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Chlorine in PDB 5jir: Crystal Structure of Treponema Pallidum Protein TP0624

Protein crystallography data

The structure of Crystal Structure of Treponema Pallidum Protein TP0624, PDB code: 5jir was solved by M.L.Parker, M.J.Boulanger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.75 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.020, 103.500, 140.680, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Treponema Pallidum Protein TP0624 (pdb code 5jir). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Treponema Pallidum Protein TP0624, PDB code: 5jir:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5jir

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Chlorine binding site 1 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:21.8
occ:1.00
 N B:VAL152 3.3 14.1 1.0
O B:HOH738 3.5 30.0 1.0
NH2 B:ARG105 3.5 13.8 1.0
O B:HOH634 3.7 19.4 1.0
CA B:ALA151 4.0 15.7 1.0
O B:VAL152 4.0 16.9 1.0
CB B:VAL152 4.1 10.6 1.0
C B:ALA151 4.1 12.6 1.0
CB B:ALA151 4.1 17.8 1.0
CA B:VAL152 4.2 13.1 1.0
C B:VAL152 4.5 14.5 1.0
CZ B:ARG105 4.6 15.3 1.0
CG2 B:VAL152 4.6 15.1 1.0
NE B:ARG105 4.9 15.0 1.0

Chlorine binding site 2 out of 8 in 5jir

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Chlorine binding site 2 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:21.7
occ:1.00
 NH2 B:ARG425 3.0 35.5 1.0
N B:ALA410 3.5 24.3 1.0
CD B:ARG467 3.7 32.6 1.0
CB B:THR409 3.7 24.8 1.0
CA B:THR409 4.0 22.2 1.0
CG B:ARG467 4.0 37.9 1.0
CZ B:ARG425 4.1 35.5 1.0
NH2 B:ARG467 4.1 40.8 1.0
CB B:ARG467 4.2 28.4 1.0
CD2 B:LEU412 4.3 34.0 1.0
CB B:ALA410 4.3 26.2 1.0
CG2 B:THR409 4.3 22.3 1.0
NH1 B:ARG425 4.3 32.2 1.0
C B:THR409 4.3 23.2 1.0
CD1 B:LEU412 4.4 34.9 1.0
CD2 B:LEU421 4.4 45.8 1.0
CA B:ALA410 4.4 25.1 1.0
CG B:LEU412 4.6 27.9 1.0
O B:ALA410 4.7 22.9 1.0
NE B:ARG467 4.8 41.4 1.0
OG1 B:THR409 4.9 26.3 1.0
CA B:ARG467 4.9 21.4 1.0
CZ B:ARG467 4.9 34.2 1.0

Chlorine binding site 3 out of 8 in 5jir

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Chlorine binding site 3 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:23.6
occ:1.00
 OG B:SER123 3.2 20.1 1.0
N B:GLN283 3.3 18.8 1.0
CG B:GLN124 3.4 27.1 1.0
NE2 B:GLN124 3.6 39.2 1.0
CA B:GLY282 3.7 22.0 1.0
CG B:GLN283 3.7 26.4 1.0
CB B:SER123 3.8 18.7 1.0
CE2 B:PHE281 4.0 31.3 1.0
O B:SER123 4.0 19.4 1.0
C B:GLY282 4.0 16.9 1.0
CD B:GLN124 4.0 34.7 1.0
CB B:GLN283 4.2 23.8 1.0
C B:SER123 4.3 17.7 1.0
CZ B:PHE281 4.3 33.1 1.0
CA B:GLN283 4.4 21.0 1.0
CD B:GLN283 4.4 30.5 1.0
NE2 B:GLN283 4.6 29.3 1.0
N B:GLN124 4.7 19.0 1.0
CA B:SER123 4.7 18.1 1.0
CB B:GLN124 4.7 23.9 1.0
CD2 B:PHE281 4.8 26.3 1.0
N B:GLY282 4.8 20.4 1.0
O B:HOH620 5.0 24.5 1.0
CA B:GLN124 5.0 19.1 1.0

Chlorine binding site 4 out of 8 in 5jir

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Chlorine binding site 4 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:24.1
occ:1.00
 O B:HOH755 3.1 35.2 1.0
N B:GLN416 3.5 21.7 1.0
NE2 A:GLN427 3.5 28.6 1.0
CD B:PRO415 3.5 26.9 1.0
N B:PRO415 3.7 23.8 1.0
CG B:GLN416 3.8 25.8 1.0
CB B:GLN416 3.8 25.0 1.0
C B:ARG414 3.8 24.5 1.0
CA B:ARG414 4.0 21.5 1.0
OE1 A:GLN427 4.3 25.7 1.0
CA B:GLN416 4.3 19.9 1.0
NE2 B:GLN416 4.3 27.1 1.0
CD B:GLN416 4.3 26.4 1.0
CD A:GLN427 4.3 24.0 1.0
CA B:PRO415 4.4 24.1 1.0
CG B:PRO415 4.4 28.1 1.0
C B:PRO415 4.4 21.8 1.0
CB B:PRO415 4.4 26.8 1.0
O B:ARG414 4.5 21.7 1.0
CB B:ARG414 4.7 26.2 1.0
CG B:ARG414 4.7 35.9 1.0
N B:GLU417 4.9 23.2 1.0

Chlorine binding site 5 out of 8 in 5jir

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Chlorine binding site 5 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:26.5
occ:1.00
 O B:HOH690 3.0 31.2 1.0
N B:LEU93 3.3 21.8 1.0
CG B:ARG160 3.8 29.3 1.0
CD1 B:LEU86 3.8 22.6 1.0
CB B:LEU93 3.9 22.8 1.0
CG B:LEU93 3.9 23.5 1.0
CB B:ARG160 4.0 22.8 1.0
CA B:ARG92 4.1 24.7 1.0
CA B:LEU93 4.1 24.1 1.0
CA B:ARG160 4.1 18.7 1.0
C B:ARG92 4.2 22.4 1.0
CD B:ARG160 4.4 33.6 1.0
O B:LEU93 4.4 26.4 1.0
CD1 B:LEU93 4.5 27.8 1.0
O B:MET91 4.6 24.1 1.0
CB B:LEU86 4.7 18.3 1.0
C B:LEU93 4.8 28.7 1.0
CB B:ARG92 4.8 26.7 1.0
CG B:LEU86 4.9 22.3 1.0
C B:ARG160 4.9 18.1 1.0
NE B:ARG160 5.0 48.0 1.0

Chlorine binding site 6 out of 8 in 5jir

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Chlorine binding site 6 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:20.1
occ:1.00
 NH2 A:ARG425 3.4 33.5 1.0
CD A:ARG467 3.4 42.7 1.0
N A:ALA410 3.5 27.2 1.0
NH1 A:ARG425 3.5 37.7 1.0
CB A:THR409 3.8 24.3 1.0
CG A:ARG467 3.8 37.5 1.0
CZ A:ARG425 3.9 34.4 1.0
CA A:THR409 4.0 25.9 1.0
CD2 A:LEU421 4.1 30.1 1.0
NH2 A:ARG467 4.1 48.0 1.0
CB A:ALA410 4.2 38.3 1.0
CD2 A:LEU412 4.2 34.5 1.0
CG2 A:THR409 4.3 21.7 1.0
C A:THR409 4.3 26.5 1.0
CB A:ARG467 4.3 32.7 1.0
CA A:ALA410 4.4 29.8 1.0
NE A:ARG467 4.6 50.6 1.0
CD1 A:LEU412 4.7 39.3 1.0
O A:ALA410 4.8 28.2 1.0
CG A:LEU412 4.8 34.3 1.0
CZ A:ARG467 4.9 48.7 1.0
OG1 A:THR409 5.0 27.8 1.0

Chlorine binding site 7 out of 8 in 5jir

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Chlorine binding site 7 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


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 Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:28.3
occ:1.00
 N A:LEU93 3.3 30.9 1.0
NE A:ARG160 3.7 49.5 1.0
CD1 A:LEU86 3.8 34.9 1.0
CA A:ARG92 3.9 34.8 1.0
CA A:ARG160 4.0 27.2 1.0
CB A:LEU93 4.0 34.0 1.0
C A:ARG92 4.1 29.8 1.0
CG A:ARG160 4.2 33.6 1.0
CA A:LEU93 4.2 31.2 1.0
CB A:ARG160 4.2 30.2 1.0
CG A:LEU93 4.3 34.7 1.0
NH1 A:ARG160 4.3 52.1 1.0
O A:LEU93 4.3 35.9 1.0
CD A:ARG160 4.5 39.4 1.0
CZ A:ARG160 4.5 50.7 1.0
CB A:ARG92 4.6 41.7 1.0
CB A:LEU86 4.6 29.2 1.0
NH1 A:ARG92 4.6 53.9 1.0
O A:MET91 4.7 30.9 1.0
C A:ARG160 4.8 25.8 1.0
C A:LEU93 4.8 34.1 1.0
CD1 A:LEU93 4.8 31.5 1.0
O A:HOH658 4.8 33.6 1.0
CG A:LEU86 4.8 27.4 1.0
CG A:ARG92 4.9 52.6 1.0
N A:ARG160 4.9 26.5 1.0

Chlorine binding site 8 out of 8 in 5jir

Go back to Chlorine Binding Sites List in 5jir
Chlorine binding site 8 out of 8 in the Crystal Structure of Treponema Pallidum Protein TP0624


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Treponema Pallidum Protein TP0624 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:30.9
occ:1.00
 N A:GLN416 3.3 28.1 1.0
CB A:GLN416 3.6 24.5 1.0
NE2 B:GLN427 3.6 28.6 1.0
CG A:GLN416 3.6 28.3 1.0
CD A:PRO415 3.6 30.2 1.0
N A:PRO415 3.7 28.8 1.0
NE2 A:GLN416 3.8 32.0 1.0
C A:ARG414 3.9 28.5 1.0
CD A:GLN416 4.0 31.7 1.0
CA A:ARG414 4.0 32.0 1.0
CA A:GLN416 4.0 26.1 1.0
OE1 B:GLN427 4.2 34.0 1.0
C A:PRO415 4.3 28.7 1.0
CA A:PRO415 4.3 28.9 1.0
CD B:GLN427 4.3 30.6 1.0
CB A:PRO415 4.4 29.6 1.0
CG A:PRO415 4.4 29.0 1.0
CB A:ARG414 4.5 34.4 1.0
O A:ARG414 4.5 29.8 1.0
N A:GLU417 4.8 26.4 1.0
CG A:ARG414 4.8 45.1 1.0
OE1 A:GLN416 4.9 37.7 1.0

Reference:

M.L.Parker, S.Houston, C.Wetherell, C.E.Cameron, M.J.Boulanger. The Structure of Treponema Pallidum TP0624 Reveals A Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains. Plos One V. 11 66274 2016.
ISSN: ESSN 1932-6203
PubMed: 27832149
DOI: 10.1371/JOURNAL.PONE.0166274
Page generated: Fri Jul 26 10:04:42 2024

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