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Chlorine in PDB 7dl7: The Wild-Type Structure of 3,5-Dahdhcca

Enzymatic activity of The Wild-Type Structure of 3,5-Dahdhcca

All present enzymatic activity of The Wild-Type Structure of 3,5-Dahdhcca:
1.4.1.11;

Protein crystallography data

The structure of The Wild-Type Structure of 3,5-Dahdhcca, PDB code: 7dl7 was solved by N.Liu, L.Wu, D.M.Zhu, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.98 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 89.604, 89.889, 123.693, 87.33, 70.97, 80.56
R / Rfree (%) 22.6 / 25.7

Other elements in 7dl7:

The structure of The Wild-Type Structure of 3,5-Dahdhcca also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Wild-Type Structure of 3,5-Dahdhcca (pdb code 7dl7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The Wild-Type Structure of 3,5-Dahdhcca, PDB code: 7dl7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7dl7

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Chlorine binding site 1 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:62.9
occ:1.00
 N A:ALA251 3.5 33.9 1.0
O A:THR249 3.8 41.6 1.0
OD1 A:ASP250 3.9 44.7 1.0
CA A:ASP250 4.1 38.2 1.0
CB A:ALA251 4.2 37.1 1.0
C A:ASP250 4.2 38.9 1.0
N A:ILE252 4.2 41.6 1.0
CD1 A:ILE252 4.2 43.9 1.0
CA A:ALA251 4.3 39.7 1.0
CD1 F:LEU20 4.5 40.0 1.0
O F:GLY18 4.5 53.1 1.0
CG1 A:ILE252 4.5 41.0 1.0
CG1 F:VAL19 4.6 54.2 1.0
CG F:LEU20 4.7 48.1 1.0
CA F:VAL19 4.7 43.0 1.0
N F:LEU20 4.7 44.3 1.0
C A:THR249 4.7 44.5 1.0
C A:ALA251 4.8 41.5 1.0
CG A:ASP250 4.8 44.2 1.0
N A:ASP250 4.9 44.4 1.0
CB A:ILE252 5.0 45.7 1.0

Chlorine binding site 2 out of 8 in 7dl7

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Chlorine binding site 2 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl406

b:76.9
occ:1.00
 OE1 C:GLU69 3.2 72.5 1.0
N C:VAL139 3.3 68.7 1.0
CA C:LYS138 3.6 58.1 1.0
CB C:GLU69 3.7 63.1 1.0
C C:LYS138 3.9 64.4 1.0
CD C:LYS138 4.0 72.7 1.0
CD C:GLU69 4.2 66.7 1.0
CB C:LYS138 4.3 57.9 1.0
CG C:LYS138 4.3 66.7 1.0
CA C:VAL139 4.4 61.9 1.0
CB C:VAL139 4.4 66.4 1.0
CG C:GLU69 4.4 63.4 1.0
O C:LYS137 4.4 62.1 1.0
N C:LYS138 4.5 62.6 1.0
O C:VAL139 4.5 68.6 1.0
O C:GLU69 4.6 66.4 1.0
C C:GLU69 4.6 63.9 1.0
CG2 C:VAL139 4.7 55.0 1.0
CA C:GLU69 4.7 66.6 1.0
CE C:LYS138 4.7 65.4 1.0
NZ C:LYS138 4.8 71.4 1.0
C C:LYS137 4.9 61.7 1.0
C C:VAL139 4.9 63.9 1.0

Chlorine binding site 3 out of 8 in 7dl7

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Chlorine binding site 3 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:61.1
occ:1.00
 ND2 D:ASN339 2.7 49.8 1.0
O D:ALA237 3.4 48.4 1.0
CG D:ASN339 3.7 54.2 1.0
C D:THR238 3.9 42.0 1.0
OD1 D:ASN339 3.9 63.2 1.0
CA D:THR238 4.0 41.6 1.0
O D:THR238 4.0 41.9 1.0
N D:GLY239 4.3 44.7 1.0
C D:ALA237 4.4 48.3 1.0
CB D:ALA210 4.6 36.6 1.0
N D:THR238 4.6 49.0 1.0
CA D:GLY239 4.8 42.0 1.0
CB D:ASN339 5.0 52.3 1.0

Chlorine binding site 4 out of 8 in 7dl7

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Chlorine binding site 4 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:71.5
occ:1.00
 O D:HOH522 4.4 37.8 1.0
CB E:SER301 4.4 35.5 1.0
CA E:SER301 4.5 42.2 1.0
O E:THR300 4.6 39.7 1.0
OG E:SER301 4.7 39.8 1.0
CE1 A:HIS65 5.0 52.2 1.0
ND1 A:HIS65 5.0 51.1 1.0

Chlorine binding site 5 out of 8 in 7dl7

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Chlorine binding site 5 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl405

b:72.0
occ:1.00
 OD1 F:ASP268 3.0 32.8 1.0
NZ F:LYS288 3.2 45.9 1.0
OD2 F:ASP268 3.7 40.9 1.0
CG F:ASP268 3.8 37.7 1.0
O F:HOH545 4.0 35.3 1.0
O F:ASP192 4.1 27.6 1.0
O F:HOH514 4.3 33.9 1.0
CE F:LYS288 4.5 41.3 1.0
OG1 F:THR194 4.6 35.1 1.0
N F:THR194 4.6 34.3 1.0
CB F:THR194 5.0 33.8 1.0
CA F:ASP193 5.0 34.3 1.0

Chlorine binding site 6 out of 8 in 7dl7

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Chlorine binding site 6 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl406

b:71.5
occ:1.00
 O G:GLY220 3.4 38.8 1.0
NZ G:LYS221 3.8 47.2 1.0
OD2 G:ASP241 4.1 47.3 1.0
O G:HOH503 4.3 34.5 1.0
CG G:ASP241 4.3 43.0 1.0
C G:GLY220 4.3 38.3 1.0
CA G:LYS221 4.4 41.9 1.0
CB G:LYS221 4.4 39.0 1.0
CB G:ASP241 4.5 42.3 1.0
CG G:LYS221 4.5 36.1 1.0
CE G:LYS221 4.7 45.4 1.0
N G:LYS221 4.8 40.7 1.0
OD1 G:ASP241 4.9 44.1 1.0
O G:ILE218 4.9 30.8 1.0
NZ G:LYS213 5.0 35.8 1.0

Chlorine binding site 7 out of 8 in 7dl7

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Chlorine binding site 7 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl406

b:69.1
occ:1.00
 CD2 H:HIS65 3.5 49.8 1.0
O H:ASP67 3.6 61.1 1.0
CB H:ASP67 3.9 56.8 1.0
N H:ASP67 4.0 66.3 1.0
CB H:HIS65 4.1 55.3 1.0
CG H:HIS65 4.2 53.3 1.0
CA H:ASP67 4.3 62.1 1.0
CA H:HIS65 4.3 56.9 1.0
N H:GLN66 4.3 61.4 1.0
C H:ASP67 4.4 53.0 1.0
CB H:ALA71 4.5 50.0 1.0
NE2 H:HIS65 4.7 54.1 1.0
C H:HIS65 4.8 55.6 1.0
N H:ALA71 4.9 47.8 1.0

Chlorine binding site 8 out of 8 in 7dl7

Go back to Chlorine Binding Sites List in 7dl7
Chlorine binding site 8 out of 8 in the The Wild-Type Structure of 3,5-Dahdhcca


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Wild-Type Structure of 3,5-Dahdhcca within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl407

b:73.7
occ:1.00
 CA H:LYS107 3.8 50.5 1.0
O H:LYS107 3.9 48.8 1.0
C H:LYS107 3.9 50.9 1.0
O H:PHE108 4.2 42.4 1.0
O H:ASP106 4.4 44.4 1.0
CB H:LYS107 4.5 46.2 1.0
N H:PHE108 4.6 45.6 1.0
C H:PHE108 4.6 43.1 1.0
CG H:LYS107 5.0 56.1 1.0
N H:LYS107 5.0 49.9 1.0

Reference:

N.Liu, L.Wu, J.Feng, X.Sheng, J.Li, X.Chen, J.Li, W.Liu, J.Zhou, Q.Wu, D.Zhu. Crystal Structures and Catalytic Mechanism of L-Erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering For Asymmetric Synthesis of Beta-Amino Acids. Angew.Chem.Int.Ed.Engl. V. 60 10203 2021.
ISSN: ESSN 1521-3773
PubMed: 33624917
DOI: 10.1002/ANIE.202017225
Page generated: Sun Jul 13 00:08:39 2025

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