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Chlorine in PDB 4e38: Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)

Enzymatic activity of Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)

All present enzymatic activity of Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156):
4.1.3.16;

Protein crystallography data

The structure of Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156), PDB code: 4e38 was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, K.N.Allen, D.Dunaway-Mariano, S.C.Almo, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.72 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.503, 80.960, 123.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) (pdb code 4e38). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156), PDB code: 4e38:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4e38

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Chlorine binding site 1 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:35.3
occ:1.00
 O A:HOH522 2.7 62.9 1.0
NZ A:LYS129 2.9 37.5 1.0
O A:HOH437 3.0 40.3 1.0
N A:THR69 3.0 23.0 1.0
N A:PRO90 3.5 19.8 1.0
C A:SER89 3.6 20.4 1.0
CA A:THR69 3.8 22.9 1.0
CD A:PRO90 3.8 24.1 1.0
CG A:PRO90 3.8 22.9 1.0
O A:VAL88 3.9 22.4 1.0
CG1 A:VAL88 3.9 25.1 1.0
CE A:LYS129 3.9 32.5 1.0
CA A:PRO90 3.9 19.9 1.0
OE2 A:GLU41 3.9 38.4 1.0
CA A:SER89 4.0 20.6 1.0
O A:SER89 4.0 21.4 1.0
C A:GLY68 4.0 26.6 1.0
C A:VAL88 4.0 22.5 1.0
CA A:GLY68 4.1 24.0 1.0
N A:SER89 4.1 21.8 1.0
OG1 A:THR69 4.2 30.5 1.0
CB A:PRO90 4.2 23.5 1.0
CB A:VAL88 4.3 26.1 1.0
CD A:LYS129 4.4 28.1 1.0
O A:HOH445 4.4 48.1 1.0
CB A:THR69 4.6 29.5 1.0
CA A:VAL88 4.9 22.9 1.0
C A:THR69 5.0 21.2 1.0

Chlorine binding site 2 out of 7 in 4e38

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Chlorine binding site 2 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:47.9
occ:1.00
 ND2 A:ASN113 3.1 24.3 1.0
ND2 B:ASN113 3.2 22.9 1.0
ND2 C:ASN113 3.2 23.7 1.0
O B:HOH464 3.5 36.2 1.0
O A:HOH429 3.7 37.8 1.0
OG1 B:THR116 3.7 21.2 1.0
O C:HOH474 3.8 38.3 1.0
OG1 A:THR116 3.8 21.8 1.0
OG1 C:THR116 4.0 22.2 1.0
CG A:ASN113 4.1 23.9 1.0
OD1 A:ASN113 4.1 23.7 1.0
CG B:ASN113 4.1 18.9 1.0
OD1 B:ASN113 4.2 21.8 1.0
CG C:ASN113 4.2 21.6 1.0
OD1 C:ASN113 4.3 21.3 1.0
O B:HOH412 4.5 20.9 1.0
O A:HOH515 4.6 23.1 1.0
O C:HOH435 4.7 22.3 1.0
O B:HOH488 4.9 53.3 1.0
O A:HOH455 5.0 48.5 1.0

Chlorine binding site 3 out of 7 in 4e38

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Chlorine binding site 3 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:34.9
occ:1.00
 O C:HOH470 2.7 41.4 1.0
O C:HOH618 2.8 46.2 1.0
N A:ALA135 3.1 21.3 1.0
OG C:SER144 3.2 34.4 1.0
O A:GLY158 3.3 25.8 1.0
C A:GLY158 3.4 25.6 1.0
N A:GLU134 3.5 20.3 1.0
CB A:ALA135 3.6 23.9 1.0
CB A:PRO132 3.6 20.3 1.0
CB A:GLU134 3.7 21.9 1.0
CA A:GLY158 3.9 23.0 1.0
CA A:GLU134 3.9 22.9 1.0
N A:GLY159 3.9 24.6 1.0
CA A:ALA135 3.9 23.8 1.0
C A:GLU134 4.0 22.5 1.0
C A:PRO132 4.0 21.0 1.0
N A:ALA133 4.2 20.0 1.0
CB C:SER144 4.2 23.6 1.0
CA A:GLY159 4.2 26.7 1.0
CA A:PRO132 4.3 21.4 1.0
O A:PRO132 4.3 22.4 1.0
C A:ALA133 4.4 20.9 1.0
OG C:SER140 4.6 16.4 0.1
O C:HOH421 4.6 35.1 1.0
CG A:PRO132 4.6 23.7 1.0
CG A:GLU134 4.7 25.0 1.0
O C:HOH461 4.8 33.2 1.0
CA A:ALA133 4.9 19.5 1.0

Chlorine binding site 4 out of 7 in 4e38

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Chlorine binding site 4 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:38.4
occ:1.00
 NZ B:LYS129 2.9 38.9 1.0
N B:THR69 3.0 20.3 1.0
O B:HOH540 3.1 32.7 1.0
N B:PRO90 3.5 21.2 1.0
C B:SER89 3.6 20.1 1.0
O B:VAL88 3.6 20.8 1.0
CA B:THR69 3.7 24.4 1.0
CG1 B:VAL88 3.8 23.0 1.0
OE2 B:GLU41 3.8 39.8 1.0
CD B:PRO90 3.8 24.8 1.0
CG B:PRO90 3.8 27.2 1.0
C B:VAL88 3.9 20.0 1.0
CA B:SER89 3.9 21.6 1.0
CA B:PRO90 4.0 22.5 1.0
C B:GLY68 4.0 24.0 1.0
CE B:LYS129 4.0 30.2 1.0
CA B:GLY68 4.0 22.7 1.0
N B:SER89 4.1 21.7 1.0
O B:SER89 4.1 22.8 1.0
CB B:VAL88 4.2 24.0 1.0
OG1 B:THR69 4.2 31.2 1.0
CB B:PRO90 4.4 24.0 1.0
CD B:LYS129 4.5 22.1 1.0
CB B:THR69 4.6 27.2 1.0
CA B:VAL88 4.8 21.2 1.0
CD B:GLU41 4.8 33.3 1.0
C B:THR69 4.9 23.0 1.0
N B:ILE70 4.9 23.1 1.0

Chlorine binding site 5 out of 7 in 4e38

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Chlorine binding site 5 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:36.7
occ:1.00
 O A:HOH440 2.8 40.0 1.0
O A:HOH420 2.8 36.3 1.0
N B:ALA135 3.0 20.5 1.0
O B:GLY158 3.3 24.4 1.0
C B:GLY158 3.4 21.3 1.0
N B:GLU134 3.4 23.3 1.0
CB B:ALA135 3.6 23.3 1.0
CB B:GLU134 3.6 22.6 1.0
CB B:PRO132 3.6 21.9 1.0
OG A:SER144 3.8 31.5 1.0
CA B:GLU134 3.8 21.9 1.0
C B:GLU134 3.9 22.1 1.0
CA B:ALA135 3.9 22.9 1.0
N B:GLY159 3.9 22.5 1.0
CA B:GLY158 3.9 21.3 1.0
C B:PRO132 4.0 19.6 1.0
N B:ALA133 4.0 18.8 1.0
CA B:GLY159 4.2 27.7 1.0
OG A:SER140 4.2 35.7 0.6
CA B:PRO132 4.3 20.1 1.0
O B:PRO132 4.3 19.6 1.0
C B:ALA133 4.4 21.2 1.0
O A:HOH442 4.5 38.6 1.0
CG B:PRO132 4.6 26.1 1.0
O A:HOH486 4.6 54.6 1.0
CG B:GLU134 4.7 22.7 1.0
CA B:ALA133 4.8 19.6 1.0
O A:HOH543 4.9 38.9 1.0
CB A:SER144 5.0 27.7 1.0

Chlorine binding site 6 out of 7 in 4e38

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Chlorine binding site 6 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:35.8
occ:1.00
 NZ C:LYS129 2.7 32.8 1.0
N C:THR69 3.0 19.0 1.0
O C:HOH576 3.1 41.7 1.0
N C:PRO90 3.4 18.8 1.0
C C:SER89 3.5 21.6 1.0
CA C:THR69 3.6 21.6 1.0
CD C:PRO90 3.7 21.4 1.0
CG C:PRO90 3.7 25.7 1.0
O C:VAL88 3.8 19.5 1.0
CA C:PRO90 3.9 17.3 1.0
CA C:SER89 3.9 18.9 1.0
O C:SER89 4.0 20.8 1.0
CG1 C:VAL88 4.0 27.6 1.0
CE C:LYS129 4.0 28.3 1.0
C C:GLY68 4.0 19.8 1.0
C C:VAL88 4.1 17.8 1.0
O C:HOH606 4.1 47.5 1.0
CB C:PRO90 4.1 22.4 1.0
OG1 C:THR69 4.2 28.6 1.0
N C:SER89 4.2 19.5 1.0
CA C:GLY68 4.2 19.4 1.0
OE2 C:GLU41 4.4 31.4 1.0
CB C:VAL88 4.5 23.0 1.0
CB C:THR69 4.5 27.4 1.0
CD C:LYS129 4.5 21.6 1.0
C C:THR69 4.8 21.4 1.0
N C:ILE70 4.9 21.6 1.0
CA C:VAL88 4.9 17.8 1.0

Chlorine binding site 7 out of 7 in 4e38

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Chlorine binding site 7 out of 7 in the Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156)


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 Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:33.8
occ:1.00
 O B:HOH541 2.7 46.1 1.0
O B:HOH426 2.8 40.8 1.0
N C:ALA135 3.1 20.5 1.0
O C:GLY158 3.3 21.4 1.0
C C:GLY158 3.4 21.7 1.0
N C:GLU134 3.5 20.4 1.0
CB C:PRO132 3.6 22.9 1.0
CB C:ALA135 3.6 21.3 1.0
CB C:GLU134 3.7 22.7 1.0
OG B:SER144 3.8 33.1 1.0
CA C:GLY158 3.9 21.6 1.0
N C:GLY159 3.9 21.6 1.0
CA C:GLU134 3.9 21.0 1.0
C C:GLU134 3.9 21.4 1.0
CA C:ALA135 3.9 22.0 1.0
C C:PRO132 4.0 22.2 1.0
N C:ALA133 4.1 19.1 1.0
CA C:GLY159 4.3 25.8 1.0
O B:HOH457 4.3 39.0 1.0
OG B:SER140 4.3 39.7 0.6
CA C:PRO132 4.3 19.9 1.0
O C:PRO132 4.4 20.9 1.0
C C:ALA133 4.4 19.5 1.0
CG C:PRO132 4.6 23.1 1.0
O C:HOH491 4.7 40.4 1.0
CG C:GLU134 4.7 22.5 1.0
CA C:ALA133 4.8 18.8 1.0
O B:HOH543 4.9 34.7 1.0
CB B:SER144 4.9 32.2 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, K.N.Allen, D.Dunaway-Mariano, J.A.Gerlt, S.C.Almo. Crystal Structure of Probable Keto-Hydroxyglutarate-Aldolase From Vibrionales Bacterium Swat-3 (Target Efi-502156) To Be Published.
Page generated: Sat Dec 12 10:33:27 2020

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