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Chlorine in PDB 1w15: Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium

Protein crystallography data

The structure of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium, PDB code: 1w15 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 / 1.93
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.490, 91.490, 122.142, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 23.3

Other elements in 1w15:

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

Calcium (Ca) 3 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium (pdb code 1w15). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium, PDB code: 1w15:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 1w15

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Chlorine binding site 1 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3001

b:40.4
occ:0.33
 ND2 A:ASN355 3.2 40.2 1.0
CB A:ASN355 3.8 38.5 1.0
CG A:ASN355 4.0 41.1 1.0
O A:ASN355 5.0 40.6 1.0

Chlorine binding site 2 out of 9 in 1w15

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Chlorine binding site 2 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3002

b:48.6
occ:1.00
 O A:HOH2087 3.0 61.5 1.0
N A:TRP419 3.2 33.8 1.0
CA A:LYS418 3.7 35.0 1.0
CB A:TRP419 3.9 33.5 1.0
C A:LYS418 4.0 34.3 1.0
CA A:TRP419 4.1 33.9 1.0
CB A:LYS418 4.1 35.8 1.0
CD1 A:TRP419 4.2 32.3 1.0
O A:TRP419 4.3 34.1 1.0
CG A:TRP419 4.4 34.1 1.0
C A:TRP419 4.7 34.7 1.0
O A:HOH2003 4.8 87.1 1.0
CG A:LYS418 4.8 44.9 1.0
O A:ALA417 4.8 35.2 1.0
N A:LYS418 4.9 33.8 1.0

Chlorine binding site 3 out of 9 in 1w15

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Chlorine binding site 3 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3003

b:45.3
occ:0.50
 O A:HOH2018 2.2 68.6 1.0
OH A:TYR326 3.1 36.5 1.0
CD A:LYS328 3.2 49.0 1.0
NZ A:LYS328 3.6 45.4 1.0
CE2 A:TYR326 3.8 37.8 1.0
CD1 A:LEU377 3.8 38.7 1.0
CZ A:TYR326 3.9 38.0 1.0
CE A:LYS328 4.1 48.3 1.0
CB A:LYS328 4.4 37.4 1.0
CG A:LYS328 4.4 39.9 1.0
CD2 A:LEU377 4.5 35.6 1.0
O A:HOH2019 4.7 59.6 1.0
CG A:LEU377 4.7 36.3 1.0

Chlorine binding site 4 out of 9 in 1w15

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Chlorine binding site 4 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3004

b:37.7
occ:1.00
 N A:VAL359 3.2 34.0 1.0
NZ A:LYS341 3.3 44.5 1.0
CA A:PHE358 3.7 34.0 1.0
CE A:LYS341 3.7 41.4 1.0
O A:VAL359 3.8 34.9 1.0
CB A:PHE358 4.0 33.7 1.0
C A:PHE358 4.0 34.6 1.0
CD1 A:PHE358 4.0 32.5 1.0
CD A:LYS341 4.0 40.9 1.0
CA A:VAL359 4.2 35.0 1.0
C A:VAL359 4.4 36.3 1.0
CB A:VAL359 4.5 35.1 1.0
CG A:PHE358 4.5 35.2 1.0
O A:HOH2040 4.6 67.2 1.0
O A:LEU357 4.6 32.5 1.0
N A:PHE358 4.9 32.5 1.0
CG2 A:VAL359 5.0 35.6 1.0

Chlorine binding site 5 out of 9 in 1w15

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Chlorine binding site 5 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3005

b:43.2
occ:1.00
 O A:HOH2077 3.1 51.8 1.0
ND2 A:ASN330 3.2 36.6 1.0
NZ A:LYS328 3.4 45.4 1.0
CE A:LYS328 3.5 48.3 1.0
NH1 A:ARG337 3.8 45.1 1.0
CD A:LYS328 3.9 49.0 1.0
CD1 A:LEU375 3.9 39.3 1.0
CG A:ASN330 4.1 35.7 1.0
OD1 A:ASN330 4.2 36.2 1.0
CG A:LYS328 4.4 39.9 1.0
O A:HOH2093 4.6 70.7 1.0
CL A:CL3006 4.7 66.4 1.0
O A:HOH2020 5.0 45.8 1.0
CZ A:ARG337 5.0 47.2 1.0

Chlorine binding site 6 out of 9 in 1w15

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Chlorine binding site 6 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3006

b:66.4
occ:1.00
 NZ A:LYS340 3.0 56.2 1.0
NZ A:LYS328 3.0 45.4 1.0
O A:HOH2019 3.3 59.6 1.0
NH2 A:ARG337 3.4 47.8 1.0
NH1 A:ARG337 3.5 45.1 1.0
CD A:LYS340 3.6 47.9 1.0
CZ A:ARG337 3.9 47.2 1.0
CE A:LYS340 3.9 51.3 1.0
CE A:LYS328 4.0 48.3 1.0
CL A:CL3005 4.7 43.2 1.0
O A:HOH2093 5.0 70.7 1.0

Chlorine binding site 7 out of 9 in 1w15

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Chlorine binding site 7 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence 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 Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3007

b:92.1
occ:1.00
 O A:HOH2005 2.9 63.8 1.0
NE2 A:HIS313 3.4 43.2 1.0
CZ A:ARG312 3.7 36.6 1.0
NH1 A:ARG312 3.8 38.4 1.0
NE A:ARG312 4.0 34.8 1.0
NH2 A:ARG312 4.0 33.4 1.0
CE1 A:HIS313 4.2 43.9 1.0
CD2 A:HIS313 4.4 41.1 1.0
CD A:ARG312 4.4 39.0 1.0
OE2 A:GLU290 4.6 49.6 1.0
O A:HOH2016 4.9 53.8 1.0

Chlorine binding site 8 out of 9 in 1w15

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Chlorine binding site 8 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3008

b:87.0
occ:1.00
 O A:HOH2028 3.7 54.1 1.0
O A:HOH2025 3.7 65.5 1.0
NE A:ARG337 3.8 46.0 1.0
N A:SER339 3.8 38.1 1.0
CA A:SER339 3.9 37.8 1.0
C A:ILE338 4.0 38.6 1.0
C A:SER339 4.0 38.5 1.0
O A:ARG337 4.1 38.8 1.0
O A:ILE338 4.2 39.2 1.0
CG A:ARG337 4.2 41.0 1.0
CG A:LYS340 4.3 43.0 1.0
N A:LYS340 4.3 37.6 1.0
CD A:ARG337 4.4 41.9 1.0
CZ A:ARG337 4.5 47.2 1.0
O A:SER339 4.5 37.4 1.0
C A:ARG337 4.5 39.9 1.0
CD A:LYS340 4.6 47.9 1.0
NH2 A:ARG337 4.6 47.8 1.0
CA A:ILE338 4.6 38.6 1.0
CB A:LYS340 4.7 38.5 1.0
CB A:ARG337 4.7 39.7 1.0
N A:ILE338 4.8 39.1 1.0

Chlorine binding site 9 out of 9 in 1w15

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Chlorine binding site 9 out of 9 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3009

b:61.6
occ:1.00
 O A:HOH2073 2.9 52.0 1.0
O A:HOH2000 3.3 63.8 1.0
N A:LEU367 3.3 42.9 1.0
CB A:LEU367 3.7 42.7 1.0
SG A:CYS409 3.8 41.2 1.0
CB A:SER366 3.8 43.5 1.0
CE2 A:TYR297 3.9 35.2 1.0
CB A:CYS409 3.9 37.2 1.0
CA A:LEU367 4.1 43.4 1.0
CA A:SER366 4.1 42.8 1.0
C A:SER366 4.2 43.5 1.0
CA A:CYS409 4.4 37.9 1.0
CD2 A:TYR297 4.5 34.3 1.0
N A:GLU368 4.5 43.5 1.0
C A:LEU367 4.6 43.4 1.0
CZ A:TYR297 4.7 35.9 1.0
CD2 A:LEU367 4.7 43.6 1.0
OG A:SER366 4.7 42.1 1.0
CG A:LEU367 4.7 46.9 1.0
O A:CYS409 4.8 35.5 1.0
OH A:TYR297 4.8 32.6 1.0

Reference:

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
Page generated: Sat Jul 20 03:30:20 2024

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