Calcium in PDB 6jlh: Structure of Scgn in Complex with A SNAP25 Peptide

The structure of Structure of Scgn in Complex with A SNAP25 Peptide, PDB code: 6jlh was solved by J.Qin, Q.Sun, D.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.96 / 2.37
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.524, 107.049, 54.770, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.7

The structure of Structure of Scgn in Complex with A SNAP25 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Structure of Scgn in Complex with A SNAP25 Peptide (pdb code 6jlh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structure of Scgn in Complex with A SNAP25 Peptide, PDB code: 6jlh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:26.7 occ:1.00 OD1 A:ASP67 2.3 29.7 1.0 OD1 A:ASP71 2.4 29.6 1.0 O A:ARG73 2.4 26.3 1.0 OE1 A:GLU78 2.4 22.6 1.0 OE2 A:GLU78 2.5 23.6 1.0 OG1 A:THR69 2.5 26.1 1.0 O A:HOH415 2.5 18.4 1.0 CD A:GLU78 2.8 22.9 1.0 CG A:ASP71 3.3 30.4 1.0 CG A:ASP67 3.4 29.8 1.0 C A:ARG73 3.5 28.4 1.0 OD2 A:ASP71 3.7 31.7 1.0 CB A:THR69 3.8 25.7 1.0 OD2 A:ASP67 4.1 32.8 1.0 N A:THR69 4.1 25.4 1.0 CG2 A:THR69 4.3 25.7 1.0 CG A:GLU78 4.3 23.2 1.0 CA A:THR69 4.3 26.2 1.0 N A:ARG73 4.3 30.1 1.0 N A:LEU74 4.4 27.3 1.0 CA A:LEU74 4.4 26.7 1.0 CA A:ASP67 4.4 26.6 1.0 N A:PHE70 4.4 27.1 1.0 CA A:ARG73 4.4 29.9 1.0 CB A:ASP67 4.4 28.1 1.0 N A:ASP71 4.5 30.3 1.0 N A:GLN75 4.5 25.4 1.0 C A:THR69 4.6 27.2 1.0 CB A:ASP71 4.6 29.9 1.0 C A:ASP67 4.6 25.3 1.0 OE1 A:GLN75 4.7 25.4 1.0 CB A:ARG73 4.7 32.2 1.0 CG A:GLN75 4.7 24.8 1.0 C A:LEU74 4.8 26.1 1.0 N A:ALA68 4.8 24.9 1.0 CD A:GLN75 4.9 25.1 1.0 N A:GLY72 5.0 29.9 1.0

Calcium binding site 2 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:31.6 occ:1.00 OD1 A:ASP114 2.3 26.3 1.0 O A:HOH420 2.3 23.2 1.0 OG A:SER118 2.4 30.3 1.0 OE1 A:GLU125 2.4 32.9 1.0 O A:TYR120 2.4 30.8 1.0 OE2 A:GLU125 2.6 32.3 1.0 OD1 A:ASP116 2.7 35.4 1.0 CD A:GLU125 2.8 33.1 1.0 CG A:ASP114 3.4 25.9 1.0 CB A:SER118 3.5 29.4 1.0 CG A:ASP116 3.6 36.0 1.0 C A:TYR120 3.6 29.7 1.0 OD2 A:ASP116 3.8 35.9 1.0 CD1 A:TYR120 3.9 47.6 1.0 CA A:ASP114 4.0 27.5 1.0 N A:SER118 4.0 32.0 1.0 CE1 A:TYR120 4.1 50.7 1.0 CB A:ASP114 4.2 26.0 1.0 CA A:SER118 4.3 29.2 1.0 CG A:GLU125 4.3 31.9 1.0 OD2 A:ASP114 4.3 26.1 1.0 N A:TYR120 4.4 29.6 1.0 C A:ASP114 4.4 29.1 1.0 N A:ILE121 4.5 27.7 1.0 CA A:ILE121 4.5 25.6 1.0 CG A:TYR120 4.5 44.1 1.0 CA A:TYR120 4.6 31.6 1.0 N A:ALA115 4.6 31.1 1.0 O A:HOH413 4.7 28.3 1.0 N A:SER122 4.7 25.1 1.0 CZ A:TYR120 4.8 53.1 1.0 N A:GLY119 4.8 26.7 1.0 C A:SER118 4.8 26.8 1.0 N A:SER117 4.9 37.7 1.0 N A:ASP116 5.0 35.1 1.0 CB A:ASP116 5.0 36.9 1.0

Calcium binding site 3 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:33.9 occ:1.00 OD1 A:ASP250 2.2 38.6 1.0 OE1 A:GLN258 2.3 26.5 1.0 OD1 A:ASN252 2.4 40.1 1.0 OE1 A:GLU261 2.4 28.4 1.0 OE2 A:GLU261 2.4 28.9 1.0 O A:LYS256 2.4 30.7 1.0 OD1 A:ASP254 2.5 36.0 1.0 CD A:GLU261 2.7 29.0 1.0 CG A:ASP254 3.3 36.6 1.0 CG A:ASP250 3.3 39.4 1.0 CG A:ASN252 3.4 38.7 1.0 CD A:GLN258 3.5 28.1 1.0 C A:LYS256 3.5 31.0 1.0 OD2 A:ASP254 3.6 36.1 1.0 ND2 A:ASN252 4.0 39.4 1.0 NE2 A:GLN258 4.1 29.1 1.0 CA A:ASP250 4.1 38.0 1.0 OD2 A:ASP250 4.2 39.0 1.0 N A:GLN258 4.2 27.6 1.0 CG A:GLU261 4.2 28.3 1.0 CB A:ASP250 4.2 38.2 1.0 N A:LYS256 4.2 33.5 1.0 N A:ASP254 4.3 35.2 1.0 CA A:LYS256 4.3 32.8 1.0 N A:ILE257 4.4 29.4 1.0 CA A:ILE257 4.5 28.8 1.0 CB A:ASP254 4.5 36.1 1.0 CB A:LYS256 4.5 35.0 1.0 N A:ASN252 4.5 38.1 1.0 C A:ASP250 4.5 38.5 1.0 O A:HOH436 4.5 39.5 1.0 N A:LYS253 4.6 38.8 1.0 CB A:ASN252 4.6 38.5 1.0 N A:MSE251 4.7 38.6 1.0 CG A:GLN258 4.7 28.5 1.0 CB A:GLN258 4.8 28.3 1.0 CA A:ASP254 4.8 35.7 1.0 C A:ILE257 4.9 28.4 1.0 C A:ASN252 4.9 39.0 1.0 CA A:ASN252 4.9 38.5 1.0 N A:GLY255 4.9 34.5 1.0

Calcium binding site 4 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:36.5 occ:1.00 OD1 A:ASP21 2.2 35.0 1.0 OD1 A:ASN25 2.3 36.8 1.0 O A:HOH432 2.3 32.5 1.0 O A:TYR27 2.4 37.4 1.0 OD1 A:ASP23 2.5 51.9 1.0 OE1 A:GLU32 2.5 43.1 1.0 OE2 A:GLU32 2.6 41.9 1.0 CD A:GLU32 2.9 41.2 1.0 CG A:ASN25 3.2 37.4 1.0 CG A:ASP23 3.3 50.9 1.0 CG A:ASP21 3.5 35.4 1.0 OD2 A:ASP23 3.6 48.8 1.0 C A:TYR27 3.6 35.4 1.0 ND2 A:ASN25 4.0 37.2 1.0 N A:ASN25 4.2 41.8 1.0 CB A:ASN25 4.2 37.2 1.0 CA A:ASP21 4.2 39.1 1.0 N A:TYR27 4.2 34.0 1.0 OD2 A:ASP21 4.3 30.4 1.0 OE2 A:GLU29 4.3 37.3 1.0 C A:ASP21 4.4 41.1 1.0 O A:HOH422 4.4 42.0 1.0 CA A:TYR27 4.4 34.8 1.0 CB A:ASP21 4.4 36.4 1.0 N A:ASP23 4.4 46.8 1.0 CG A:GLU32 4.5 40.2 1.0 CG A:GLU29 4.5 35.8 1.0 O A:HOH403 4.5 44.4 1.0 CB A:ASP23 4.6 49.5 1.0 N A:ASP24 4.6 45.2 1.0 N A:ALA22 4.6 43.4 1.0 CA A:ASN25 4.6 37.8 1.0 N A:ILE28 4.6 34.5 1.0 CB A:TYR27 4.7 34.4 1.0 CA A:ASP23 4.8 47.4 1.0 C A:ASP23 4.8 45.9 1.0 CA A:ILE28 4.8 34.4 1.0 N A:GLY26 4.8 35.8 1.0 CD A:GLU29 4.9 37.4 1.0 N A:GLU29 4.9 33.0 1.0 O A:ASP21 4.9 39.5 1.0 C A:ASN25 4.9 36.2 1.0

Calcium binding site 5 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:43.0 occ:1.00 OD1 A:ASP158 2.3 23.6 1.0 O A:HOH438 2.3 34.9 1.0 OD1 A:ASN160 2.3 26.8 1.0 O A:HOH406 2.4 16.1 1.0 O A:ARG164 2.4 30.8 1.0 OD1 A:ASP162 2.5 25.9 1.0 CG A:ASP158 3.3 23.6 1.0 CG A:ASP162 3.4 27.6 1.0 CG A:ASN160 3.5 28.4 1.0 C A:ARG164 3.6 30.9 1.0 OD2 A:ASP162 3.8 28.4 1.0 OD2 A:ASP158 4.0 23.7 1.0 ND2 A:ASN160 4.1 30.1 1.0 N A:ASN160 4.1 28.6 1.0 OD2 A:ASP169 4.1 22.7 1.0 CA A:ASP158 4.2 24.1 1.0 N A:LYS159 4.2 28.3 1.0 N A:ASP162 4.2 28.6 1.0 CB A:ASP158 4.2 23.6 1.0 N A:ARG164 4.2 33.3 1.0 C A:ASP158 4.3 25.4 1.0 N A:LYS161 4.3 29.4 1.0 O A:HOH459 4.4 38.4 1.0 CA A:ARG164 4.4 33.7 1.0 O A:HOH447 4.4 37.7 1.0 N A:LEU165 4.6 26.9 1.0 CB A:ASP162 4.6 28.6 1.0 CB A:ASN160 4.6 28.8 1.0 C A:ASN160 4.7 29.7 1.0 CA A:ASN160 4.7 29.4 1.0 CA A:LEU165 4.8 24.4 1.0 CB A:ARG164 4.8 37.4 1.0 CA A:ASP162 4.8 29.3 1.0 N A:ASP166 4.9 20.9 1.0 N A:GLY163 4.9 29.3 1.0

Calcium binding site 6 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:61.1 occ:1.00 OD1 A:ASP206 2.3 36.3 1.0 O A:ALA212 2.3 32.8 1.0 OE1 A:GLU217 2.4 27.5 1.0 OG A:SER208 2.6 39.0 1.0 OE1 A:GLU214 2.9 47.1 1.0 OG1 A:THR210 2.9 40.1 1.0 CD A:GLU217 3.2 27.5 1.0 OE2 A:GLU217 3.3 27.6 1.0 CG A:ASP206 3.4 35.6 1.0 C A:ALA212 3.6 31.7 1.0 N A:THR210 3.8 41.1 1.0 CD A:GLU214 3.9 44.1 1.0 CB A:SER208 3.9 40.2 1.0 CA A:ASP206 3.9 33.8 1.0 CB A:THR210 4.0 40.6 1.0 N A:ARG209 4.0 45.4 1.0 N A:SER208 4.1 37.5 1.0 CG2 A:THR210 4.1 41.3 1.0 C A:ASP206 4.1 34.4 1.0 CB A:ASP206 4.2 34.5 1.0 OD2 A:ASP206 4.2 36.9 1.0 CA A:SER208 4.3 40.0 1.0 C A:SER208 4.3 42.9 1.0 OE2 A:GLU214 4.4 47.6 1.0 CA A:THR210 4.4 40.8 1.0 N A:ALA212 4.4 33.9 1.0 CA A:LEU213 4.4 30.0 1.0 N A:LEU213 4.4 30.8 1.0 N A:GLU214 4.4 31.9 1.0 N A:VAL207 4.5 34.9 1.0 O A:ASP206 4.5 35.1 1.0 CA A:ALA212 4.6 33.1 1.0 CG A:GLU217 4.6 26.7 1.0 N A:GLY211 4.7 39.0 1.0 C A:ARG209 4.8 44.1 1.0 C A:THR210 4.8 39.8 1.0 CA A:ARG209 4.8 46.1 1.0 C A:LEU213 4.8 30.4 1.0 CG A:GLU214 4.9 40.4 1.0

Calcium binding site 7 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:28.6 occ:1.00 OD1 C:ASP71 2.3 38.8 1.0 O C:ARG73 2.3 30.0 1.0 OD1 C:ASP67 2.4 30.3 1.0 OE1 C:GLU78 2.4 25.3 1.0 OE2 C:GLU78 2.5 24.4 1.0 OG1 C:THR69 2.5 29.3 1.0 O C:HOH412 2.5 29.1 1.0 CD C:GLU78 2.8 25.3 1.0 CG C:ASP71 3.3 41.8 1.0 CG C:ASP67 3.4 30.2 1.0 C C:ARG73 3.5 31.4 1.0 OD2 C:ASP71 3.6 43.3 1.0 CB C:THR69 3.8 30.3 1.0 OD2 C:ASP67 4.0 31.9 1.0 N C:THR69 4.1 30.4 1.0 N C:ARG73 4.3 34.2 1.0 CG C:GLU78 4.3 25.4 1.0 CG2 C:THR69 4.3 28.6 1.0 CA C:THR69 4.3 32.0 1.0 N C:LEU74 4.4 30.0 1.0 CA C:ASP67 4.4 28.3 1.0 CA C:ARG73 4.4 34.4 1.0 N C:PHE70 4.4 37.8 1.0 CA C:LEU74 4.4 29.2 1.0 NE2 C:GLN75 4.4 25.6 1.0 N C:ASP71 4.4 40.2 1.0 CB C:ASP67 4.4 29.7 1.0 N C:GLN75 4.5 28.1 1.0 C C:THR69 4.6 34.8 1.0 CB C:ASP71 4.6 40.2 1.0 C C:ASP67 4.6 28.4 1.0 CB C:ARG73 4.7 37.3 1.0 CG C:GLN75 4.7 26.9 1.0 N C:ALA68 4.8 27.8 1.0 O C:HOH456 4.9 36.6 1.0 C C:LEU74 4.9 29.3 1.0 N C:GLY72 4.9 36.5 1.0 CA C:ASP71 5.0 39.7 1.0 CD C:GLN75 5.0 26.1 1.0

Calcium binding site 8 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:44.4 occ:1.00 OD1 C:ASN25 2.3 50.7 1.0 OD1 C:ASP21 2.3 32.8 1.0 OE1 C:GLU32 2.4 44.5 1.0 O C:TYR27 2.4 42.9 1.0 O C:HOH419 2.5 39.5 1.0 OD1 C:ASP23 2.6 57.5 1.0 OE2 C:GLU32 2.6 50.6 1.0 CD C:GLU32 2.8 46.6 1.0 CG C:ASN25 3.3 50.0 1.0 CG C:ASP23 3.3 59.2 1.0 OD2 C:ASP23 3.5 63.0 1.0 CG C:ASP21 3.5 33.5 1.0 C C:TYR27 3.7 39.3 1.0 ND2 C:ASN25 4.0 49.6 1.0 CA C:ASP21 4.2 37.5 1.0 CB C:ASN25 4.3 50.2 1.0 N C:ASN25 4.3 52.4 1.0 OE2 C:GLU29 4.3 48.0 1.0 OD2 C:ASP21 4.3 32.1 1.0 N C:TYR27 4.3 41.3 1.0 CG C:GLU32 4.4 45.1 1.0 CB C:ASP21 4.4 34.8 1.0 CG C:GLU29 4.5 46.5 1.0 C C:ASP21 4.5 40.6 1.0 CA C:TYR27 4.5 41.7 1.0 N C:ASP23 4.5 55.0 1.0 CB C:ASP23 4.6 58.0 1.0 N C:ILE28 4.6 37.0 1.0 N C:ALA22 4.7 43.9 1.0 N C:ASP24 4.7 55.1 1.0 CA C:ASN25 4.7 50.4 1.0 CA C:ILE28 4.7 36.9 1.0 N C:GLU29 4.8 41.4 1.0 CB C:TYR27 4.8 43.6 1.0 CD C:GLU29 4.8 47.6 1.0 CA C:ASP23 4.9 56.0 1.0 C C:ASP23 4.9 56.0 1.0 N C:GLY26 4.9 46.6 1.0 O C:ASP21 5.0 43.4 1.0

Calcium binding site 9 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:46.6 occ:1.00 O C:HOH411 2.1 44.0 1.0 OD1 C:ASP158 2.3 30.4 1.0 O C:HOH448 2.3 26.9 1.0 OD1 C:ASP162 2.3 29.8 1.0 OD1 C:ASN160 2.3 29.7 1.0 O C:ARG164 2.4 28.0 1.0 CG C:ASP162 3.2 31.4 1.0 CG C:ASP158 3.2 30.4 1.0 CG C:ASN160 3.5 30.5 1.0 OD2 C:ASP162 3.5 33.1 1.0 C C:ARG164 3.6 29.0 1.0 OD2 C:ASP158 3.9 30.9 1.0 N C:ASP162 4.0 31.7 1.0 ND2 C:ASN160 4.1 30.2 1.0 CA C:ASP158 4.1 30.0 1.0 CB C:ASP158 4.1 30.0 1.0 N C:ARG164 4.2 31.7 1.0 N C:ASN160 4.2 32.3 1.0 N C:LYS161 4.3 32.6 1.0 N C:LYS159 4.3 34.5 1.0 O C:HOH454 4.3 23.6 1.0 C C:ASP158 4.4 31.9 1.0 CA C:ARG164 4.4 31.6 1.0 OD2 C:ASP169 4.4 19.7 1.0 CB C:ASP162 4.4 31.8 1.0 C C:ASN160 4.6 31.9 1.0 N C:LEU165 4.6 26.9 1.0 CA C:ASP162 4.6 31.8 1.0 CB C:ASN160 4.7 31.2 1.0 CA C:ASN160 4.7 31.9 1.0 CB C:ARG164 4.7 35.4 1.0 N C:GLY163 4.8 31.7 1.0 CA C:LEU165 4.9 24.9 1.0 C C:ASP162 4.9 31.8 1.0

Calcium binding site 10 out of 12 in the Structure of Scgn in Complex with A SNAP25 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Scgn in Complex with A SNAP25 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:31.4 occ:1.00 OD1 C:ASP114 2.3 26.5 1.0 OD1 C:ASP116 2.4 34.5 1.0 OE2 C:GLU125 2.4 28.4 1.0 O C:TYR120 2.4 29.0 1.0 O C:HOH451 2.4 43.0 1.0 OE1 C:GLU125 2.5 27.8 1.0 OG C:SER118 2.7 29.9 1.0 CD C:GLU125 2.8 28.5 1.0 CG C:ASP116 3.2 35.6 1.0 CG C:ASP114 3.5 26.0 1.0 OD2 C:ASP116 3.5 36.0 1.0 CB C:SER118 3.6 31.1 1.0 C C:TYR120 3.7 29.9 1.0 N C:SER118 4.0 33.6 1.0 CA C:ASP114 4.1 27.8 1.0 CB C:ASP114 4.3 26.6 1.0 CG C:GLU125 4.3 28.4 1.0 OD2 C:ASP114 4.3 24.7 1.0 CA C:SER118 4.3 32.1 1.0 C C:ASP114 4.4 30.4 1.0 N C:ASP116 4.4 35.1 1.0 N C:TYR120 4.5 31.5 1.0 CA C:ILE121 4.5 27.0 1.0 N C:ALA115 4.5 32.0 1.0 N C:ILE121 4.5 28.2 1.0 CB C:ASP116 4.5 35.7 1.0 O C:HOH431 4.6 43.6 1.0 N C:SER122 4.6 26.8 1.0 N C:SER117 4.6 36.3 1.0 CA C:TYR120 4.6 32.0 1.0 CA C:ASP116 4.8 36.3 1.0 N C:GLY119 4.9 30.7 1.0 C C:ASP116 4.9 36.9 1.0 C C:SER118 5.0 31.0 1.0 CB C:TYR120 5.0 36.3 1.0

J.Qin, Q.Liu, Z.Liu, Y.Z.Pan, L.Sifuentes-Dominguez, K.Stepien, Y.Wang, Y.Tu, S.Tan, Y.Wang, Q.Sun, X.Mo, J.Rizo-Rey, E.Burstein, D.Jia. Structural and Mechanistic Insights Into Secretagogin-Mediated Exocytosis Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1919698117