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Chlorine in PDB 2x2j: Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin

Enzymatic activity of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin

All present enzymatic activity of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin:
4.2.2.13;

Protein crystallography data

The structure of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin, PDB code: 2x2j was solved by H.J.Rozeboom, S.Yu, S.Madrid, K.H.Kalk, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.19 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.314, 91.707, 192.899, 90.00, 99.33, 90.00
R / Rfree (%) 23.4 / 29.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin (pdb code 2x2j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin, PDB code: 2x2j:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2x2j

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Chlorine binding site 1 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin


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 the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2044

b:34.6
occ:1.00
 OG1 A:THR555 2.8 39.3 1.0
NE A:ARG649 3.0 38.5 1.0
NH2 A:ARG649 3.1 39.1 1.0
N A:THR555 3.2 39.4 1.0
CZ A:ARG649 3.5 38.9 1.0
CB A:THR555 3.8 39.3 1.0
N A:VAL556 3.9 39.7 1.0
CG2 A:VAL556 3.9 39.8 1.0
CD1 A:TYR266 3.9 36.7 1.0
CA A:THR555 3.9 39.5 1.0
CB A:ARG649 3.9 37.9 1.0
O A:HOH3250 4.1 36.9 1.0
C A:MET554 4.2 39.5 1.0
CD A:ARG649 4.2 38.2 1.0
CG2 A:THR555 4.2 39.2 1.0
N A:GLY650 4.2 37.8 1.0
CA A:MET554 4.3 39.5 1.0
CG A:ARG649 4.3 37.8 1.0
C A:ARG649 4.3 37.5 1.0
N A:MET554 4.3 39.3 1.0
C A:THR555 4.4 39.7 1.0
O A:ARG649 4.6 37.4 1.0
CE1 A:TYR266 4.6 37.0 1.0
CA A:GLY650 4.6 37.8 1.0
O A:TYR238 4.7 37.2 1.0
CA A:ARG649 4.8 37.6 1.0
NH1 A:ARG649 4.8 39.0 1.0
CG A:TYR266 4.8 36.3 1.0
CB A:TYR266 4.8 36.0 1.0
CB A:VAL556 4.9 40.0 1.0
CA A:VAL556 4.9 39.9 1.0
CB A:ALA558 5.0 40.0 1.0

Chlorine binding site 2 out of 4 in 2x2j

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Chlorine binding site 2 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin


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 the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2040

b:41.6
occ:1.00
 OG1 B:THR555 2.9 40.5 1.0
NE B:ARG649 2.9 37.0 1.0
NH2 B:ARG649 3.0 37.7 1.0
N B:THR555 3.2 39.8 1.0
CZ B:ARG649 3.4 37.4 1.0
CG2 B:VAL556 3.7 41.4 1.0
O B:HOH3203 3.7 37.1 1.0
N B:VAL556 3.8 40.5 1.0
CD1 B:TYR266 3.9 36.1 1.0
CB B:THR555 3.9 40.0 1.0
CA B:THR555 4.0 39.9 1.0
CB B:ARG649 4.0 36.4 1.0
C B:MET554 4.1 39.8 1.0
CD B:ARG649 4.1 36.8 1.0
CA B:MET554 4.2 40.0 1.0
N B:GLY650 4.2 36.4 1.0
C B:ARG649 4.2 36.2 1.0
CG B:ARG649 4.3 36.4 1.0
O B:ARG649 4.3 36.1 1.0
C B:THR555 4.4 40.2 1.0
N B:MET554 4.4 39.9 1.0
CA B:GLY650 4.4 36.5 1.0
CG2 B:THR555 4.5 39.8 1.0
CE1 B:TYR266 4.6 36.2 1.0
CB B:VAL556 4.7 41.1 1.0
CA B:VAL556 4.7 40.9 1.0
O B:TYR238 4.7 37.4 1.0
NH1 B:ARG649 4.8 37.6 1.0
CA B:ARG649 4.8 36.1 1.0
CB B:TYR266 4.8 35.8 1.0
CG B:TYR266 4.8 35.9 1.0

Chlorine binding site 3 out of 4 in 2x2j

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Chlorine binding site 3 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin


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 the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2043

b:37.4
occ:1.00
 NE C:ARG649 2.9 34.0 1.0
OG1 C:THR555 3.0 34.5 1.0
NH2 C:ARG649 3.1 34.5 1.0
O C:HOH3133 3.4 33.4 1.0
CZ C:ARG649 3.4 34.4 1.0
N C:THR555 3.6 34.7 1.0
CD1 C:TYR266 3.7 33.3 1.0
CG2 C:VAL556 3.8 34.7 1.0
CB C:ARG649 3.9 33.4 1.0
N C:GLY650 3.9 33.0 1.0
N C:VAL556 4.0 34.6 1.0
CD C:ARG649 4.0 33.8 1.0
C C:ARG649 4.1 32.8 1.0
CG C:ARG649 4.1 33.3 1.0
CA C:GLY650 4.2 33.0 1.0
CB C:THR555 4.2 34.6 1.0
CE1 C:TYR266 4.2 33.6 1.0
O C:ARG649 4.2 32.6 1.0
CA C:THR555 4.3 34.6 1.0
C C:MET554 4.4 34.9 1.0
CA C:MET554 4.5 35.0 1.0
N C:MET554 4.5 35.0 1.0
C C:THR555 4.5 34.6 1.0
CA C:ARG649 4.6 33.0 1.0
NH1 C:ARG649 4.8 34.7 1.0
CG C:TYR266 4.8 33.0 1.0
O C:TYR238 4.8 34.0 1.0
CB C:VAL556 4.9 34.7 1.0
CG2 C:THR555 4.9 34.7 1.0
CA C:VAL556 4.9 34.6 1.0
CB C:ALA558 5.0 35.5 1.0

Chlorine binding site 4 out of 4 in 2x2j

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Chlorine binding site 4 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin


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 the Gracilariopsis Lemaneiformis Alpha- 1,4- Glucan Lyase with Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2040

b:35.5
occ:1.00
 OG1 D:THR555 3.0 42.7 1.0
NE D:ARG649 3.0 41.8 1.0
N D:THR555 3.1 43.0 1.0
NH2 D:ARG649 3.2 42.7 1.0
O D:HOH3065 3.4 42.7 1.0
CZ D:ARG649 3.5 42.2 1.0
CG2 D:VAL556 3.7 44.8 1.0
CA D:THR555 3.8 42.9 1.0
CB D:THR555 3.8 42.5 1.0
CD1 D:TYR266 3.9 42.2 1.0
N D:VAL556 3.9 43.8 1.0
CB D:ARG649 3.9 41.0 1.0
O D:ARG649 4.0 41.4 1.0
C D:MET554 4.1 43.2 1.0
C D:ARG649 4.1 41.2 1.0
CD D:ARG649 4.2 41.3 1.0
CG D:ARG649 4.2 41.0 1.0
C D:THR555 4.2 43.4 1.0
CG2 D:THR555 4.2 42.1 1.0
CA D:MET554 4.2 43.4 1.0
N D:GLY650 4.3 41.5 1.0
N D:MET554 4.5 42.9 1.0
CA D:GLY650 4.5 41.9 1.0
CE1 D:TYR266 4.5 42.4 1.0
CA D:ARG649 4.6 40.9 1.0
CA D:VAL556 4.8 44.5 1.0
NH1 D:ARG649 4.8 42.2 1.0
CG D:TYR266 4.8 42.1 1.0
CB D:VAL556 4.9 45.0 1.0
CB D:TYR266 4.9 41.9 1.0
O D:TYR238 5.0 43.6 1.0

Reference:

H.J.Rozeboom, S.Yu, S.Madrid, K.H.Kalk, R.Zhang, B.W.Dijkstra. Crystal Structure of Alpha-1,4-Glucan Lyase, A Unique Glycoside Hydrolase Family Member with A Novel Catalytic Mechanism. J.Biol.Chem. V. 288 26764 2013.
ISSN: ISSN 0021-9258
PubMed: 23902768
DOI: 10.1074/JBC.M113.485896
Page generated: Sat Jul 20 13:29:07 2024

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