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Chlorine in PDB 3e8m: Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily

Protein crystallography data

The structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily, PDB code: 3e8m was solved by Z.Lu, L.Wang, D.Dunaway-Mariano, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.78 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.243, 107.482, 75.093, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 14.1

Other elements in 3e8m:

The structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily (pdb code 3e8m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily, PDB code: 3e8m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3e8m

Go back to Chlorine Binding Sites List in 3e8m
Chlorine binding site 1 out of 5 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl166

b:11.5
occ:1.00
 H A:GLY55 2.3 12.2 1.0
HD21 A:ASN106 2.4 16.6 1.0
HZ1 A:LYS80 2.6 13.3 1.0
N A:GLY55 3.1 10.1 1.0
O A:HOH222 3.1 15.6 1.0
O A:HOH190 3.2 10.8 1.0
HA3 A:GLY55 3.2 12.9 1.0
NZ A:LYS80 3.3 11.1 1.0
HZ2 A:LYS80 3.3 13.3 1.0
ND2 A:ASN106 3.3 13.8 1.0
HE3 A:LYS80 3.3 13.0 1.0
HG1 A:THR54 3.4 12.4 1.0
O A:HOH183 3.6 10.1 1.0
CA A:GLY55 3.6 10.7 1.0
H A:GLU56 3.6 12.3 1.0
HA A:THR54 3.7 11.8 1.0
O A:HOH196 3.7 14.6 1.0
OD2 A:ASP10 3.7 10.2 1.0
CE A:LYS80 3.8 10.8 1.0
HG2 A:GLU56 3.9 13.7 1.0
HD22 A:ASN106 3.9 16.6 1.0
O A:HOH185 3.9 10.9 1.0
OD1 A:ASN106 4.0 12.4 1.0
OG1 A:THR54 4.0 10.3 1.0
HZ3 A:LYS80 4.1 13.3 1.0
O B:HOH191 4.1 13.4 1.0
CG A:ASN106 4.1 12.2 1.0
HE2 A:LYS80 4.1 13.0 1.0
C A:THR54 4.2 9.6 1.0
N A:GLU56 4.2 10.2 1.0
O A:HOH449 4.3 27.8 1.0
CA A:THR54 4.4 9.8 1.0
C A:GLY55 4.4 10.4 1.0
HA2 A:GLY55 4.5 12.9 1.0
CG A:ASP10 4.7 9.8 1.0
O A:HOH252 4.7 19.8 1.0
MG A:MG165 4.8 10.0 1.0
CB A:THR54 4.8 10.2 1.0
O A:HOH414 4.8 38.4 1.0
CG A:GLU56 4.8 11.3 1.0

Chlorine binding site 2 out of 5 in 3e8m

Go back to Chlorine Binding Sites List in 3e8m
Chlorine binding site 2 out of 5 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl167

b:12.7
occ:1.00
 H41 A:PG4172 2.9 30.3 1.0
HE1 D:PHE21 3.2 13.1 1.0
HE1 C:PHE21 3.2 13.0 1.0
O B:HOH201 3.2 15.0 1.0
O A:HOH212 3.2 13.9 1.0
HE2 B:PHE21 3.2 13.3 1.0
O B:HOH216 3.2 15.1 1.0
O C:HOH459 3.2 16.1 1.0
HE2 A:PHE21 3.3 13.3 1.0
HZ C:PHE21 3.4 12.8 1.0
HZ B:PHE21 3.4 12.6 1.0
HZ D:PHE21 3.4 12.8 1.0
HZ A:PHE21 3.5 12.5 1.0
H51 A:PG4172 3.6 29.9 1.0
CE1 D:PHE21 3.9 10.9 1.0
C4 A:PG4172 3.9 25.2 1.0
CE1 C:PHE21 3.9 10.8 1.0
CE2 B:PHE21 3.9 11.0 1.0
CE2 A:PHE21 4.0 11.0 1.0
CZ C:PHE21 4.0 10.6 1.0
H42 A:PG4172 4.0 30.3 1.0
CZ D:PHE21 4.0 10.7 1.0
CZ B:PHE21 4.0 10.4 1.0
HD2 A:LYS31 4.0 13.5 1.0
HD2 C:LYS31 4.0 13.9 1.0
CZ A:PHE21 4.0 10.3 1.0
HD2 D:LYS31 4.0 13.5 1.0
HD2 B:LYS31 4.1 13.3 1.0
HZ1 B:LYS31 4.2 18.0 1.0
HZ2 D:LYS31 4.2 18.1 1.0
HZ2 C:LYS31 4.3 19.2 1.0
HZ1 A:LYS31 4.4 17.6 1.0
C5 A:PG4172 4.5 24.9 1.0
O3 A:PG4172 4.5 26.0 1.0
H62 A:PG4172 5.0 28.1 1.0
CD A:LYS31 5.0 11.2 1.0
CD D:LYS31 5.0 11.2 1.0
CD C:LYS31 5.0 11.6 1.0

Chlorine binding site 3 out of 5 in 3e8m

Go back to Chlorine Binding Sites List in 3e8m
Chlorine binding site 3 out of 5 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl166

b:12.4
occ:1.00
 H B:GLY55 2.3 12.4 1.0
HD21 B:ASN106 2.4 19.3 1.0
HZ1 B:LYS80 2.6 15.0 1.0
N B:GLY55 3.1 10.3 1.0
O B:HOH186 3.1 11.7 1.0
O B:HOH199 3.1 14.5 1.0
HA3 B:GLY55 3.2 13.2 1.0
NZ B:LYS80 3.3 12.5 1.0
ND2 B:ASN106 3.3 16.0 1.0
HZ2 B:LYS80 3.3 15.0 1.0
HE3 B:LYS80 3.4 15.0 1.0
HG1 B:THR54 3.4 12.8 1.0
O B:HOH180 3.6 10.7 1.0
O B:HOH214 3.6 16.6 1.0
CA B:GLY55 3.7 10.9 1.0
HA B:THR54 3.7 11.6 1.0
H B:GLU56 3.8 12.3 1.0
OD2 B:ASP10 3.8 10.7 1.0
CE B:LYS80 3.8 12.5 1.0
O B:HOH188 3.9 11.9 1.0
HD22 B:ASN106 3.9 19.3 1.0
HG2 B:GLU56 4.0 13.4 1.0
OD1 B:ASN106 4.0 13.6 1.0
OG1 B:THR54 4.1 10.6 1.0
HZ3 B:LYS80 4.1 15.0 1.0
O D:HOH297 4.1 15.5 1.0
CG B:ASN106 4.1 13.2 1.0
HE2 B:LYS80 4.1 15.0 1.0
C B:THR54 4.2 9.9 1.0
N B:GLU56 4.3 10.2 1.0
CA B:THR54 4.4 9.6 1.0
C B:GLY55 4.4 10.5 1.0
HA2 B:GLY55 4.5 13.2 1.0
O B:HOH407 4.5 34.0 1.0
O B:HOH230 4.7 20.8 1.0
CG B:ASP10 4.7 10.0 1.0
MG B:MG165 4.8 10.2 1.0
CB B:THR54 4.8 10.0 1.0
CG B:GLU56 4.9 11.2 1.0
OD1 B:ASP10 5.0 11.2 1.0

Chlorine binding site 4 out of 5 in 3e8m

Go back to Chlorine Binding Sites List in 3e8m
Chlorine binding site 4 out of 5 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl166

b:13.1
occ:1.00
 H C:GLY55 2.3 14.1 1.0
HD21 C:ASN106 2.3 20.3 1.0
HZ1 C:LYS80 2.6 15.2 1.0
N C:GLY55 3.1 11.7 1.0
O C:HOH183 3.1 11.3 1.0
O C:HOH201 3.2 15.1 1.0
HA3 C:GLY55 3.2 15.1 1.0
ND2 C:ASN106 3.3 16.9 1.0
NZ C:LYS80 3.3 12.6 1.0
HZ2 C:LYS80 3.3 15.2 1.0
HE3 C:LYS80 3.4 15.6 1.0
HG1 C:THR54 3.4 14.1 1.0
O C:HOH177 3.6 11.4 1.0
O C:HOH206 3.6 17.6 1.0
CA C:GLY55 3.7 12.5 1.0
HA C:THR54 3.7 13.2 1.0
OD2 C:ASP10 3.7 10.7 1.0
H C:GLU56 3.7 14.2 1.0
CE C:LYS80 3.8 13.0 1.0
HD22 C:ASN106 3.9 20.3 1.0
HG2 C:GLU56 3.9 15.0 1.0
O C:HOH185 4.0 12.2 1.0
OD1 C:ASN106 4.0 14.6 1.0
O A:HOH207 4.1 17.9 1.0
OG1 C:THR54 4.1 11.7 1.0
CG C:ASN106 4.1 14.4 1.0
HZ3 C:LYS80 4.1 15.2 1.0
HE2 C:LYS80 4.2 15.6 1.0
C C:THR54 4.2 11.3 1.0
N C:GLU56 4.3 11.8 1.0
CA C:THR54 4.4 10.9 1.0
O C:HOH301 4.4 34.4 1.0
C C:GLY55 4.4 12.3 1.0
HA2 C:GLY55 4.5 15.1 1.0
O C:HOH214 4.6 17.5 1.0
CG C:ASP10 4.7 10.6 1.0
MG C:MG165 4.8 10.7 1.0
CB C:THR54 4.8 11.3 1.0
CG C:GLU56 4.9 12.4 1.0
OD1 C:ASP10 5.0 11.7 1.0

Chlorine binding site 5 out of 5 in 3e8m

Go back to Chlorine Binding Sites List in 3e8m
Chlorine binding site 5 out of 5 in the Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl166

b:12.8
occ:1.00
 H D:GLY55 2.3 13.4 1.0
HD21 D:ASN106 2.4 19.4 1.0
HZ1 D:LYS80 2.6 15.1 1.0
N D:GLY55 3.1 11.1 1.0
O D:HOH308 3.1 16.2 1.0
O D:HOH291 3.1 12.0 1.0
HA3 D:GLY55 3.2 13.8 1.0
HZ2 D:LYS80 3.3 15.1 1.0
NZ D:LYS80 3.3 12.5 1.0
HE3 D:LYS80 3.3 14.5 1.0
ND2 D:ASN106 3.3 16.2 1.0
HG1 D:THR54 3.5 13.4 1.0
O D:HOH285 3.6 11.4 1.0
O D:HOH300 3.6 16.0 1.0
CA D:GLY55 3.7 11.5 1.0
HA D:THR54 3.7 12.7 1.0
H D:GLU56 3.7 13.5 1.0
OD1 D:ASP10 3.7 11.3 1.0
CE D:LYS80 3.8 12.1 1.0
O D:HOH294 3.9 12.2 1.0
HG2 D:GLU56 3.9 14.2 1.0
HD22 D:ASN106 4.0 19.4 1.0
OD1 D:ASN106 4.0 13.7 1.0
O C:HOH204 4.1 15.0 1.0
OG1 D:THR54 4.1 11.1 1.0
CG D:ASN106 4.1 13.3 1.0
HZ3 D:LYS80 4.1 15.1 1.0
HE2 D:LYS80 4.2 14.5 1.0
C D:THR54 4.2 10.6 1.0
N D:GLU56 4.3 11.2 1.0
O D:HOH394 4.4 26.4 1.0
CA D:THR54 4.4 10.6 1.0
C D:GLY55 4.4 11.4 1.0
HA2 D:GLY55 4.5 13.8 1.0
CG D:ASP10 4.7 10.6 1.0
O D:HOH355 4.7 21.0 1.0
MG D:MG165 4.8 10.8 1.0
CB D:THR54 4.9 11.0 1.0
CG D:GLU56 4.9 11.8 1.0
OD2 D:ASP10 5.0 11.9 1.0

Reference:

Z.Lu, L.Wang, D.Dunaway-Mariano, K.N.Allen. Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members. J.Biol.Chem. V. 284 1224 2009.
ISSN: ISSN 0021-9258
PubMed: 18986982
DOI: 10.1074/JBC.M807056200
Page generated: Fri Jul 11 04:44:31 2025

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