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Chlorine in PDB 3hyc: Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form

Enzymatic activity of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form

All present enzymatic activity of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form, PDB code: 3hyc was solved by O.V.Tsodikov, T.Biswas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.08 / 3.06
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 122.219, 122.219, 202.173, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 25.7

Other elements in 3hyc:

The structure of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form (pdb code 3hyc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form, PDB code: 3hyc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3hyc

Go back to Chlorine Binding Sites List in 3hyc
Chlorine binding site 1 out of 5 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


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 E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:40.0
occ:1.00
 NZ B:LYS102 3.1 36.0 1.0
OD2 B:ASP32 3.4 37.5 1.0
CE B:LYS102 3.5 36.3 1.0
N B:GLY77 3.6 36.3 1.0
O A:SER187 3.7 36.4 1.0
MG B:MG202 3.7 14.8 1.0
CG2 B:ILE128 3.8 36.6 1.0
CB A:SER187 4.0 36.5 1.0
CG B:ASP32 4.1 37.1 1.0
CA B:GLY77 4.2 36.3 1.0
OD1 B:ASP32 4.2 37.3 1.0
C A:SER187 4.5 36.5 1.0
C B:THR76 4.5 36.3 1.0
CA B:THR76 4.6 36.3 1.0
CA A:SER187 4.6 36.5 1.0
OG1 B:THR76 4.6 36.6 1.0
OD1 B:ASP129 4.7 36.7 1.0
N A:SER187 4.8 36.5 1.0
OG A:SER187 5.0 36.4 1.0
CD B:LYS102 5.0 36.4 1.0

Chlorine binding site 2 out of 5 in 3hyc

Go back to Chlorine Binding Sites List in 3hyc
Chlorine binding site 2 out of 5 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


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 E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl205

b:40.0
occ:1.00
 NZ D:LYS102 3.0 36.4 1.0
N D:GLY77 3.2 36.5 1.0
OD2 D:ASP32 3.4 36.9 1.0
CE D:LYS102 3.5 36.5 1.0
CG2 D:ILE128 3.8 36.4 1.0
O C:SER187 3.8 36.6 1.0
CA D:GLY77 3.9 36.5 1.0
OG1 D:THR76 4.0 36.8 1.0
C D:THR76 4.1 36.5 1.0
CA D:THR76 4.1 36.5 1.0
MG D:MG204 4.1 23.0 1.0
CB C:SER187 4.2 36.6 1.0
CG D:ASP32 4.3 36.8 1.0
OD1 D:ASP32 4.5 36.8 1.0
C C:SER187 4.6 36.7 1.0
CB D:THR76 4.7 36.6 1.0
CA C:SER187 4.8 36.6 1.0
N C:SER187 4.8 36.6 1.0
OD1 D:ASP129 4.8 36.7 1.0
CD D:LYS102 4.9 36.6 1.0

Chlorine binding site 3 out of 5 in 3hyc

Go back to Chlorine Binding Sites List in 3hyc
Chlorine binding site 3 out of 5 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


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 E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl189

b:40.0
occ:1.00
 NZ F:LYS102 3.1 36.1 1.0
CE F:LYS102 3.3 36.1 1.0
OD2 F:ASP32 3.4 36.7 1.0
N F:GLY77 3.4 36.7 1.0
CG2 F:ILE128 3.6 36.3 1.0
O E:SER187 3.7 36.9 1.0
CA F:GLY77 3.9 36.7 1.0
MG F:MG206 4.0 37.0 1.0
CB E:SER187 4.0 37.1 1.0
CG F:ASP32 4.1 36.7 1.0
OD1 F:ASP32 4.3 36.4 1.0
C F:THR76 4.4 36.7 1.0
CA F:THR76 4.5 36.7 1.0
C E:SER187 4.5 37.0 1.0
OG1 F:THR76 4.5 36.8 1.0
CA E:SER187 4.7 37.0 1.0
OD1 F:ASP129 4.8 36.8 1.0
N E:SER187 4.8 37.0 1.0
CD F:LYS102 4.8 36.4 1.0
CB F:ILE128 4.8 36.4 1.0
CG1 F:ILE128 5.0 36.4 1.0

Chlorine binding site 4 out of 5 in 3hyc

Go back to Chlorine Binding Sites List in 3hyc
Chlorine binding site 4 out of 5 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


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 E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl189

b:40.0
occ:1.00
 OD2 G:ASP32 2.8 36.3 1.0
CE G:LYS102 3.3 37.4 1.0
NZ G:LYS102 3.4 37.6 1.0
CD1 G:ILE128 3.6 37.1 1.0
CG G:ASP32 3.6 36.3 1.0
OD1 G:ASP32 3.8 36.1 1.0
OD1 G:ASP129 3.9 37.2 1.0
MG G:MG207 4.1 30.0 1.0
CG1 G:ILE128 4.5 36.9 1.0
CD G:LYS102 4.8 37.2 1.0
O G:ILE75 4.8 37.0 1.0
CB F:SER187 4.9 37.1 1.0
CG G:ASP129 4.9 36.9 1.0
CB G:ASP32 4.9 36.4 1.0

Chlorine binding site 5 out of 5 in 3hyc

Go back to Chlorine Binding Sites List in 3hyc
Chlorine binding site 5 out of 5 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


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 E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl189

b:40.0
occ:1.00
 N H:GLY77 3.1 36.7 1.0
NZ H:LYS102 3.1 35.4 1.0
CE H:LYS102 3.2 35.9 1.0
CA H:GLY77 3.5 36.7 1.0
OD2 H:ASP32 3.8 37.2 1.0
CG2 H:ILE128 3.8 36.7 1.0
O G:SER187 4.0 36.8 1.0
C H:THR76 4.1 36.7 1.0
CB G:SER187 4.2 36.7 1.0
MG H:MG208 4.4 32.4 1.0
CA H:THR76 4.4 36.7 1.0
CD H:LYS102 4.5 36.1 1.0
OD1 H:ASP129 4.7 37.4 1.0
CG H:ASP32 4.7 36.7 1.0
C G:SER187 4.7 36.7 1.0
N G:SER187 4.8 36.7 1.0
C H:GLY77 4.8 36.8 1.0
OG1 H:THR76 4.8 37.0 1.0
CA G:SER187 4.8 36.7 1.0

Reference:

T.Biswas, L.Yi, P.Aggarwal, J.Wu, J.R.Rubin, J.A.Stuckey, R.W.Woodard, O.V.Tsodikov. The Tail of Kdsc: Conformational Changes Control the Activity of A Haloacid Dehalogenase Superfamily Phosphatase. J.Biol.Chem. V. 284 30594 2009.
ISSN: ISSN 0021-9258
PubMed: 19726684
DOI: 10.1074/JBC.M109.012278
Page generated: Sat Dec 12 09:46:41 2020

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