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Chlorine in PDB 1lk5: Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii

Enzymatic activity of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii

All present enzymatic activity of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii:
5.3.1.6;

Protein crystallography data

The structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii, PDB code: 1lk5 was solved by K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.548, 114.932, 119.017, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.5

Other elements in 1lk5:

The structure of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii (pdb code 1lk5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii, PDB code: 1lk5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 1lk5

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Chlorine binding site 1 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:17.8
occ:1.00
 OE2 A:GLU107 3.0 18.7 1.0
O A:HOH1032 3.1 18.5 1.0
N A:GLY101 3.2 17.8 1.0
N A:ALA103 3.4 16.7 1.0
CA A:GLY101 3.4 17.5 1.0
N A:ALA102 3.5 17.1 1.0
C A:GLY101 3.6 17.3 1.0
CA A:GLY99 3.6 17.8 1.0
OE1 A:GLU107 3.7 18.4 1.0
CD A:GLU107 3.7 16.1 1.0
C A:GLY99 3.8 18.6 1.0
N A:GLY99 3.9 17.9 1.0
CB A:ALA103 4.0 16.6 1.0
CA A:ALA103 4.0 16.5 1.0
N A:ARG100 4.1 18.5 1.0
N A:LEU104 4.2 16.8 1.0
C A:ALA103 4.3 16.4 1.0
O A:GLY99 4.3 17.8 1.0
O A:GLY101 4.3 17.0 1.0
C A:ALA102 4.3 17.0 1.0
C A:ARG100 4.4 18.6 1.0
CA A:ALA102 4.4 17.4 1.0
CG2 A:THR28 4.5 18.5 1.0
O A:HOH1017 4.6 24.5 1.0
OD2 C:ASP168 4.8 19.6 1.0
CB A:THR28 4.8 17.8 1.0
CA A:ARG100 4.8 19.7 1.0
CA A:LEU104 5.0 17.0 1.0

Chlorine binding site 2 out of 10 in 1lk5

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Chlorine binding site 2 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:16.6
occ:1.00
 OD2 A:ASP174 2.9 16.8 1.0
O A:HOH1031 3.2 16.2 1.0
N A:TYR58 3.3 18.5 1.0
O C:ASP168 3.4 17.5 1.0
NZ C:LYS167 3.4 16.2 1.0
N A:GLN59 3.5 19.4 1.0
OD1 A:ASP174 3.5 13.8 1.0
CB A:TYR58 3.6 18.7 1.0
CA C:GLY169 3.7 17.3 1.0
CG A:ASP174 3.7 16.9 1.0
CB A:SER57 3.7 17.8 1.0
CD C:PRO170 3.9 17.5 1.0
CA A:TYR58 3.9 18.6 1.0
CD1 A:TYR58 4.0 17.9 1.0
C C:ASP168 4.1 17.9 1.0
C A:TYR58 4.2 19.3 1.0
N C:GLY169 4.2 17.9 1.0
C A:SER57 4.2 18.3 1.0
OG A:SER57 4.2 17.1 1.0
CG A:TYR58 4.2 18.6 1.0
CB A:GLN59 4.3 19.6 1.0
CA A:SER57 4.4 17.6 1.0
C C:GLY169 4.4 17.4 1.0
N C:PRO170 4.4 17.2 1.0
CA A:GLN59 4.5 19.4 1.0
CE C:LYS167 4.6 16.9 1.0
O A:HOH1028 4.9 18.1 1.0

Chlorine binding site 3 out of 10 in 1lk5

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Chlorine binding site 3 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1009

b:18.0
occ:1.00
 N C:VAL165 3.2 18.9 1.0
N A:VAL165 3.2 19.6 1.0
O A:HOH1128 3.3 25.3 1.0
N C:ASN166 3.3 18.6 1.0
N A:ASN166 3.4 18.6 1.0
CB C:VAL165 3.9 20.0 1.0
CA A:GLY164 3.9 19.2 1.0
CA C:VAL165 3.9 19.7 1.0
CA C:GLY164 4.0 18.5 1.0
CA A:VAL165 4.0 20.2 1.0
C C:GLY164 4.1 18.7 1.0
C A:GLY164 4.1 19.5 1.0
C C:VAL165 4.1 19.2 1.0
CB A:VAL165 4.2 20.5 1.0
C A:VAL165 4.2 19.7 1.0
CA C:ASN166 4.2 18.3 1.0
CA A:ASN166 4.2 17.8 1.0
CB C:ASN166 4.3 18.8 1.0
CB A:ASN166 4.3 18.4 1.0
N A:LYS167 4.5 16.3 1.0
N C:LYS167 4.5 17.8 1.0
CG2 C:VAL165 4.5 21.5 1.0
C C:ASN166 4.7 18.1 1.0
C A:ASN166 4.7 17.2 1.0
CG2 C:VAL171 4.9 15.4 1.0
CG2 A:VAL165 4.9 22.1 1.0
CG2 A:VAL171 4.9 16.9 1.0

Chlorine binding site 4 out of 10 in 1lk5

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Chlorine binding site 4 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:17.2
occ:1.00
 OE2 B:GLU107 3.0 17.2 1.0
O B:HOH1017 3.1 17.8 1.0
N B:GLY101 3.2 16.3 1.0
N B:ALA103 3.3 14.9 1.0
CA B:GLY101 3.4 16.1 1.0
N B:ALA102 3.5 15.4 1.0
C B:GLY101 3.6 15.5 1.0
CA B:GLY99 3.6 18.1 1.0
OE1 B:GLU107 3.6 17.1 1.0
CD B:GLU107 3.7 16.9 1.0
C B:GLY99 3.7 18.1 1.0
N B:GLY99 3.8 18.3 1.0
N B:ARG100 4.0 17.7 1.0
CB B:ALA103 4.0 15.0 1.0
CA B:ALA103 4.1 15.0 1.0
O B:GLY99 4.2 17.9 1.0
N B:LEU104 4.3 14.9 1.0
C B:ALA102 4.3 15.3 1.0
C B:ALA103 4.3 14.6 1.0
C B:ARG100 4.3 17.6 1.0
O B:GLY101 4.4 15.8 1.0
CA B:ALA102 4.4 15.4 1.0
CG2 B:THR28 4.4 16.2 1.0
O B:HOH1037 4.6 21.4 1.0
CB B:THR28 4.7 15.7 1.0
CA B:ARG100 4.8 18.2 1.0
OD2 D:ASP168 4.8 16.8 1.0

Chlorine binding site 5 out of 10 in 1lk5

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Chlorine binding site 5 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1006

b:16.6
occ:1.00
 OD2 B:ASP174 2.9 17.1 1.0
O B:HOH1034 3.2 16.8 1.0
N B:TYR58 3.3 15.7 1.0
N B:GLN59 3.4 16.2 1.0
NZ D:LYS167 3.5 13.2 1.0
O D:ASP168 3.5 15.9 1.0
CB B:TYR58 3.6 15.6 1.0
OD1 B:ASP174 3.6 13.1 1.0
CA D:GLY169 3.6 16.9 1.0
CG B:ASP174 3.7 15.9 1.0
CB B:SER57 3.7 15.7 1.0
CA B:TYR58 3.9 15.7 1.0
CD D:PRO170 3.9 16.6 1.0
CD1 B:TYR58 4.0 17.1 1.0
C D:ASP168 4.1 16.4 1.0
C B:TYR58 4.1 15.9 1.0
N D:GLY169 4.2 16.2 1.0
CG B:TYR58 4.2 16.5 1.0
C B:SER57 4.2 16.0 1.0
OG B:SER57 4.3 16.3 1.0
CB B:GLN59 4.3 16.6 1.0
CA B:SER57 4.4 15.8 1.0
C D:GLY169 4.4 16.4 1.0
CA B:GLN59 4.4 16.5 1.0
N D:PRO170 4.5 16.6 1.0
CE D:LYS167 4.7 14.6 1.0
O B:HOH1029 4.9 17.9 1.0

Chlorine binding site 6 out of 10 in 1lk5

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Chlorine binding site 6 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1010

b:17.4
occ:1.00
 O D:HOH1106 3.2 26.7 1.0
N B:VAL165 3.2 17.4 1.0
N D:VAL165 3.2 18.5 1.0
O D:HOH1139 3.3 28.2 1.0
N B:ASN166 3.3 16.5 1.0
N D:ASN166 3.4 17.4 1.0
CA B:GLY164 4.0 17.4 1.0
CA D:GLY164 4.0 17.6 1.0
CA B:VAL165 4.0 18.1 1.0
CA D:VAL165 4.0 19.0 1.0
C B:GLY164 4.1 17.9 1.0
CB D:VAL165 4.1 19.6 1.0
C D:GLY164 4.1 18.5 1.0
CB B:VAL165 4.1 18.4 1.0
C B:VAL165 4.2 17.5 1.0
CA B:ASN166 4.2 16.9 1.0
C D:VAL165 4.2 18.5 1.0
CB B:ASN166 4.3 17.1 1.0
CA D:ASN166 4.3 17.3 1.0
CB D:ASN166 4.3 16.9 1.0
N B:LYS167 4.5 16.9 1.0
N D:LYS167 4.7 16.3 1.0
C B:ASN166 4.7 17.3 1.0
C D:ASN166 4.7 16.9 1.0
CG2 D:VAL171 4.8 17.5 1.0
CG2 D:VAL165 4.8 21.8 1.0
CG2 B:VAL165 4.9 20.3 1.0
CG2 B:VAL171 4.9 16.5 1.0

Chlorine binding site 7 out of 10 in 1lk5

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Chlorine binding site 7 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1003

b:18.4
occ:1.00
 OE2 C:GLU107 3.0 19.9 1.0
O C:HOH1020 3.1 18.6 1.0
N C:GLY101 3.3 18.0 1.0
N C:ALA103 3.3 16.7 1.0
CA C:GLY101 3.4 17.8 1.0
N C:ALA102 3.5 17.1 1.0
C C:GLY101 3.6 16.9 1.0
OE1 C:GLU107 3.6 18.1 1.0
CA C:GLY99 3.6 18.0 1.0
CD C:GLU107 3.7 18.7 1.0
C C:GLY99 3.8 18.6 1.0
N C:GLY99 3.8 17.9 1.0
CB C:ALA103 3.9 17.4 1.0
CA C:ALA103 4.0 16.5 1.0
O C:HOH1174 4.0 36.3 1.0
N C:ARG100 4.1 18.8 1.0
N C:LEU104 4.2 16.6 1.0
C C:ALA103 4.2 17.3 1.0
O C:GLY99 4.2 18.6 1.0
O C:GLY101 4.3 16.5 1.0
C C:ALA102 4.3 16.4 1.0
CG2 C:THR28 4.4 20.0 1.0
CA C:ALA102 4.4 16.5 1.0
C C:ARG100 4.4 18.8 1.0
CB C:THR28 4.6 18.3 1.0
O C:HOH1059 4.7 21.4 1.0
OD2 A:ASP168 4.8 19.3 1.0
CA C:ARG100 4.9 19.6 1.0
O C:ALA103 5.0 16.6 1.0
CA C:LEU104 5.0 17.0 1.0

Chlorine binding site 8 out of 10 in 1lk5

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Chlorine binding site 8 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1007

b:20.5
occ:1.00
 OD2 C:ASP174 2.9 19.0 1.0
O C:HOH1027 3.2 17.7 1.0
N C:GLN59 3.3 18.4 1.0
O A:ASP168 3.3 17.4 1.0
N C:TYR58 3.3 17.2 1.0
NZ A:LYS167 3.4 15.1 1.0
OD1 C:ASP174 3.5 16.9 1.0
CB C:TYR58 3.6 17.5 1.0
CG C:ASP174 3.6 17.8 1.0
CA A:GLY169 3.6 17.0 1.0
CB C:SER57 3.7 17.2 1.0
CA C:TYR58 3.8 17.6 1.0
CD A:PRO170 3.9 17.8 1.0
C C:TYR58 4.0 17.9 1.0
C A:ASP168 4.0 17.1 1.0
CB C:GLN59 4.1 18.7 1.0
OG C:SER57 4.1 17.8 1.0
C C:SER57 4.2 17.5 1.0
N A:GLY169 4.2 17.3 1.0
CA C:GLN59 4.2 18.7 1.0
CD1 C:TYR58 4.3 19.1 1.0
CA C:SER57 4.3 17.1 1.0
CG C:TYR58 4.4 17.5 1.0
C A:GLY169 4.4 17.2 1.0
N A:PRO170 4.4 17.2 1.0
CE A:LYS167 4.6 15.1 1.0

Chlorine binding site 9 out of 10 in 1lk5

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Chlorine binding site 9 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1004

b:19.1
occ:1.00
 OE2 D:GLU107 3.1 19.8 1.0
O D:HOH1020 3.1 22.4 1.0
N D:GLY101 3.2 18.6 1.0
CA D:GLY101 3.3 18.4 1.0
N D:ALA103 3.3 16.9 1.0
C D:GLY101 3.5 17.6 1.0
N D:ALA102 3.5 17.2 1.0
CA D:GLY99 3.6 18.1 1.0
OE1 D:GLU107 3.7 18.5 1.0
CD D:GLU107 3.7 18.8 1.0
C D:GLY99 3.8 18.8 1.0
N D:GLY99 3.8 18.6 1.0
CB D:ALA103 3.9 17.4 1.0
O D:HOH1128 4.0 36.2 1.0
CA D:ALA103 4.0 17.0 1.0
N D:ARG100 4.1 19.5 1.0
O D:GLY101 4.2 18.0 1.0
N D:LEU104 4.2 17.0 1.0
O D:GLY99 4.2 18.5 1.0
C D:ALA103 4.2 17.5 1.0
C D:ALA102 4.3 17.0 1.0
C D:ARG100 4.4 19.5 1.0
CA D:ALA102 4.4 17.3 1.0
CG2 D:THR28 4.5 20.5 1.0
O D:HOH1024 4.7 24.3 1.0
OD2 B:ASP168 4.8 22.9 1.0
CB D:THR28 4.8 20.1 1.0
CA D:ARG100 4.8 19.9 1.0
O D:ALA103 5.0 17.8 1.0

Chlorine binding site 10 out of 10 in 1lk5

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Chlorine binding site 10 out of 10 in the Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1008

b:18.3
occ:1.00
 OD2 D:ASP174 2.9 15.6 1.0
O D:HOH1034 3.2 18.9 1.0
N D:TYR58 3.4 19.3 1.0
NZ B:LYS167 3.4 15.8 1.0
N D:GLN59 3.5 20.5 1.0
OD1 D:ASP174 3.5 16.6 1.0
O B:ASP168 3.5 17.3 1.0
CB D:SER57 3.6 18.6 1.0
CG D:ASP174 3.7 17.6 1.0
CB D:TYR58 3.7 19.3 1.0
CA B:GLY169 3.7 18.0 1.0
CD B:PRO170 3.9 17.3 1.0
CA D:TYR58 3.9 19.6 1.0
CD1 D:TYR58 4.1 18.2 1.0
OG D:SER57 4.1 18.5 1.0
C B:ASP168 4.2 18.1 1.0
C D:SER57 4.2 19.2 1.0
C D:TYR58 4.2 20.2 1.0
N B:GLY169 4.2 18.1 1.0
CB D:GLN59 4.3 21.4 1.0
CA D:SER57 4.3 18.6 1.0
CG D:TYR58 4.3 18.9 1.0
CA D:GLN59 4.5 20.9 1.0
C B:GLY169 4.5 17.5 1.0
N B:PRO170 4.5 17.3 1.0
CE B:LYS167 4.6 15.4 1.0
O D:HOH1027 5.0 17.9 1.0

Reference:

K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel. A Hyperthermostable D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii Characterization and Three-Dimensional Structure. Structure V. 10 877 2002.
ISSN: ISSN 0969-2126
PubMed: 12057201
DOI: 10.1016/S0969-2126(02)00779-7
Page generated: Fri Jul 19 23:51:13 2024

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