Chlorine in PDB 1w16: Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium

The structure of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium, PDB code: 1w16 was solved by H.Dai, O.-H.Shin, M.Machius, D.R.Tomchick, T.C.Sudhof, J.Rizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.061, 91.061, 122.860, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 25.7

The structure of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium (pdb code 1w16). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium, PDB code: 1w16:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3001 b:49.4 occ:0.33 ND2 A:ASN355 3.2 55.2 1.0 CB A:ASN355 3.8 55.9 1.0 CG A:ASN355 4.0 57.9 1.0

Chlorine binding site 2 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3002 b:57.6 occ:1.00 N A:TRP419 3.2 44.2 1.0 O A:HOH2046 3.3 65.5 1.0 CA A:LYS418 3.8 45.7 1.0 CG A:LYS418 3.8 51.0 1.0 CB A:TRP419 3.9 43.8 1.0 C A:LYS418 4.0 45.8 1.0 CA A:TRP419 4.1 44.1 1.0 CD1 A:TRP419 4.3 41.1 1.0 CB A:LYS418 4.3 45.3 1.0 O A:TRP419 4.4 43.9 1.0 CG A:TRP419 4.5 42.6 1.0 C A:TRP419 4.7 44.6 1.0 O A:ALA417 4.8 43.0 1.0 N A:LYS418 4.9 44.6 1.0

Chlorine binding site 3 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3003 b:56.5 occ:0.50 NZ A:LYS328 3.3 58.8 1.0 OH A:TYR326 3.4 49.6 1.0 CD A:LYS328 3.5 60.4 1.0 CE2 A:TYR326 4.0 47.6 1.0 CD1 A:LEU377 4.0 52.4 1.0 CE A:LYS328 4.1 60.5 1.0 CZ A:TYR326 4.1 48.3 1.0 CB A:LYS328 4.3 51.1 1.0 CG A:LYS328 4.4 53.7 1.0 CD2 A:LEU377 4.7 51.2 1.0 CG A:LEU377 5.0 54.4 1.0 NZ A:LYS342 5.0 71.3 1.0

Chlorine binding site 4 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3004 b:45.6 occ:1.00 N A:VAL359 3.1 50.5 1.0 NZ A:LYS341 3.2 52.2 1.0 O A:VAL359 3.7 51.8 1.0 CA A:PHE358 3.7 48.8 1.0 CE A:LYS341 3.7 49.8 1.0 C A:PHE358 3.9 50.0 1.0 CB A:PHE358 4.0 47.6 1.0 CD1 A:PHE358 4.0 44.6 1.0 CA A:VAL359 4.1 51.5 1.0 CD A:LYS341 4.2 50.0 1.0 C A:VAL359 4.3 51.8 1.0 CB A:VAL359 4.4 51.0 1.0 CG A:PHE358 4.5 49.8 1.0 O A:LEU357 4.7 45.4 1.0 CG2 A:VAL359 4.9 49.3 1.0 N A:PHE358 4.9 47.9 1.0

Chlorine binding site 5 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3005 b:54.7 occ:1.00 O A:HOH2051 3.1 53.0 1.0 NZ A:LYS328 3.1 58.8 1.0 ND2 A:ASN330 3.3 46.2 1.0 CE A:LYS328 3.5 60.5 1.0 NH1 A:ARG337 3.7 55.4 1.0 CD1 A:LEU375 4.1 52.1 1.0 CD A:LYS328 4.1 60.4 1.0 OD1 A:ASN330 4.1 50.5 1.0 CG A:ASN330 4.2 48.7 1.0 CG A:LYS328 4.2 53.7 1.0 CL A:CL3006 4.4 72.9 1.0 CZ A:ARG337 4.7 56.5 1.0

Chlorine binding site 6 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3006 b:72.9 occ:1.00 NZ A:LYS328 3.0 58.8 1.0 NZ A:LYS340 3.0 69.3 1.0 NH2 A:ARG337 3.2 55.0 1.0 NH1 A:ARG337 3.3 55.4 1.0 CZ A:ARG337 3.7 56.5 1.0 CD A:LYS340 3.7 61.2 1.0 CE A:LYS328 3.8 60.5 1.0 CE A:LYS340 4.0 65.9 1.0 CL A:CL3005 4.4 54.7 1.0 O A:HOH2051 4.9 53.0 1.0

Chlorine binding site 7 out of 7 in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3007 b:90.8 occ:1.00 NE2 A:HIS313 3.3 53.0 1.0 CZ A:ARG312 3.6 49.8 1.0 NH1 A:ARG312 3.6 46.4 1.0 NE A:ARG312 3.9 49.9 1.0 NH2 A:ARG312 4.0 48.8 1.0 CE1 A:HIS313 4.0 53.2 1.0 CD A:ARG312 4.2 50.7 1.0 CD2 A:HIS313 4.4 53.6 1.0 OE2 A:GLU290 5.0 53.3 1.0

H.Dai, O.-H.Shin, M.Machius, D.R.Tomchick, T.C.Sudhof, J.Rizo. Structural Basis For the Evolutionary Inactivation of CA2+ Binding to Synaptotagmin 4 Nat.Struct.Mol.Biol. V. 11 844 2004.
ISSN: ISSN 1545-9993
PubMed: 15311271
DOI: 10.1038/NSMB817