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Tungsten in PDB 3e84: 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: 3e84 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) 21.93 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.086, 107.336, 75.310, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.8

Other elements in 3e84:

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

Tungsten Binding Sites:

The binding sites of Tungsten 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 3e84). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 4 binding sites of Tungsten 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: 3e84:
Jump to Tungsten binding site number: 1; 2; 3; 4;

Tungsten binding site 1 out of 4 in 3e84

Go back to Tungsten Binding Sites List in 3e84
Tungsten binding site 1 out of 4 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 Tungsten with other atoms in the W 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:W801

b:30.2
occ:1.00
W A:WO4801 0.0 30.2 1.0
O4 A:WO4801 2.0 30.4 1.0
O3 A:WO4801 2.0 30.1 1.0
O1 A:WO4801 2.0 30.4 1.0
O2 A:WO4801 2.1 30.1 1.0
OD2 A:ASP10 2.5 14.8 1.0
OG1 A:THR54 3.3 26.8 1.0
CG A:ASP10 3.5 17.2 1.0
MG A:MG701 3.7 20.0 1.0
OD2 A:ASP12 3.8 31.9 1.0
OD1 A:ASP10 3.8 18.5 1.0
N A:ASP12 3.9 13.5 1.0
N A:GLY55 4.0 16.9 1.0
O B:HOH882 4.0 24.6 1.0
NZ A:LYS80 4.1 18.5 1.0
CB A:ASP12 4.1 17.1 1.0
O B:HOH857 4.2 37.9 1.0
CB A:THR54 4.3 23.9 1.0
CA A:THR54 4.4 14.8 1.0
N A:ILE11 4.4 14.7 1.0
ND2 A:ASN106 4.4 31.9 1.0
CG A:ASP12 4.4 24.1 1.0
O A:ASP12 4.5 15.1 1.0
CA A:ASP12 4.5 14.7 1.0
O B:HOH1001 4.5 19.6 1.0
C A:THR54 4.7 16.7 1.0
O B:HOH990 4.7 24.4 1.0
N A:GLU56 4.7 16.0 1.0
CG A:GLU56 4.8 22.7 1.0
CA A:GLY55 4.8 21.6 1.0
C A:ILE11 4.8 13.6 1.0
CB A:ASP10 4.9 14.0 1.0
OD1 A:ASN106 4.9 35.5 1.0
CE A:LYS80 5.0 15.4 1.0
CA A:ILE11 5.0 15.7 1.0

Tungsten binding site 2 out of 4 in 3e84

Go back to Tungsten Binding Sites List in 3e84
Tungsten binding site 2 out of 4 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 Tungsten with other atoms in the W 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
B:W802

b:32.1
occ:1.00
W B:WO4802 0.0 32.1 1.0
O2 B:WO4802 2.0 31.9 1.0
O3 B:WO4802 2.0 32.0 1.0
O1 B:WO4802 2.0 32.1 1.0
O4 B:WO4802 2.1 32.4 1.0
OD1 B:ASP10 2.5 16.4 1.0
OG1 B:THR54 3.3 23.4 1.0
O B:HOH900 3.5 36.3 1.0
CG B:ASP10 3.5 20.4 1.0
MG B:MG702 3.6 21.7 1.0
OD2 B:ASP12 3.7 36.0 1.0
OD2 B:ASP10 3.9 20.1 1.0
N B:ASP12 3.9 15.8 1.0
O B:HOH832 4.0 21.8 1.0
O B:HOH1248 4.0 36.3 1.0
N B:GLY55 4.0 16.2 1.0
NZ B:LYS80 4.1 20.6 1.0
CB B:ASP12 4.1 18.2 1.0
CB B:THR54 4.3 22.4 1.0
N B:ILE11 4.4 14.2 1.0
CA B:THR54 4.4 13.3 1.0
CG B:ASP12 4.4 27.1 1.0
ND2 B:ASN106 4.4 31.8 1.0
O B:ASP12 4.4 17.0 1.0
CA B:ASP12 4.5 14.9 1.0
O B:HOH1143 4.7 23.3 1.0
O B:HOH898 4.7 22.1 1.0
C B:THR54 4.7 18.5 1.0
N B:GLU56 4.8 19.4 1.0
C B:ILE11 4.8 18.5 1.0
CB B:ASP10 4.9 13.4 1.0
CE B:LYS80 4.9 14.6 1.0
CA B:GLY55 5.0 17.4 1.0
CG B:GLU56 5.0 23.4 1.0
C B:ASP12 5.0 17.4 1.0
CA B:ILE11 5.0 14.7 1.0

Tungsten binding site 3 out of 4 in 3e84

Go back to Tungsten Binding Sites List in 3e84
Tungsten binding site 3 out of 4 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 Tungsten with other atoms in the W 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
C:W803

b:33.9
occ:1.00
W C:WO4803 0.0 33.9 1.0
O3 C:WO4803 2.0 32.8 1.0
O4 C:WO4803 2.0 33.5 1.0
O2 C:WO4803 2.0 33.3 1.0
O1 C:WO4803 2.0 34.0 1.0
OD2 C:ASP10 2.5 19.1 1.0
OG1 C:THR54 3.3 31.4 1.0
CG C:ASP10 3.5 24.2 1.0
OD1 C:ASP12 3.7 40.4 1.0
MG C:MG703 3.7 24.9 1.0
OD1 C:ASP10 3.7 27.0 1.0
O B:HOH936 3.8 27.1 1.0
N C:ASP12 3.9 17.5 1.0
N C:GLY55 4.0 24.9 1.0
CB C:ASP12 4.1 24.0 1.0
NZ C:LYS80 4.1 26.6 1.0
O B:HOH937 4.2 39.6 1.0
CB C:THR54 4.3 28.9 1.0
ND2 C:ASN106 4.3 31.1 1.0
O B:HOH1215 4.3 42.4 1.0
CA C:THR54 4.3 25.0 1.0
CG C:ASP12 4.3 31.2 1.0
N C:ILE11 4.3 17.7 1.0
O C:ASP12 4.5 18.9 1.0
CA C:ASP12 4.5 18.7 1.0
O B:HOH917 4.6 29.8 1.0
O B:HOH935 4.6 17.6 1.0
C C:THR54 4.7 25.3 1.0
N C:GLU56 4.8 26.7 1.0
CB C:ASP10 4.8 22.1 1.0
C C:ILE11 4.9 20.4 1.0
CA C:GLY55 4.9 22.9 1.0
OD1 C:ASN106 4.9 27.7 0.7
CG C:GLU56 5.0 31.2 1.0
CA C:ILE11 5.0 18.0 1.0

Tungsten binding site 4 out of 4 in 3e84

Go back to Tungsten Binding Sites List in 3e84
Tungsten binding site 4 out of 4 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 Tungsten with other atoms in the W 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
D:W804

b:35.4
occ:1.00
W D:WO4804 0.0 35.4 1.0
O3 D:WO4804 2.0 34.9 1.0
O4 D:WO4804 2.0 35.8 1.0
O2 D:WO4804 2.0 35.6 1.0
O1 D:WO4804 2.0 35.3 1.0
OD1 D:ASP10 2.6 21.7 1.0
OG1 D:THR54 3.5 24.9 1.0
CG D:ASP10 3.5 23.6 1.0
MG D:MG704 3.6 28.2 1.0
OD2 D:ASP12 3.8 41.3 1.0
OD2 D:ASP10 3.8 26.1 1.0
N D:ASP12 3.9 21.4 1.0
N D:GLY55 4.0 30.9 1.0
O B:HOH1093 4.0 22.9 1.0
CB D:ASP12 4.0 19.4 1.0
NZ D:LYS80 4.1 28.1 1.0
CG D:ASP12 4.4 31.3 1.0
CA D:THR54 4.4 26.2 1.0
N D:ILE11 4.4 20.0 1.0
CB D:THR54 4.4 25.8 1.0
ND2 D:ASN106 4.4 34.0 1.0
O D:ASP12 4.5 20.1 1.0
CA D:ASP12 4.5 19.8 1.0
O B:HOH1086 4.6 18.6 1.0
C D:THR54 4.7 28.7 1.0
N D:GLU56 4.7 32.7 1.0
O B:HOH851 4.8 25.6 1.0
CA D:GLY55 4.8 33.0 1.0
C D:ILE11 4.9 20.0 1.0
CB D:ASP10 4.9 22.6 1.0
CG D:GLU56 4.9 29.8 1.0
CE D:LYS80 4.9 25.2 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: Thu Oct 29 07:08:22 2020

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