Atomistry » Magnesium » PDB 3hx0-3i5x » 3hyc
Atomistry »
  Magnesium »
    PDB 3hx0-3i5x »
      3hyc »

Magnesium 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:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form, PDB code: 3hyc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 1 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg201

b:23.5
occ:1.00
O A:ASP34 2.3 37.0 1.0
OD2 A:ASP125 2.4 35.8 1.0
OD1 A:ASP32 2.4 36.4 1.0
CG A:ASP32 3.4 36.5 1.0
C A:ASP34 3.4 36.8 1.0
CG A:ASP125 3.4 36.2 1.0
OD2 A:ASP32 3.6 36.9 1.0
CB A:ASP34 3.7 36.8 1.0
OD1 A:ASP125 3.7 36.3 1.0
CA A:ASP34 3.9 36.7 1.0
N A:ASP34 4.0 36.7 1.0
OD2 A:ASP129 4.4 36.7 1.0
N A:GLY35 4.6 36.7 1.0
CB A:ASP125 4.7 36.3 1.0
CB A:ASP32 4.8 36.5 1.0
CB A:ASP126 4.8 36.2 1.0
OD1 A:ASP129 4.8 36.9 1.0
CG A:ASP34 4.9 36.8 1.0
OD2 A:ASP34 4.9 36.8 1.0
CG2 D:VAL56 5.0 36.4 1.0

Magnesium binding site 2 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 2 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg202

b:14.8
occ:1.00
O B:ASP34 2.3 36.5 1.0
OD1 B:ASP32 2.4 37.3 1.0
OD2 B:ASP125 2.5 37.3 1.0
CG B:ASP32 3.4 37.1 1.0
C B:ASP34 3.5 36.6 1.0
CG B:ASP125 3.5 36.8 1.0
OG A:SER187 3.6 36.4 1.0
OD2 B:ASP32 3.7 37.5 1.0
CL B:CL204 3.7 40.0 1.0
CG1 A:VAL56 3.8 36.2 1.0
OD1 B:ASP125 3.8 36.9 1.0
CB A:SER187 3.8 36.5 1.0
CB B:ASP34 4.2 36.6 1.0
CA B:ASP34 4.2 36.6 1.0
O A:SER187 4.3 36.4 1.0
OD2 B:ASP129 4.4 36.8 1.0
N B:ASP34 4.4 36.6 1.0
N B:GLY35 4.5 36.6 1.0
CB B:ASP126 4.6 36.4 1.0
CB B:ASP32 4.8 36.7 1.0
CA B:GLY35 4.8 36.6 1.0
CB B:ASP125 4.9 36.6 1.0

Magnesium binding site 3 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 3 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg203

b:27.3
occ:1.00
OD1 C:ASP32 2.2 36.7 1.0
OD2 C:ASP125 2.4 37.4 1.0
O C:ASP34 2.6 36.8 1.0
CG C:ASP32 3.2 36.8 1.0
CG C:ASP125 3.5 36.9 1.0
OD2 C:ASP32 3.5 37.3 1.0
C C:ASP34 3.7 36.7 1.0
OD1 C:ASP125 3.8 37.2 1.0
CB C:ASP34 4.0 36.6 1.0
OD2 C:ASP129 4.1 36.7 1.0
CA C:ASP34 4.2 36.6 1.0
N C:ASP34 4.4 36.5 1.0
CB C:ASP32 4.6 36.5 1.0
CD1 C:ILE128 4.6 36.9 1.0
CB C:ASP126 4.7 36.4 1.0
OD1 C:ASP129 4.7 36.6 1.0
CB C:ASP125 4.8 36.6 1.0
N C:GLY35 4.8 36.7 1.0
CG C:ASP129 4.8 36.5 1.0
N C:ASP126 4.9 36.4 1.0

Magnesium binding site 4 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 4 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg204

b:23.0
occ:1.00
O D:ASP34 2.3 36.5 1.0
OD2 D:ASP125 2.4 36.6 1.0
OD1 D:ASP32 2.6 36.8 1.0
CG D:ASP125 3.3 36.5 1.0
C D:ASP34 3.5 36.5 1.0
OD1 D:ASP125 3.5 36.5 1.0
OG C:SER187 3.6 36.5 1.0
CG D:ASP32 3.6 36.8 1.0
CG1 C:VAL56 3.8 36.6 1.0
CB C:SER187 3.8 36.6 1.0
OD2 D:ASP32 4.0 36.9 1.0
CL D:CL205 4.1 40.0 1.0
OD2 D:ASP129 4.3 36.5 1.0
CB D:ASP34 4.3 36.5 1.0
CA D:ASP34 4.3 36.5 1.0
O C:SER187 4.3 36.6 1.0
CB D:ASP126 4.4 36.5 1.0
N D:GLY35 4.5 36.5 1.0
N D:ASP34 4.6 36.5 1.0
CB D:ASP125 4.7 36.5 1.0
CA D:GLY35 4.8 36.5 1.0
N D:ASP126 4.8 36.5 1.0
CB D:ASP32 4.9 36.6 1.0

Magnesium binding site 5 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 5 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
E:Mg205

b:40.0
occ:1.00
OD1 E:ASP32 2.1 36.5 1.0
O E:ASP34 2.2 36.9 1.0
OD2 E:ASP125 2.4 36.7 1.0
CG E:ASP32 3.3 36.7 1.0
C E:ASP34 3.3 36.8 1.0
CG E:ASP125 3.4 36.6 1.0
OD1 E:ASP125 3.7 36.9 1.0
OD2 E:ASP32 3.8 36.8 1.0
OD2 E:ASP129 4.0 36.7 1.0
CA E:ASP34 4.0 36.8 1.0
CB E:ASP34 4.1 36.8 1.0
N E:ASP34 4.1 36.8 1.0
OG H:SER187 4.2 37.4 1.0
N E:GLY35 4.4 36.9 1.0
CB E:ASP32 4.4 36.6 1.0
CB H:SER187 4.6 37.2 1.0
CB E:ASP126 4.7 36.3 1.0
CA E:GLY35 4.7 36.8 1.0
CB E:ASP125 4.7 36.5 1.0
CG2 H:VAL56 4.8 36.8 1.0
OD1 E:ASP129 4.8 36.9 1.0
CG E:ASP129 4.8 36.7 1.0
N E:ASP126 4.9 36.4 1.0
C E:VAL33 5.0 36.8 1.0

Magnesium binding site 6 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 6 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg206

b:37.0
occ:1.00
OD1 F:ASP32 2.4 36.4 1.0
OD2 F:ASP125 2.5 36.6 1.0
O F:ASP34 2.7 36.7 1.0
CG F:ASP32 3.4 36.7 1.0
CG F:ASP125 3.4 36.7 1.0
OG E:SER187 3.5 37.3 1.0
OD1 F:ASP125 3.6 36.9 1.0
CB E:SER187 3.8 37.1 1.0
OD2 F:ASP32 3.8 36.7 1.0
C F:ASP34 3.8 36.7 1.0
CL F:CL189 4.0 40.0 1.0
CG1 E:VAL56 4.0 36.7 1.0
CB F:ASP126 4.2 36.2 1.0
OD2 F:ASP129 4.3 37.0 1.0
CB F:ASP34 4.4 36.8 1.0
O E:SER187 4.5 36.9 1.0
N F:ASP126 4.5 36.4 1.0
CA F:ASP34 4.5 36.7 1.0
N F:ASP34 4.7 36.7 1.0
CB F:ASP32 4.7 36.6 1.0
CB F:ASP125 4.8 36.5 1.0
N F:GLY35 4.9 36.7 1.0
CG2 F:ILE128 5.0 36.3 1.0

Magnesium binding site 7 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 7 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg207

b:30.0
occ:1.00
OD2 G:ASP125 2.2 36.5 1.0
OD1 G:ASP32 2.3 36.1 1.0
O G:ASP34 2.4 36.5 1.0
CG G:ASP125 3.2 36.5 1.0
C G:ASP34 3.5 36.6 1.0
CG G:ASP32 3.5 36.3 1.0
OD1 G:ASP125 3.6 36.6 1.0
OG F:SER187 3.8 37.1 1.0
CB G:ASP34 4.0 36.6 1.0
OD2 G:ASP32 4.0 36.3 1.0
CL G:CL189 4.1 40.0 1.0
OD2 G:ASP129 4.1 37.0 1.0
CA G:ASP34 4.1 36.6 1.0
CB F:SER187 4.3 37.1 1.0
N G:ASP34 4.4 36.5 1.0
CB G:ASP126 4.4 36.5 1.0
N G:GLY35 4.5 36.6 1.0
CB G:ASP125 4.6 36.5 1.0
CB G:ASP32 4.7 36.4 1.0
N G:ASP126 4.7 36.5 1.0
OD1 G:ASP129 4.8 37.2 1.0
CG2 F:VAL56 4.8 36.7 1.0
CA G:GLY35 4.8 36.6 1.0
CG G:ASP129 4.9 36.9 1.0
N G:ASP125 4.9 36.5 1.0
O F:SER187 5.0 37.2 1.0

Magnesium binding site 8 out of 8 in 3hyc

Go back to Magnesium Binding Sites List in 3hyc
Magnesium binding site 8 out of 8 in the Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of E. Coli Phosphatase Yrbi, with Mg, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg208

b:32.4
occ:1.00
O H:ASP34 2.2 36.8 1.0
OD2 H:ASP125 2.5 37.1 1.0
OD1 H:ASP32 2.6 36.4 1.0
OG G:SER187 3.4 36.6 1.0
C H:ASP34 3.4 36.8 1.0
CG H:ASP125 3.5 36.8 1.0
CG H:ASP32 3.5 36.7 1.0
OD1 H:ASP125 3.7 37.3 1.0
OD2 H:ASP32 3.7 37.2 1.0
CB G:SER187 3.7 36.7 1.0
CG1 G:VAL56 4.0 36.5 1.0
CB H:ASP34 4.1 36.9 1.0
OD2 H:ASP129 4.1 37.4 1.0
CA H:ASP34 4.2 36.8 1.0
CL H:CL189 4.4 40.0 1.0
N H:GLY35 4.4 36.8 1.0
CB H:ASP126 4.5 36.6 1.0
N H:ASP34 4.5 36.7 1.0
O G:SER187 4.5 36.8 1.0
CA H:GLY35 4.7 36.7 1.0
CB H:ASP125 4.9 36.6 1.0
CB H:ASP32 4.9 36.6 1.0
N H:ASP126 4.9 36.6 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: Mon Dec 14 08:15:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy