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Chlorine in PDB 3w5f: Crystal Structure of Tomato Beta-Galactosidase 4

Enzymatic activity of Crystal Structure of Tomato Beta-Galactosidase 4

All present enzymatic activity of Crystal Structure of Tomato Beta-Galactosidase 4:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Tomato Beta-Galactosidase 4, PDB code: 3w5f was solved by M.Eda, T.Tada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.09 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.820, 96.300, 159.267, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Tomato Beta-Galactosidase 4 (pdb code 3w5f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Tomato Beta-Galactosidase 4, PDB code: 3w5f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3w5f

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Chlorine binding site 1 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


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 Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl807

b:8.4
occ:1.00
 OG A:SER45 3.1 7.7 1.0
NE2 A:HIS47 3.1 6.6 1.0
NH2 A:ARG112 3.2 8.1 1.0
NE A:ARG112 3.3 7.5 1.0
N A:TYR74 3.7 7.4 1.0
CA A:THR73 3.7 7.3 1.0
CG A:GLU72 3.7 7.1 1.0
CB A:SER45 3.7 7.3 1.0
CD2 A:HIS47 3.7 7.0 1.0
CZ A:ARG112 3.7 7.6 1.0
OE1 A:GLU72 3.8 8.0 1.0
C A:THR73 3.8 7.2 1.0
N A:THR73 3.9 7.0 1.0
O A:GLU72 3.9 7.4 1.0
C A:GLU72 3.9 6.9 1.0
CD2 A:TYR74 4.0 7.5 1.0
CE2 A:TYR289 4.1 7.5 1.0
CD2 A:TYR289 4.2 6.5 1.0
CE2 A:TYR74 4.2 6.6 1.0
CD A:GLU72 4.2 7.0 1.0
CB A:GLU72 4.3 6.8 1.0
CG A:TYR74 4.3 6.5 1.0
CE1 A:HIS47 4.3 7.2 1.0
CD A:ARG112 4.5 7.4 1.0
CA A:SER45 4.6 6.3 1.0
CZ A:TYR74 4.6 7.4 1.0
O A:THR73 4.6 7.3 1.0
CG A:ARG112 4.7 6.4 1.0
CD1 A:TYR74 4.7 6.9 1.0
CA A:TYR74 4.7 7.5 1.0
CA A:GLU72 4.7 6.0 1.0
CE1 A:TYR74 4.8 6.9 1.0
CB A:TYR74 4.9 7.0 1.0

Chlorine binding site 2 out of 9 in 3w5f

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Chlorine binding site 2 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


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 Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl808

b:27.3
occ:1.00
 O A:HOH1444 3.1 32.6 1.0
N A:GLY210 3.2 10.9 1.0
CA A:GLY210 3.4 11.7 1.0
O A:HOH972 3.6 12.6 1.0
CA A:LYS208 3.8 12.5 1.0
C A:LYS208 3.9 12.3 1.0
N A:THR209 4.0 10.5 1.0
O A:HOH941 4.1 11.2 1.0
CD A:LYS208 4.2 24.3 1.0
C A:GLY210 4.3 11.1 1.0
CB A:LYS208 4.3 16.4 1.0
C A:THR209 4.4 11.2 1.0
O A:LYS208 4.6 14.1 1.0
N A:VAL211 4.7 9.5 1.0
CA A:THR209 4.8 10.5 1.0
O A:HOH1206 4.9 27.0 1.0
CG A:LYS208 4.9 21.1 1.0
N A:LYS208 5.0 11.4 1.0
O A:GLY210 5.0 11.6 1.0

Chlorine binding site 3 out of 9 in 3w5f

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Chlorine binding site 3 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


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 Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl809

b:21.1
occ:1.00
 OG A:SER695 2.9 18.1 1.0
OG1 A:THR52 2.9 15.4 1.0
O A:HOH1323 3.0 26.8 1.0
O A:HOH1664 3.2 37.6 1.0
N A:SER695 3.2 16.2 1.0
CB A:SER695 3.4 16.3 1.0
N A:ARG694 3.6 20.2 1.0
CB A:PRO693 3.6 14.6 1.0
CG A:MET55 3.7 13.6 1.0
C A:PRO693 3.9 16.6 1.0
CA A:SER695 3.9 16.0 1.0
CB A:THR52 4.0 12.3 1.0
CA A:PRO693 4.0 14.4 1.0
NE2 A:GLN54 4.0 33.5 1.0
CG2 A:THR52 4.0 14.3 1.0
CB A:GLN54 4.1 18.3 1.0
CA A:ARG694 4.2 18.5 1.0
C A:ARG694 4.2 17.9 1.0
SD A:MET55 4.2 13.2 1.0
CB A:ARG694 4.2 20.4 1.0
CG A:GLN54 4.2 23.9 1.0
CD A:GLN54 4.4 29.3 1.0
N A:MET55 4.6 12.5 1.0
O A:PRO693 4.7 16.9 1.0
O A:HOH1030 4.8 18.6 1.0
CB A:MET55 4.9 12.3 1.0
CG A:PRO693 4.9 14.4 1.0
C A:GLN54 5.0 13.4 1.0
C A:SER695 5.0 16.7 1.0
CA A:GLN54 5.0 13.5 1.0

Chlorine binding site 4 out of 9 in 3w5f

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Chlorine binding site 4 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


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 Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl810

b:47.0
occ:1.00
 O A:HOH1545 3.4 32.4 1.0
N A:ARG92 3.8 11.3 1.0
O A:HOH1572 3.8 38.6 1.0
NE1 A:TRP696 3.9 16.8 1.0
NH1 A:ARG92 3.9 15.8 1.0
CB A:ARG92 4.0 11.4 1.0
CG A:ARG92 4.1 11.9 1.0
CD A:PRO53 4.3 11.4 1.0
CD A:ARG92 4.3 12.3 1.0
O A:HOH1722 4.4 42.0 1.0
CA A:ARG92 4.5 10.7 1.0
CE2 A:TRP696 4.5 15.2 1.0
CA A:GLY91 4.5 11.4 1.0
C A:GLY91 4.5 10.6 1.0
CZ2 A:TRP696 4.6 15.6 1.0
CD1 A:TRP696 4.8 16.9 1.0
CZ A:ARG92 4.9 15.7 1.0
O A:HOH1715 4.9 47.3 1.0
OE2 A:GLU649 4.9 21.1 1.0

Chlorine binding site 5 out of 9 in 3w5f

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Chlorine binding site 5 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl807

b:8.7
occ:1.00
 NE2 B:HIS47 3.1 7.3 1.0
OG B:SER45 3.1 7.6 1.0
NH2 B:ARG112 3.2 8.4 1.0
NE B:ARG112 3.3 8.4 1.0
N B:TYR74 3.7 7.7 1.0
CA B:THR73 3.7 7.6 1.0
CZ B:ARG112 3.7 8.4 1.0
CG B:GLU72 3.7 7.5 1.0
CB B:SER45 3.7 6.8 1.0
CD2 B:HIS47 3.7 7.2 1.0
OE1 B:GLU72 3.8 8.3 1.0
C B:THR73 3.9 7.8 1.0
CD2 B:TYR74 3.9 8.0 1.0
O B:GLU72 4.0 7.8 1.0
N B:THR73 4.0 7.6 1.0
CE2 B:TYR289 4.0 6.9 1.0
C B:GLU72 4.0 7.2 1.0
CE2 B:TYR74 4.1 8.3 1.0
CD2 B:TYR289 4.1 6.7 1.0
CE1 B:HIS47 4.2 7.0 1.0
CG B:TYR74 4.2 7.6 1.0
CD B:GLU72 4.3 7.7 1.0
CB B:GLU72 4.4 6.9 1.0
CD B:ARG112 4.5 8.4 1.0
CZ B:TYR74 4.6 8.2 1.0
CA B:SER45 4.6 7.0 1.0
CD1 B:TYR74 4.7 8.0 1.0
CA B:TYR74 4.7 7.6 1.0
O B:THR73 4.7 8.1 1.0
CG B:ARG112 4.7 8.3 1.0
CB B:TYR74 4.8 7.5 1.0
CE1 B:TYR74 4.8 8.1 1.0
CA B:GLU72 4.9 6.9 1.0

Chlorine binding site 6 out of 9 in 3w5f

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Chlorine binding site 6 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl808

b:32.5
occ:1.00
 N B:GLU219 3.6 12.2 1.0
O B:HOH1754 3.7 36.8 1.0
CG B:GLU219 3.7 25.3 1.0
O B:HOH1128 3.8 17.5 1.0
CA B:GLY183 3.8 11.8 1.0
O B:LYS217 3.8 11.3 1.0
C B:LYS217 3.9 11.0 1.0
N B:GLN218 4.1 10.6 1.0
CB B:GLU219 4.1 16.5 1.0
C B:GLY183 4.1 12.9 1.0
CA B:GLN218 4.2 11.4 1.0
C B:GLN218 4.4 11.0 1.0
O B:HOH1111 4.4 20.6 1.0
CA B:GLU219 4.4 12.4 1.0
O B:HOH1211 4.5 22.5 1.0
CD B:PRO184 4.5 11.6 1.0
N B:PRO184 4.5 12.1 1.0
CD B:GLU219 4.6 35.1 1.0
O B:GLY183 4.6 14.2 1.0
CA B:LYS217 4.7 10.4 1.0
N B:GLY183 4.9 11.1 1.0
OE1 B:GLU219 4.9 33.9 1.0
CB B:LYS217 5.0 13.9 1.0

Chlorine binding site 7 out of 9 in 3w5f

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Chlorine binding site 7 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl809

b:13.3
occ:1.00
 OG B:SER695 3.0 14.4 1.0
O B:HOH1034 3.1 14.9 1.0
OG1 B:THR52 3.1 11.8 1.0
N B:SER695 3.3 11.7 1.0
CB B:SER695 3.4 13.3 1.0
N B:ARG694 3.7 11.2 1.0
CB B:PRO693 3.8 9.2 1.0
CG B:MET55 3.8 9.8 1.0
CB B:GLN54 3.9 14.2 1.0
CA B:SER695 4.0 12.8 1.0
CB B:THR52 4.1 10.1 1.0
C B:PRO693 4.1 9.7 1.0
CG2 B:THR52 4.2 10.9 1.0
CA B:PRO693 4.2 9.6 1.0
C B:ARG694 4.3 11.1 1.0
SD B:MET55 4.4 11.2 1.0
CA B:ARG694 4.4 10.8 1.0
N B:MET55 4.4 10.0 1.0
CB B:ARG694 4.6 12.1 1.0
C B:GLN54 4.7 11.3 1.0
O B:HOH1158 4.8 23.5 1.0
CA B:GLN54 4.8 11.7 1.0
O B:HOH1106 4.8 19.5 1.0
O B:PRO693 4.9 10.7 1.0
CG B:GLN54 4.9 16.7 1.0
CB B:MET55 4.9 9.3 1.0

Chlorine binding site 8 out of 9 in 3w5f

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Chlorine binding site 8 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl810

b:29.9
occ:1.00
 O B:HOH1476 3.0 30.2 1.0
NE1 B:TRP696 3.1 13.0 1.0
O B:HOH1106 3.3 19.5 1.0
CD B:PRO53 3.6 12.3 1.0
CB B:THR52 3.8 10.1 1.0
CG2 B:THR52 3.8 10.9 1.0
CD1 B:TRP696 4.0 13.1 1.0
CE2 B:TRP696 4.0 12.8 1.0
CA B:THR52 4.3 9.2 1.0
CZ2 B:TRP696 4.3 13.8 1.0
O B:HOH1101 4.5 21.3 1.0
N B:PRO53 4.6 10.4 1.0
CG B:PRO53 4.6 11.6 1.0
CB B:ARG92 4.7 15.4 1.0
N B:ARG92 5.0 12.2 1.0
OG B:SER695 5.0 14.4 1.0
OG1 B:THR52 5.0 11.8 1.0
O B:HOH1282 5.0 22.5 1.0

Chlorine binding site 9 out of 9 in 3w5f

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Chlorine binding site 9 out of 9 in the Crystal Structure of Tomato Beta-Galactosidase 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Tomato Beta-Galactosidase 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl811

b:31.8
occ:1.00
 O B:HOH1421 2.7 31.8 1.0
NH1 B:ARG721 3.2 15.7 1.0
CB B:ALA427 3.5 20.3 1.0
CD B:ARG721 3.8 11.5 1.0
O B:HOH1741 3.9 45.0 1.0
CB B:PRO626 4.1 17.5 1.0
N B:GLY428 4.1 27.6 1.0
CA B:ALA427 4.1 16.9 1.0
N B:GLY627 4.2 18.9 1.0
CZ B:ARG721 4.2 13.9 1.0
CA B:PRO626 4.4 16.5 1.0
NE B:ARG721 4.5 11.9 1.0
O B:HOH1680 4.5 38.0 1.0
C B:ALA427 4.5 22.1 1.0
C B:PRO626 4.8 15.8 1.0

Reference:

M.Eda, T.Tada. Crystal Structure of Tomato Beta-Galactosidase 4 To Be Published.
Page generated: Fri Jul 11 11:54:07 2025

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