Chlorine in PDB 7a1r: Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)

Protein crystallography data

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r was solved by G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.908, 57.532, 84.57, 90, 90, 90
R / Rfree (%) 17 / 19.1

Other elements in 7a1r:

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) (pdb code 7a1r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7a1r

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Chlorine binding site 1 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:26.9
occ:1.00
O A:HOH764 3.3 32.1 1.0
O A:HOH740 3.3 26.5 1.0
N A:ARG559 3.3 17.2 1.0
O A:HOH718 3.4 30.2 1.0
CA A:LEU558 3.8 14.6 1.0
CD1 A:LEU558 3.8 19.7 1.0
CG A:ARG559 3.9 36.3 1.0
C A:LEU558 4.0 16.2 1.0
O A:ARG559 4.3 23.7 1.0
CA A:ARG559 4.3 20.9 1.0
O A:THR557 4.4 15.9 1.0
CB A:ARG559 4.5 30.9 1.0
O A:HOH865 4.6 26.5 1.0
CG A:LEU558 4.6 19.5 1.0
CB A:LEU558 4.6 17.7 1.0
NE A:ARG559 4.6 50.4 1.0
N A:LEU558 4.7 15.8 1.0
CD A:ARG559 4.8 42.2 1.0
C A:ARG559 4.8 18.3 1.0
CB A:ASP580 4.9 17.7 1.0
C A:THR557 4.9 14.8 1.0

Chlorine binding site 2 out of 7 in 7a1r

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Chlorine binding site 2 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:14.4
occ:1.00
O A:HOH824 2.7 48.5 1.0
O B:HOH803 3.1 34.9 1.0
NE B:ARG510 3.2 14.1 1.0
NE A:ARG510 3.2 14.2 1.0
N A:ALA528 3.2 15.9 1.0
N B:ALA528 3.3 12.6 1.0
CD A:ARG510 3.5 13.8 1.0
CD B:ARG510 3.5 13.3 1.0
CA A:ALA527 3.6 12.8 1.0
O A:ALA528 3.6 15.8 1.0
CA B:ALA527 3.6 12.0 1.0
O B:ALA528 3.6 16.3 1.0
CB B:ALA527 3.7 15.4 1.0
CB A:ALA527 3.7 17.5 1.0
C A:ALA527 3.9 14.7 1.0
C B:ALA527 3.9 12.2 1.0
CA A:ALA528 4.2 15.2 1.0
CZ B:ARG510 4.3 17.4 1.0
CA B:ALA528 4.3 12.4 1.0
CZ A:ARG510 4.3 16.5 1.0
C A:ALA528 4.4 19.2 1.0
CG A:ARG510 4.4 12.8 1.0
C B:ALA528 4.4 12.6 1.0
CG B:ARG510 4.4 14.5 1.0
NH2 B:ARG510 4.6 15.8 1.0
NH2 A:ARG510 4.6 15.2 1.0
CB A:ALA528 4.7 16.1 1.0
CB B:ALA528 4.7 14.7 1.0
O A:GLU526 4.8 17.8 1.0
O B:GLU526 4.8 17.8 1.0
N A:ALA527 4.9 13.0 1.0
N B:ALA527 4.9 13.7 1.0

Chlorine binding site 3 out of 7 in 7a1r

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Chlorine binding site 3 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:25.2
occ:1.00
O A:HOH790 3.2 37.5 1.0
O A:HOH722 3.3 25.4 1.0
O A:HOH784 3.6 32.7 1.0
CA A:ARG506 3.7 17.5 1.0
CG A:ARG506 4.0 22.0 1.0
N A:ARG506 4.0 18.2 1.0
CB A:ARG506 4.3 21.2 1.0
NE2 A:GLN504 4.5 16.0 0.4
C A:ARG506 4.7 18.2 1.0
O A:ARG506 4.9 19.8 1.0

Chlorine binding site 4 out of 7 in 7a1r

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Chlorine binding site 4 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:23.1
occ:1.00
O B:HOH730 2.9 25.4 1.0
O A:HOH748 3.0 23.8 1.0
N A:TYR514 3.4 14.0 1.0
N B:TYR514 3.4 14.7 1.0
CA B:PRO513 3.5 13.7 1.0
CD2 A:TYR514 3.5 17.9 1.0
CA A:PRO513 3.5 10.8 1.0
CD2 B:TYR514 3.5 17.7 1.0
CB B:PRO513 3.7 14.8 1.0
CB A:PRO513 3.7 15.1 1.0
CE2 A:TYR514 3.8 20.0 1.0
CE2 B:TYR514 3.9 17.0 1.0
C A:PRO513 4.0 11.3 1.0
C B:PRO513 4.0 14.6 1.0
CG A:TYR514 4.4 17.0 1.0
CG B:TYR514 4.4 16.6 1.0
O B:HOH833 4.4 34.1 1.0
O B:HOH759 4.5 24.9 1.0
CA A:TYR514 4.6 13.4 1.0
O A:HOH749 4.6 23.9 1.0
CA B:TYR514 4.6 13.6 1.0
O A:TYR514 4.6 14.6 1.0
O B:TYR514 4.6 16.9 1.0
O A:HOH820 4.7 35.0 1.0
CG B:PRO513 4.7 14.3 1.0
CG A:PRO513 4.7 12.8 1.0
N B:PRO513 4.8 12.8 1.0
N A:PRO513 4.8 12.2 1.0
CB A:TYR514 4.8 14.5 1.0
CB B:TYR514 4.8 16.9 1.0
CZ A:TYR514 4.9 21.6 1.0
CZ B:TYR514 5.0 21.6 1.0

Chlorine binding site 5 out of 7 in 7a1r

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Chlorine binding site 5 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl604

b:27.5
occ:1.00
N B:ASP552 3.2 18.1 1.0
CG B:ASP552 3.7 20.7 1.0
CA B:LYS551 3.8 17.8 1.0
OD1 B:ASP552 3.8 22.2 1.0
CB B:ASP552 3.9 18.9 1.0
CG B:LYS551 4.0 27.2 1.0
C B:LYS551 4.0 17.6 1.0
OD2 B:ASP552 4.1 22.2 1.0
CA B:ASP552 4.2 18.5 1.0
O B:HOH721 4.4 39.9 1.0
CB B:LYS551 4.4 22.6 1.0
O B:HOH766 4.7 39.9 1.0
O B:VAL550 4.7 20.5 1.0
CD B:LYS551 4.9 43.1 1.0
N B:LYS551 4.9 22.1 1.0

Chlorine binding site 6 out of 7 in 7a1r

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Chlorine binding site 6 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:26.9
occ:1.00
O B:HOH844 3.2 32.0 1.0
O B:HOH716 3.2 38.0 1.0
N B:LYS507 3.3 15.4 1.0
CB B:ARG506 3.6 17.1 1.0
CG B:GLN508 3.6 14.8 1.0
NE2 B:GLN508 3.7 21.2 1.0
CB B:LYS507 3.7 22.1 1.0
N B:GLN508 3.8 14.9 1.0
CA B:LYS507 3.9 18.6 1.0
CE2 B:TYR532 3.9 29.8 1.0
CD B:GLN508 4.1 16.3 1.0
O B:LEU505 4.1 15.6 1.0
C B:LYS507 4.1 16.4 1.0
C B:ARG506 4.3 15.9 1.0
O B:HOH824 4.4 37.2 1.0
CG B:LYS507 4.4 33.1 1.0
CA B:ARG506 4.5 15.2 1.0
CD2 B:TYR532 4.6 34.8 1.0
CD B:ARG506 4.6 23.9 1.0
CB B:GLN508 4.6 13.7 1.0
O B:HOH852 4.6 29.8 1.0
CG B:ARG506 4.7 16.7 1.0
CA B:GLN508 4.7 13.3 1.0
CZ B:TYR532 4.8 38.0 1.0
OH B:TYR532 4.9 33.6 1.0

Chlorine binding site 7 out of 7 in 7a1r

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Chlorine binding site 7 out of 7 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:26.6
occ:1.00
O B:HOH839 3.2 50.2 1.0
NZ B:LYS507 3.2 23.9 1.0
O B:HOH821 3.4 50.8 1.0
CD B:LYS507 3.6 25.5 1.0
CE B:LYS507 4.1 26.1 1.0
NE2 B:GLN504 4.5 53.2 1.0
CG B:LYS507 4.8 33.1 1.0
CA B:LYS507 4.9 18.6 1.0
O B:ARG506 5.0 19.6 1.0

Reference:

E.Stepinac, N.Landrein, D.Skwarzynska, P.Wojcik, J.Lesigang, I.Lucic, C.Y.He, M.Bonhivers, D.R.Robinson, G.Dong. Structural Studies of the Shortest Extended Synaptotagmin with Only Two C2 Domains From Trypanosoma Brucei . Iscience V. 24 02422 2021.
ISSN: ESSN 2589-0042
PubMed: 33997700
DOI: 10.1016/J.ISCI.2021.102422
Page generated: Sat Jul 10 12:29:39 2021

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