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Chlorine in PDB 5c9f: Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii

Protein crystallography data

The structure of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii, PDB code: 5c9f was solved by M.Li, A.Gustchina, R.Cruz, M.Simoes, P.Curto, J.Martinez, C.Faro, I.Simoes, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.102, 94.153, 118.636, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.5

Other elements in 5c9f:

The structure of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii (pdb code 5c9f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii, PDB code: 5c9f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5c9f

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Chlorine binding site 1 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:40.7
occ:1.00
 N A:ARG120 3.2 37.2 1.0
O A:HOH431 3.4 51.1 1.0
CG A:ARG120 3.4 40.0 1.0
CG A:ASN119 3.6 38.6 1.0
ND2 A:ASN119 3.6 33.9 1.0
OD1 A:ASN119 3.7 36.5 1.0
CB A:ARG120 3.8 45.1 1.0
CA A:ASN119 4.0 36.1 1.0
C A:ASN119 4.1 33.7 1.0
CA A:ARG120 4.2 37.5 1.0
CB A:ASN119 4.4 29.8 1.0
CD A:ARG120 4.7 51.8 1.0

Chlorine binding site 2 out of 12 in 5c9f

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Chlorine binding site 2 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:47.9
occ:1.00
 N A:ALA232 3.2 36.0 1.0
N A:LYS218 3.3 39.7 1.0
CA A:TYR231 3.4 28.3 1.0
O A:HOH418 3.5 51.3 1.0
CB A:TYR231 3.5 26.7 1.0
O A:ALA232 3.7 40.9 1.0
CD A:LYS190 3.8 44.9 1.0
C A:TYR231 3.8 34.5 1.0
CB A:LYS218 3.8 46.4 1.0
O A:ARG216 4.0 47.4 1.0
CA A:LYS218 4.0 45.3 1.0
NZ A:LYS190 4.1 67.3 1.0
C A:PHE217 4.1 39.9 1.0
CA A:PHE217 4.1 36.8 1.0
CA A:ALA232 4.3 32.2 1.0
O A:ASN230 4.3 24.9 1.0
C A:ALA232 4.4 43.0 1.0
NZ A:LYS218 4.4 73.3 1.0
CE A:LYS190 4.5 57.9 1.0
CE A:LYS218 4.6 70.5 1.0
N A:TYR231 4.6 24.0 1.0
CB A:ALA232 4.7 27.2 1.0
CG A:LYS218 4.9 63.1 1.0
C A:ASN230 4.9 26.9 1.0
CG A:TYR231 4.9 28.3 1.0
C A:ARG216 4.9 42.7 1.0
CG A:LYS190 4.9 52.2 1.0

Chlorine binding site 3 out of 12 in 5c9f

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Chlorine binding site 3 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:53.4
occ:1.00
 O A:HOH417 3.0 32.8 1.0
NH2 A:ARG216 3.5 54.6 1.0
NE A:ARG216 3.6 69.2 1.0
CB A:SER212 3.7 38.1 1.0
N A:LYS196 3.8 30.2 1.0
CG2 A:ILE195 3.9 37.0 1.0
CZ A:ARG216 4.0 60.3 1.0
C A:SER212 4.0 35.9 1.0
O A:SER212 4.0 34.4 1.0
N A:LEU213 4.3 30.1 1.0
CB A:LYS196 4.3 45.9 1.0
CD1 A:ILE195 4.3 32.3 1.0
CA A:ILE195 4.3 32.1 1.0
CA A:SER212 4.5 30.1 1.0
C A:ILE195 4.6 32.5 1.0
CA A:LYS196 4.6 40.5 1.0
CB A:ILE195 4.6 38.7 1.0
CA A:LEU213 4.6 24.2 1.0
O A:LYS196 4.6 35.9 1.0
O A:HOH407 4.7 47.6 1.0
CD A:ARG216 4.7 52.9 1.0
OG A:SER212 4.9 45.2 1.0

Chlorine binding site 4 out of 12 in 5c9f

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Chlorine binding site 4 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:75.1
occ:1.00
 N A:GLU191 3.4 41.6 1.0
CB A:ALA233 3.4 37.4 1.0
CB A:LYS190 3.7 40.8 1.0
O A:GLU191 3.9 42.2 1.0
CB A:GLU191 4.0 38.8 1.0
CA A:GLU191 4.1 40.2 1.0
CA A:LYS190 4.1 44.2 1.0
C A:LYS190 4.3 47.1 1.0
CE A:LYS190 4.5 57.9 1.0
C A:GLU191 4.5 37.7 1.0
CA A:ALA233 4.5 44.8 1.0
CG A:LYS190 4.7 52.2 1.0
CD A:LYS190 4.9 44.9 1.0

Chlorine binding site 5 out of 12 in 5c9f

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Chlorine binding site 5 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:51.9
occ:1.00
 N B:LYS218 3.2 53.2 1.0
N B:ALA232 3.3 24.2 1.0
CA B:TYR231 3.5 22.6 1.0
CB B:LYS218 3.7 49.6 1.0
O B:ALA232 3.7 44.5 1.0
CB B:TYR231 3.8 27.7 1.0
CD B:LYS190 3.9 48.7 1.0
CA B:LYS218 3.9 53.3 1.0
C B:TYR231 3.9 27.6 1.0
NZ B:LYS190 4.0 64.2 1.0
O B:ARG216 4.1 47.4 1.0
C B:PHE217 4.1 58.3 1.0
CA B:PHE217 4.2 56.0 1.0
CA B:ALA232 4.3 33.0 1.0
C B:ALA232 4.4 39.3 1.0
O B:ASN230 4.4 29.2 1.0
CE B:LYS190 4.5 85.0 1.0
CD B:LYS218 4.7 76.6 1.0
N B:TYR231 4.8 23.5 1.0
CB B:ALA232 4.8 33.4 1.0
CG B:LYS218 4.8 69.5 1.0
CE B:LYS218 4.9 72.4 1.0
C B:ARG216 5.0 58.2 1.0

Chlorine binding site 6 out of 12 in 5c9f

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Chlorine binding site 6 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:42.1
occ:1.00
 N C:ILE222 3.2 35.0 1.0
O C:HOH413 3.5 54.6 1.0
CA C:ARG221 3.9 37.0 1.0
O C:ILE222 4.0 47.6 1.0
C C:ARG221 4.0 40.4 1.0
CB C:ILE222 4.0 39.2 1.0
CA C:ILE222 4.1 37.3 1.0
NH2 C:ARG221 4.2 80.4 1.0
NE C:ARG221 4.4 95.4 1.0
CG1 C:ILE222 4.5 44.8 1.0
CZ C:ARG221 4.5 92.2 1.0
C C:ILE222 4.5 39.6 1.0
O C:PHE220 4.5 39.3 1.0
CG C:ARG221 4.6 49.2 1.0
CZ C:PHE220 4.7 58.0 1.0
CE2 C:PHE220 4.7 71.9 1.0
CD1 C:ILE222 4.7 53.2 1.0
N C:ARG221 4.8 39.4 1.0
CB C:ARG221 4.8 40.6 1.0
C C:PHE220 5.0 38.2 1.0

Chlorine binding site 7 out of 12 in 5c9f

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Chlorine binding site 7 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:46.3
occ:1.00
 N C:LYS218 3.3 42.1 1.0
N C:ALA232 3.4 30.0 1.0
CD C:LYS190 3.5 58.4 1.0
CA C:TYR231 3.6 28.3 1.0
CB C:TYR231 3.7 31.0 1.0
O C:ALA232 3.8 28.8 1.0
NZ C:LYS190 3.8 70.0 1.0
CB C:LYS218 3.9 41.4 1.0
O C:ARG216 3.9 35.2 1.0
C C:TYR231 4.0 29.5 1.0
C C:PHE217 4.1 40.4 1.0
CA C:LYS218 4.1 41.8 1.0
CA C:PHE217 4.1 36.3 1.0
CE C:LYS190 4.2 59.6 1.0
CA C:ALA232 4.4 41.2 1.0
C C:ALA232 4.4 45.2 1.0
O C:ASN230 4.4 27.6 1.0
NZ C:LYS218 4.5 66.1 1.0
CE C:LYS218 4.6 65.5 1.0
CG C:LYS190 4.8 53.0 1.0
N C:TYR231 4.8 23.0 1.0
C C:ARG216 4.8 39.5 1.0
CB C:ALA232 4.9 29.3 1.0
N C:PHE217 5.0 37.4 1.0
CG C:LYS218 5.0 48.3 1.0

Chlorine binding site 8 out of 12 in 5c9f

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Chlorine binding site 8 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:47.2
occ:1.00
 O C:HOH429 3.1 39.5 1.0
NH2 C:ARG216 3.3 53.6 1.0
NE C:ARG216 3.4 45.0 1.0
N C:LYS196 3.6 37.2 1.0
CG2 C:ILE195 3.7 39.8 1.0
CZ C:ARG216 3.8 51.4 1.0
CB C:SER212 3.9 38.6 1.0
CD1 C:ILE195 3.9 43.3 1.0
CA C:ILE195 4.0 42.2 1.0
C C:SER212 4.2 41.1 1.0
O C:SER212 4.2 47.0 1.0
CB C:LYS196 4.3 52.6 1.0
C C:ILE195 4.3 46.6 1.0
CB C:ILE195 4.3 41.7 1.0
N C:LEU213 4.4 36.1 1.0
CA C:LYS196 4.5 41.7 1.0
CD C:ARG216 4.6 46.0 1.0
O C:LYS196 4.7 36.9 1.0
CA C:LEU213 4.7 33.0 1.0
CA C:SER212 4.7 35.9 1.0
CG1 C:ILE195 4.8 51.1 1.0
O C:HOH408 4.9 46.7 1.0

Chlorine binding site 9 out of 12 in 5c9f

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Chlorine binding site 9 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:59.1
occ:1.00
 N D:ALA232 3.4 31.5 1.0
N D:LYS218 3.4 48.1 1.0
CA D:TYR231 3.5 22.2 1.0
CD D:LYS190 3.6 69.4 1.0
CB D:TYR231 3.7 25.4 1.0
CB D:LYS218 3.7 52.3 1.0
O D:ALA232 3.8 34.8 1.0
NZ D:LYS190 3.8 85.0 1.0
C D:TYR231 4.0 35.6 1.0
CA D:LYS218 4.1 64.4 1.0
CE D:LYS218 4.2 61.6 1.0
CE D:LYS190 4.3 79.6 1.0
C D:PHE217 4.3 55.8 1.0
O D:ARG216 4.4 41.0 1.0
CA D:PHE217 4.4 46.6 1.0
O D:ASN230 4.4 24.8 1.0
CA D:ALA232 4.5 32.3 1.0
C D:ALA232 4.5 47.3 1.0
CD D:LYS218 4.7 76.7 1.0
N D:TYR231 4.7 17.0 1.0
CG D:LYS218 4.8 63.4 1.0
CG D:LYS190 4.9 53.7 1.0
CB D:ALA232 5.0 37.5 1.0

Chlorine binding site 10 out of 12 in 5c9f

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Chlorine binding site 10 out of 12 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:53.5
occ:1.00
 O D:HOH408 3.0 34.9 1.0
NH2 D:ARG216 3.3 73.6 1.0
N D:LYS196 3.5 33.7 1.0
NE D:ARG216 3.6 71.0 1.0
CG2 D:ILE195 3.7 37.2 1.0
CZ D:ARG216 3.9 67.7 1.0
CD1 D:ILE195 3.9 37.6 1.0
CA D:ILE195 3.9 27.7 1.0
CB D:SER212 4.0 54.4 1.0
CB D:LYS196 4.2 47.0 1.0
C D:ILE195 4.3 36.9 1.0
CB D:ILE195 4.3 34.2 1.0
C D:SER212 4.4 65.8 1.0
CA D:LYS196 4.5 36.5 1.0
O D:SER212 4.5 56.1 1.0
N D:LEU213 4.6 36.9 1.0
O D:LYS196 4.7 35.2 1.0
CG1 D:ILE195 4.7 35.1 1.0
CD D:ARG216 4.8 66.7 1.0
O D:HOH427 4.8 55.5 1.0
CA D:SER212 4.9 53.0 1.0
CA D:LEU213 4.9 37.5 1.0
OG D:SER212 5.0 52.7 1.0

Reference:

M.Li, A.Gustchina, R.Cruz, M.Simoes, P.Curto, J.Martinez, C.Faro, I.Simoes, A.Wlodawer. Structure of RC1339/Aprc From Rickettsia Conorii, A Retropepsin-Like Aspartic Protease. Acta Crystallogr. D Biol. V. 71 2109 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26457434
DOI: 10.1107/S1399004715013905
Page generated: Fri Jul 26 05:59:31 2024

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