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Chlorine in PDB 1lk7: Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid

Enzymatic activity of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid

All present enzymatic activity of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid:
5.3.1.6;

Protein crystallography data

The structure of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid, PDB code: 1lk7 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.689, 114.923, 119.578, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.7

Other elements in 1lk7:

The structure of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid (pdb code 1lk7). 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 D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid, PDB code: 1lk7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 1lk7

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Chlorine binding site 1 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2001

b:22.1
occ:0.30
 OH2 A:DER1001 1.7 36.2 0.7
C1 A:DER1001 2.7 34.4 0.7
OH1 A:DER1001 3.0 29.2 0.7
N A:ALA103 3.2 28.2 1.0
N A:ALA102 3.2 27.0 1.0
N A:GLY101 3.2 28.6 1.0
CA A:GLY101 3.3 28.3 1.0
OE2 A:GLU107 3.3 39.0 1.0
C A:GLY101 3.4 27.8 1.0
OE1 A:GLU107 3.5 36.6 1.0
CA A:GLY99 3.6 30.7 1.0
CD A:GLU107 3.7 36.0 1.0
C A:GLY99 3.7 30.7 1.0
CB A:ALA103 3.8 28.1 1.0
N A:GLY99 3.8 30.3 1.0
CA A:ALA103 3.9 27.7 1.0
C2 A:DER1001 4.0 34.6 0.7
O A:GLY99 4.1 31.5 1.0
N A:ARG100 4.1 30.8 1.0
N A:LEU104 4.1 28.9 1.0
C A:ALA103 4.1 28.0 1.0
C A:ALA102 4.1 28.0 1.0
CA A:ALA102 4.1 28.1 1.0
O A:GLY101 4.2 27.2 1.0
C A:ARG100 4.4 30.2 1.0
CG2 A:THR28 4.5 30.5 1.0
CB A:THR28 4.7 31.4 1.0
O2 A:DER1001 4.8 30.2 0.7
CA A:LEU104 4.9 29.2 1.0
CA A:ARG100 4.9 31.1 1.0
O A:ALA103 4.9 27.7 1.0
C3 A:DER1001 4.9 37.2 0.7

Chlorine binding site 2 out of 10 in 1lk7

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Chlorine binding site 2 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2005

b:29.8
occ:1.00
 OD2 A:ASP174 2.9 26.1 1.0
O A:HOH2012 3.2 25.8 1.0
N A:TYR58 3.2 30.8 1.0
O C:ASP168 3.4 29.1 1.0
N A:GLN59 3.5 31.5 1.0
NZ C:LYS167 3.5 24.3 1.0
OD1 A:ASP174 3.5 24.4 1.0
CB A:TYR58 3.5 31.9 1.0
CG A:ASP174 3.6 23.4 1.0
CB A:SER57 3.7 30.4 1.0
CA C:GLY169 3.7 29.8 1.0
CA A:TYR58 3.8 31.2 1.0
CD C:PRO170 3.9 29.0 1.0
C C:ASP168 4.0 30.1 1.0
CD1 A:TYR58 4.1 33.8 1.0
C A:SER57 4.1 30.9 1.0
C A:TYR58 4.2 31.3 1.0
N C:GLY169 4.2 29.9 1.0
CG A:TYR58 4.2 32.4 1.0
OG A:SER57 4.3 27.8 1.0
CA A:SER57 4.3 29.9 1.0
CB A:GLN59 4.4 32.5 1.0
C C:GLY169 4.5 29.8 1.0
N C:PRO170 4.5 28.9 1.0
CA A:GLN59 4.5 32.6 1.0
CE C:LYS167 4.8 28.5 1.0
O A:HOH2043 4.9 28.4 1.0

Chlorine binding site 3 out of 10 in 1lk7

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Chlorine binding site 3 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2009

b:30.3
occ:1.00
 N C:VAL165 3.2 31.9 1.0
N A:VAL165 3.2 32.1 1.0
N A:ASN166 3.3 30.4 1.0
N C:ASN166 3.3 30.6 1.0
CA C:GLY164 4.0 30.6 1.0
CA C:VAL165 4.0 32.5 1.0
CA A:GLY164 4.0 30.9 1.0
CA A:VAL165 4.0 32.4 1.0
C C:GLY164 4.1 31.2 1.0
CB A:VAL165 4.1 33.0 1.0
CB C:VAL165 4.1 32.8 1.0
CA A:ASN166 4.1 30.0 1.0
C A:GLY164 4.2 31.8 1.0
C C:VAL165 4.2 31.6 1.0
C A:VAL165 4.2 31.5 1.0
CB A:ASN166 4.2 29.6 1.0
CA C:ASN166 4.2 30.2 1.0
CB C:ASN166 4.3 29.6 1.0
N A:LYS167 4.5 29.6 1.0
N C:LYS167 4.6 28.5 1.0
C A:ASN166 4.7 29.3 1.0
CG2 A:VAL165 4.7 34.1 1.0
C C:ASN166 4.8 29.4 1.0
CG2 A:VAL171 4.9 28.7 1.0
CG2 C:VAL165 4.9 34.4 1.0
CG2 C:VAL171 5.0 28.8 1.0

Chlorine binding site 4 out of 10 in 1lk7

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Chlorine binding site 4 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2002

b:20.4
occ:0.30
 OH2 B:DER1002 1.7 35.8 0.7
C1 B:DER1002 2.7 36.9 0.7
OE2 B:GLU107 3.0 37.0 1.0
N B:ALA103 3.1 26.6 1.0
OH1 B:DER1002 3.1 29.6 0.7
OE1 B:GLU107 3.2 33.4 1.0
N B:GLY101 3.3 27.6 1.0
N B:ALA102 3.4 26.7 1.0
CD B:GLU107 3.4 33.5 1.0
CA B:GLY101 3.5 27.4 1.0
CA B:GLY99 3.5 29.9 1.0
C B:GLY101 3.5 27.1 1.0
CB B:ALA103 3.6 25.7 1.0
CA B:ALA103 3.7 25.2 1.0
C B:GLY99 3.8 29.4 1.0
N B:GLY99 3.8 30.0 1.0
N B:LEU104 3.9 26.3 1.0
C B:ALA103 3.9 26.2 1.0
C2 B:DER1002 4.0 37.1 0.7
C B:ALA102 4.1 26.2 1.0
N B:ARG100 4.2 29.4 1.0
O B:GLY99 4.2 27.0 1.0
CA B:ALA102 4.3 26.9 1.0
O B:GLY101 4.3 26.6 1.0
C B:ARG100 4.5 29.0 1.0
CG2 B:THR28 4.5 26.8 1.0
CB B:THR28 4.6 27.9 1.0
O B:ALA103 4.7 24.7 1.0
CA B:LEU104 4.7 27.4 1.0
O3 B:DER1002 4.8 42.0 0.7
CG B:GLU107 4.8 30.1 1.0
O2 B:DER1002 4.9 35.2 0.7
C3 B:DER1002 4.9 39.9 0.7
CA B:ARG100 5.0 30.5 1.0

Chlorine binding site 5 out of 10 in 1lk7

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Chlorine binding site 5 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2006

b:27.1
occ:1.00
 OD2 B:ASP174 2.8 29.4 1.0
O B:HOH2036 3.0 27.0 1.0
N B:TYR58 3.3 27.3 1.0
N B:GLN59 3.4 26.9 1.0
NZ D:LYS167 3.5 20.8 1.0
O D:ASP168 3.5 24.8 1.0
CB B:TYR58 3.5 28.1 1.0
OD1 B:ASP174 3.5 23.9 1.0
CG B:ASP174 3.6 25.0 1.0
CB B:SER57 3.6 27.1 1.0
CA D:GLY169 3.7 26.5 1.0
CA B:TYR58 3.8 27.6 1.0
CD D:PRO170 3.9 25.8 1.0
CD2 B:TYR58 4.1 28.2 1.0
C D:ASP168 4.1 26.3 1.0
C B:TYR58 4.1 27.4 1.0
C B:SER57 4.2 26.9 1.0
N D:GLY169 4.2 26.1 1.0
CG B:TYR58 4.2 27.7 1.0
OG B:SER57 4.2 25.9 1.0
CA B:SER57 4.3 26.3 1.0
CB B:GLN59 4.3 28.7 1.0
CA B:GLN59 4.5 28.1 1.0
C D:GLY169 4.5 26.3 1.0
N D:PRO170 4.5 26.2 1.0
CE D:LYS167 4.8 19.6 1.0
O B:HOH2037 4.8 24.8 1.0

Chlorine binding site 6 out of 10 in 1lk7

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Chlorine binding site 6 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2010

b:25.5
occ:1.00
 N D:VAL165 3.2 28.4 1.0
N B:VAL165 3.3 27.3 1.0
N D:ASN166 3.3 27.5 1.0
N B:ASN166 3.4 27.5 1.0
CA D:VAL165 4.0 29.3 1.0
CB D:VAL165 4.0 29.3 1.0
CA D:GLY164 4.0 26.7 1.0
CA B:GLY164 4.0 27.1 1.0
CB B:VAL165 4.1 29.4 1.0
C D:GLY164 4.1 27.5 1.0
CA B:VAL165 4.1 29.1 1.0
C D:VAL165 4.1 28.8 1.0
C B:GLY164 4.1 27.5 1.0
CA D:ASN166 4.2 27.6 1.0
CB B:ASN166 4.3 27.8 1.0
C B:VAL165 4.3 28.4 1.0
CA B:ASN166 4.3 27.6 1.0
CB D:ASN166 4.3 28.2 1.0
CG2 D:VAL165 4.6 30.3 1.0
CG2 B:VAL165 4.6 32.2 1.0
N D:LYS167 4.6 24.8 1.0
N B:LYS167 4.7 26.2 1.0
C D:ASN166 4.7 26.3 1.0
CG2 B:VAL171 4.8 23.9 1.0
C B:ASN166 4.8 27.0 1.0
CG2 D:VAL171 4.9 27.3 1.0

Chlorine binding site 7 out of 10 in 1lk7

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Chlorine binding site 7 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2003

b:30.8
occ:0.30
 OH2 C:DER1003 1.8 31.1 0.7
C1 C:DER1003 2.8 33.2 0.7
N C:ALA103 3.1 30.2 1.0
OE2 C:GLU107 3.2 36.3 1.0
N C:ALA102 3.2 30.3 1.0
OH1 C:DER1003 3.2 26.5 0.7
N C:GLY101 3.2 32.2 1.0
OE1 C:GLU107 3.4 35.5 1.0
CA C:GLY101 3.4 31.3 1.0
C C:GLY101 3.4 30.5 1.0
CA C:GLY99 3.6 33.2 1.0
CD C:GLU107 3.6 34.2 1.0
C C:GLY99 3.7 33.7 1.0
CA C:ALA103 3.8 30.0 1.0
CB C:ALA103 3.8 30.7 1.0
N C:GLY99 3.9 33.0 1.0
C C:ALA102 4.0 30.2 1.0
CA C:ALA102 4.1 30.5 1.0
C C:ALA103 4.1 30.5 1.0
C2 C:DER1003 4.1 32.5 0.7
O C:GLY99 4.1 33.0 1.0
O C:GLY101 4.2 28.8 1.0
N C:LEU104 4.2 30.6 1.0
N C:ARG100 4.2 34.2 1.0
C C:ARG100 4.4 33.5 1.0
CG2 C:THR28 4.4 30.9 1.0
CB C:THR28 4.6 28.9 1.0
O C:ALA103 4.8 29.9 1.0
O2 C:DER1003 4.9 29.5 0.7
CA C:ARG100 4.9 34.8 1.0
CG C:GLU107 4.9 30.7 1.0
CA C:LEU104 5.0 31.8 1.0

Chlorine binding site 8 out of 10 in 1lk7

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Chlorine binding site 8 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2007

b:33.5
occ:1.00
 OD2 C:ASP174 2.8 28.0 1.0
O C:HOH2045 3.2 28.4 1.0
N C:GLN59 3.2 29.6 1.0
O A:ASP168 3.3 29.4 1.0
N C:TYR58 3.4 28.0 1.0
NZ A:LYS167 3.4 24.6 1.0
OD1 C:ASP174 3.5 25.0 1.0
CB C:SER57 3.6 29.4 1.0
CG C:ASP174 3.6 22.6 1.0
CB C:TYR58 3.7 28.9 1.0
CA A:GLY169 3.7 27.9 1.0
CA C:TYR58 3.9 28.8 1.0
CD A:PRO170 3.9 28.6 1.0
C C:TYR58 4.0 28.9 1.0
C A:ASP168 4.0 28.6 1.0
CB C:GLN59 4.1 31.2 1.0
C C:SER57 4.2 28.6 1.0
CA C:GLN59 4.2 30.4 1.0
OG C:SER57 4.2 28.3 1.0
N A:GLY169 4.2 28.3 1.0
CA C:SER57 4.3 28.4 1.0
C A:GLY169 4.4 27.4 1.0
CD1 C:TYR58 4.4 29.7 1.0
CG C:TYR58 4.5 30.8 1.0
N A:PRO170 4.5 27.2 1.0
CE A:LYS167 4.7 25.9 1.0
O C:HOH2048 4.8 26.9 1.0

Chlorine binding site 9 out of 10 in 1lk7

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Chlorine binding site 9 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2004

b:20.9
occ:0.30
 OH2 D:DER1004 2.0 30.4 0.7
C1 D:DER1004 2.9 30.6 0.7
N D:ALA103 3.0 25.6 1.0
OE1 D:GLU107 3.2 29.2 1.0
N D:ALA102 3.3 26.4 1.0
OH1 D:DER1004 3.3 22.9 0.7
CA D:GLY101 3.4 27.5 1.0
N D:GLY101 3.4 26.9 1.0
C D:GLY101 3.4 26.9 1.0
CA D:GLY99 3.4 27.6 1.0
OE2 D:GLU107 3.5 33.0 1.0
CB D:ALA103 3.6 26.6 1.0
CA D:ALA103 3.6 26.1 1.0
CD D:GLU107 3.6 30.4 1.0
C D:GLY99 3.7 27.4 1.0
N D:LEU104 3.8 26.6 1.0
N D:GLY99 3.8 28.0 1.0
C D:ALA103 3.9 26.5 1.0
C D:ALA102 3.9 25.9 1.0
CA D:ALA102 4.1 25.9 1.0
O D:GLY99 4.1 26.0 1.0
O D:GLY101 4.2 26.9 1.0
C2 D:DER1004 4.2 32.3 0.7
N D:ARG100 4.3 28.4 1.0
C D:ARG100 4.5 28.6 1.0
CG2 D:THR28 4.6 28.4 1.0
CA D:LEU104 4.6 28.1 1.0
O D:ALA103 4.7 26.1 1.0
CB D:THR28 4.8 27.9 1.0
O2 D:DER1004 5.0 29.7 0.7
CG D:GLU107 5.0 28.4 1.0

Chlorine binding site 10 out of 10 in 1lk7

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Chlorine binding site 10 out of 10 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2008

b:24.7
occ:1.00
 OD2 D:ASP174 2.8 22.8 1.0
O D:HOH2038 3.2 24.2 1.0
N D:TYR58 3.3 26.8 1.0
OD1 D:ASP174 3.5 24.8 1.0
O B:ASP168 3.5 28.1 1.0
NZ B:LYS167 3.5 22.2 1.0
N D:GLN59 3.6 26.7 1.0
CG D:ASP174 3.6 25.0 1.0
CB D:SER57 3.7 27.2 1.0
CB D:TYR58 3.7 27.0 1.0
CA B:GLY169 3.7 25.8 1.0
CA D:TYR58 3.9 26.5 1.0
CD B:PRO170 4.0 25.5 1.0
CD1 D:TYR58 4.0 27.6 1.0
C B:ASP168 4.1 27.2 1.0
C D:SER57 4.2 26.8 1.0
OG D:SER57 4.2 27.5 1.0
N B:GLY169 4.2 26.7 1.0
C D:TYR58 4.2 26.6 1.0
CA D:SER57 4.3 27.2 1.0
CG D:TYR58 4.3 27.3 1.0
CB D:GLN59 4.4 28.0 1.0
C B:GLY169 4.5 25.2 1.0
N B:PRO170 4.6 25.2 1.0
CA D:GLN59 4.6 27.8 1.0
CE B:LYS167 4.8 24.0 1.0
O D:HOH2025 4.9 25.8 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 23:51:28 2024

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