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Chlorine in PDB 5yrt: Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal, PDB code: 5yrt was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.687, 95.459, 114.567, 80.78, 87.58, 81.10
R / Rfree (%) 15 / 18.7

Other elements in 5yrt:

The structure of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Potassium (K) 8 atoms
Calcium (Ca) 4 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal (pdb code 5yrt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal, PDB code: 5yrt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5yrt

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Chlorine binding site 1 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:28.1
occ:1.00
 O A:HOH796 2.7 37.5 1.0
O D:HOH954 3.0 20.6 1.0
N A:GLU22 3.1 15.4 1.0
O D:HOH1056 3.6 35.8 1.0
CG A:GLU22 3.6 22.2 1.0
CA A:LYS21 3.8 13.2 1.0
CB A:GLU22 3.8 19.9 1.0
C A:LYS21 4.0 18.5 1.0
CG A:PRO310 4.0 15.9 1.0
CB A:LYS21 4.0 18.6 1.0
O A:HOH770 4.1 29.1 1.0
CA A:GLU22 4.1 20.4 1.0
CD A:GLU22 4.1 25.0 1.0
CD A:PRO310 4.2 15.4 1.0
OE1 A:GLU22 4.3 22.9 1.0
CD D:LYS542 4.4 18.2 1.0
CG A:LYS21 4.5 23.2 1.0
O D:HOH788 4.6 39.4 1.0
OE2 A:GLU22 4.8 18.0 1.0
CB D:LYS542 4.9 16.0 1.0
NH2 D:ARG392 4.9 15.6 1.0
CD A:LYS21 5.0 32.6 1.0
O A:VAL20 5.0 16.0 1.0

Chlorine binding site 2 out of 12 in 5yrt

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Chlorine binding site 2 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:25.6
occ:1.00
 O A:HOH1035 2.9 21.1 1.0
O D:HOH867 3.0 22.7 1.0
NH1 A:ARG532 3.3 15.4 1.0
O A:HOH932 3.3 23.8 1.0
O A:HOH944 3.5 19.4 1.0
CD A:ARG532 3.7 15.0 1.0
N D:ASN121 3.8 9.7 1.0
O D:MET120 3.8 11.9 1.0
C D:MET120 3.9 11.3 1.0
CB D:ASN121 3.9 8.7 1.0
CA D:ASN121 3.9 9.0 1.0
NH2 D:ARG314 4.1 13.6 1.0
CZ A:ARG532 4.3 19.4 1.0
NE A:ARG532 4.5 18.0 1.0
O D:HIS119 4.5 12.2 1.0
CZ D:ARG314 4.6 14.6 1.0
O A:HOH960 4.6 17.3 1.0
NE D:ARG314 4.7 13.4 1.0
O D:HOH702 4.7 23.9 1.0
C D:HIS119 4.8 13.6 1.0
CA D:MET120 4.8 13.8 1.0
N D:MET120 4.8 11.1 1.0
CG A:ARG532 4.9 14.9 1.0
O A:HOH895 4.9 16.3 1.0
O A:HOH1037 4.9 29.4 1.0
CB A:ARG532 5.0 14.1 1.0

Chlorine binding site 3 out of 12 in 5yrt

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Chlorine binding site 3 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:33.4
occ:1.00
 O C:HOH355 2.7 29.2 1.0
O C:HOH386 2.9 10.0 1.0
O A:HOH1103 3.0 31.7 1.0
N C:ARG100 3.3 14.3 1.0
N C:ASP99 3.4 13.2 1.0
CE A:LYS288 3.7 17.5 1.0
CD C:ARG100 3.7 45.7 1.0
CG C:ARG100 3.8 27.1 1.0
O A:HOH874 3.8 14.6 1.0
CB C:ARG100 3.8 14.4 1.0
C C:ARG98 3.9 14.1 1.0
CA C:ARG98 4.0 13.0 1.0
NZ A:LYS288 4.1 11.6 1.0
CA C:ASP99 4.1 12.7 1.0
O A:HOH834 4.2 30.0 1.0
CA C:ARG100 4.2 10.4 1.0
C C:ASP99 4.2 17.6 1.0
O C:GLY97 4.3 14.6 1.0
CB C:ASP99 4.3 14.2 1.0
O C:ARG98 4.8 11.0 1.0
CD A:LYS288 4.8 13.0 1.0
O C:HOH313 4.9 25.2 1.0
O A:HOH957 4.9 10.9 1.0
NE C:ARG100 5.0 55.5 1.0
N C:ARG98 5.0 10.9 1.0

Chlorine binding site 4 out of 12 in 5yrt

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Chlorine binding site 4 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl605

b:28.2
occ:1.00
 O A:HOH952 2.9 28.1 1.0
N D:GLU22 3.2 16.8 1.0
O A:HOH1104 3.6 40.6 1.0
CG D:GLU22 3.6 19.0 1.0
CA D:LYS21 3.8 17.3 1.0
CG D:PRO310 3.8 13.8 1.0
CB D:GLU22 3.9 16.4 1.0
C D:LYS21 4.0 18.4 1.0
CD D:GLU22 4.0 25.8 1.0
CB D:LYS21 4.0 19.8 1.0
CD D:PRO310 4.1 11.4 1.0
CA D:GLU22 4.1 16.4 1.0
OE1 D:GLU22 4.2 27.6 1.0
O D:HOH943 4.3 34.6 1.0
CG D:LYS21 4.5 28.4 1.0
CD A:LYS542 4.5 23.9 1.0
O A:HOH1060 4.6 34.9 1.0
OE2 D:GLU22 4.7 25.4 1.0
NH2 A:ARG392 4.7 17.4 1.0
CB A:LYS542 4.8 18.1 1.0
NZ A:LYS542 4.9 27.9 1.0
O D:VAL20 4.9 21.8 1.0

Chlorine binding site 5 out of 12 in 5yrt

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Chlorine binding site 5 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl606

b:30.3
occ:1.00
 O A:HOH862 3.0 22.2 1.0
O D:HOH985 3.1 23.2 1.0
NH1 D:ARG532 3.2 13.7 1.0
O D:HOH855 3.3 22.8 1.0
CD D:ARG532 3.5 14.2 1.0
O D:HOH958 3.6 22.9 1.0
O A:MET120 3.7 11.9 1.0
N A:ASN121 3.8 11.8 1.0
C A:MET120 3.8 13.5 1.0
CB A:ASN121 3.8 12.8 1.0
CA A:ASN121 3.9 9.1 1.0
NH2 A:ARG314 4.1 10.8 1.0
O A:HOH1055 4.2 38.8 1.0
CZ D:ARG532 4.2 17.1 1.0
NE D:ARG532 4.3 13.7 1.0
O A:HIS119 4.4 12.4 1.0
O D:HOH863 4.5 18.2 1.0
CZ A:ARG314 4.6 13.2 1.0
CA A:MET120 4.7 11.4 1.0
NE A:ARG314 4.7 10.0 1.0
C A:HIS119 4.7 10.2 1.0
N A:MET120 4.7 12.1 1.0
CG D:ARG532 4.8 12.6 1.0
CB D:ARG532 4.9 13.4 1.0
CG A:ASN121 4.9 14.9 1.0
ND2 A:ASN121 5.0 14.3 1.0

Chlorine binding site 6 out of 12 in 5yrt

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Chlorine binding site 6 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:24.2
occ:1.00
 O D:HOH1028 3.0 45.0 1.0
O F:HOH356 3.1 19.3 1.0
NH1 F:ARG100 3.2 32.1 1.0
N F:ASP99 3.4 26.9 1.0
N F:ARG100 3.4 20.0 1.0
O D:HOH827 3.7 20.8 1.0
CE D:LYS288 3.7 18.8 1.0
CG F:ARG100 3.7 22.1 1.0
CD F:ARG100 3.8 24.3 1.0
CB F:ARG100 3.9 20.3 1.0
NZ D:LYS288 4.0 15.8 1.0
C F:ARG98 4.0 25.4 1.0
CA F:ARG98 4.0 22.8 1.0
CA F:ASP99 4.1 29.0 1.0
O F:GLY97 4.2 27.1 1.0
CB F:ASP99 4.3 35.7 1.0
C F:ASP99 4.3 24.1 1.0
CZ F:ARG100 4.3 33.1 1.0
CA F:ARG100 4.3 20.8 1.0
NE F:ARG100 4.5 28.8 1.0
O F:ARG98 4.9 24.9 1.0
OD2 F:ASP99 4.9 49.9 1.0
N F:ARG98 4.9 24.1 1.0
O D:HOH896 5.0 19.1 1.0
CG F:ASP99 5.0 44.0 1.0
CD D:LYS288 5.0 16.1 1.0
C F:GLY97 5.0 28.4 1.0

Chlorine binding site 7 out of 12 in 5yrt

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Chlorine binding site 7 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl605

b:25.7
occ:1.00
 O J:HOH764 2.9 20.2 1.0
O J:HOH837 3.0 32.6 1.0
O G:HOH1135 3.0 44.0 1.0
N G:GLU22 3.2 15.2 1.0
CG G:GLU22 3.6 18.9 1.0
CA G:LYS21 3.7 16.4 1.0
CB G:GLU22 3.9 18.4 1.0
CB G:LYS21 3.9 18.2 1.0
C G:LYS21 4.0 17.3 1.0
CG G:PRO310 4.0 12.1 1.0
CD G:GLU22 4.2 22.3 1.0
CA G:GLU22 4.2 19.3 1.0
CD G:PRO310 4.2 13.4 1.0
O G:HOH808 4.2 31.9 1.0
OE1 G:GLU22 4.4 21.5 1.0
CG G:LYS21 4.4 27.5 1.0
O G:HOH771 4.4 33.9 1.0
CD J:LYS542 4.6 21.0 1.0
O J:HOH1033 4.7 42.6 1.0
NH2 J:ARG392 4.8 16.4 1.0
CB J:LYS542 4.8 13.9 1.0
OE2 G:GLU22 4.9 20.0 1.0
O G:VAL20 5.0 17.1 1.0

Chlorine binding site 8 out of 12 in 5yrt

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Chlorine binding site 8 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl606

b:28.8
occ:1.00
 O G:HOH983 3.1 18.5 1.0
O J:HOH782 3.2 16.1 1.0
NH1 G:ARG532 3.3 11.9 1.0
O G:HOH918 3.3 20.0 1.0
O G:HOH1010 3.5 23.2 1.0
CD G:ARG532 3.6 10.6 1.0
N J:ASN121 3.8 9.0 1.0
O J:MET120 3.8 11.4 1.0
C J:MET120 3.9 12.3 1.0
CB J:ASN121 3.9 11.8 1.0
CA J:ASN121 4.0 7.6 1.0
NH2 J:ARG314 4.2 14.6 1.0
CZ G:ARG532 4.3 12.4 1.0
NE G:ARG532 4.4 11.6 1.0
O J:HIS119 4.4 13.7 1.0
O G:HOH899 4.5 17.6 1.0
CZ J:ARG314 4.6 11.2 1.0
O J:HOH716 4.6 26.3 1.0
NE J:ARG314 4.7 10.3 1.0
CA J:MET120 4.7 8.3 1.0
C J:HIS119 4.7 13.7 1.0
CG G:ARG532 4.8 10.9 1.0
N J:MET120 4.8 12.1 1.0
CB G:ARG532 4.9 13.6 1.0
O G:HOH973 5.0 23.5 1.0

Chlorine binding site 9 out of 12 in 5yrt

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Chlorine binding site 9 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl201

b:16.0
occ:1.00
 O G:HOH1032 3.0 42.5 1.0
O I:HOH381 3.1 12.8 1.0
NH1 I:ARG100 3.3 20.2 1.0
N I:ASP99 3.4 16.1 1.0
N I:ARG100 3.4 12.5 1.0
O G:HOH802 3.7 14.8 1.0
CG I:ARG100 3.8 17.1 1.0
CE G:LYS288 3.9 11.4 1.0
CB I:ARG100 3.9 12.5 1.0
CD I:ARG100 3.9 18.7 1.0
C I:ARG98 4.0 12.8 1.0
CA I:ARG98 4.1 13.1 1.0
CA I:ASP99 4.1 17.7 1.0
NZ G:LYS288 4.1 11.7 1.0
O I:GLY97 4.2 35.6 1.0
C I:ASP99 4.2 17.6 1.0
CA I:ARG100 4.3 12.4 1.0
CB I:ASP99 4.3 19.3 1.0
CZ I:ARG100 4.4 20.1 1.0
NE I:ARG100 4.6 18.4 1.0
O I:ARG98 4.9 12.3 1.0
N I:ARG98 5.0 16.7 1.0
C I:GLY97 5.0 28.0 1.0

Chlorine binding site 10 out of 12 in 5yrt

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Chlorine binding site 10 out of 12 in the Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Diol Dehydratase, Adocbl/Substrate-Free, Anaerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl605

b:26.1
occ:1.00
 O G:HOH990 2.8 22.2 1.0
N J:GLU22 3.2 19.8 1.0
CG J:GLU22 3.7 18.9 1.0
CA J:LYS21 3.7 12.5 1.0
CG J:PRO310 3.9 14.9 1.0
C J:LYS21 4.0 17.9 1.0
CB J:GLU22 4.0 16.6 1.0
CB J:LYS21 4.0 16.5 1.0
CD J:GLU22 4.1 25.6 1.0
CD J:PRO310 4.1 10.2 1.0
OE1 J:GLU22 4.2 27.9 1.0
CA J:GLU22 4.2 16.1 1.0
O G:HOH1087 4.4 27.6 1.0
CG J:LYS21 4.6 22.0 1.0
CD G:LYS542 4.7 19.2 1.0
OE2 J:GLU22 4.8 19.9 1.0
O J:VAL20 4.9 16.9 1.0
NH2 G:ARG392 4.9 15.4 1.0
N J:LYS21 5.0 12.0 1.0

Reference:

N.Shibata, Y.Sueyoshi, Y.Higuchi, T.Toraya. Direct Participation of A Peripheral Side Chain of A Corrin Ring in Coenzyme B12CATALYSIS. Angew. Chem. Int. Ed. Engl. V. 57 7830 2018.
ISSN: ESSN 1521-3773
PubMed: 29797764
DOI: 10.1002/ANIE.201803591
Page generated: Sat Jul 12 11:01:27 2025

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