A:ASP261 3.1 18.7 0.3 HB3 A:ASP261 3.1 6.8 0.7 HZ2 A:LYS144 3.1 0.0 0.7 HG12 A:VAL139 3.3 56.4 1.0 O A:GLU140 3.3 7.5 1.0 H A:LEU142 3.5 8.5 0.9 CG A:ASP261 3.6 9.0 0.3 CG A:ASP261 3.6 9.0 0.7 CB A:ASP261 3.8 7.5 0.3 CB A:ASP261 3.8 7.8 0.7 CA A:LYS141 3.9 9.8 1.0 O A:HOH416 3.9 18.3 0.5 NZ A:LYS144 3.9 17.9 0.7 HG2 A:LYS141 3.9 19.2 1.0 HG11 A:VAL139 4.0 1.6 0.5 HZ3 A:LYS144 4.0 43.6 0.7 H A:GLY143 4.0 0.5 0.8 CG1 A:VAL139 4.1 9.1 1.0 N A:LEU142 4.2 7.8 1.0 C A:GLU140 4.2 7.2 1.0 HZ1 A:LYS144 4.2 0.5 0.7 O A:GLY143 4.3 6.6 1.0 O A:HOH403 4.3 49.2 0.8 HA A:ASP261 4.4 5.5 0.7 N A:LYS141 4.4 7.9 1.0 HA A:ASP261 4.4 4.6 0.3 HB2 A:ASP261 4.5 10.9 0.3 HG2 A:LYS144 4.5 0.1 0.7 C A:LYS141 4.5 8.9 1.0 HG3 A:LYS144 4.5 18.7 0.7 HB2 A:ASP261 4.6 9.8 0.7 HZ3 A:LYS141 4.6 0.3 0.5 HG13 A:VAL139 4.7 0.9 0.5 N A:GLY143 4.7 8.8 1.0 CG A:LYS141 4.7 17.5 1.0 CA A:ASP261 4.7 7.0 0.7 CA A:ASP261 4.7 6.7 0.3 CB A:LYS141 4.7 14.5 1.0 OD2 A:ASP261 4.8 9.6 0.3 OD1 A:ASP261 4.8 9.2 0.7 HB3 A:LYS141 4.8 0.2 0.3 HB A:VAL139 4.8 93.5 1.0 O A:VAL139 4.9 8.2 1.0 O A:HOH420 4.9 29.2 0.8 HG3 A:LYS141 4.9 18.9 1.0 HE3 A:LYS144 4.9 0.7 0.7 CG A:LYS144 5.0 10.0 0.7

R.B.Sutton, R.B.Sutton, K.L.Fuson. N/A N/A.