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Magnesium in PDB 2r8e: Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg

Enzymatic activity of Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg

All present enzymatic activity of Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg, PDB code: 2r8e was solved by O.V.Tsodikov, P.Aggarwal, J.R.Rubin, J.A.Stuckey, R.Woodard, T.Biswas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.34 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.877, 83.005, 85.864, 118.84, 118.77, 90.06
R / Rfree (%) 15.9 / 18.8

Other elements in 2r8e:

The structure of Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg (pdb code 2r8e). 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 Yrbi From Escherichia Coli in Complex with Mg, PDB code: 2r8e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2r8e

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Magnesium binding site 1 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:13.0
occ:1.00
 O A:HOH346 2.0 15.1 1.0
OD2 A:ASP125 2.0 13.2 1.0
OD1 A:ASP32 2.0 13.8 1.0
O A:ASP34 2.1 13.0 1.0
O A:HOH347 2.1 14.5 1.0
O A:HOH345 2.2 16.8 1.0
CG A:ASP125 3.1 13.3 1.0
CG A:ASP32 3.1 14.6 1.0
C A:ASP34 3.3 12.4 1.0
OD1 A:ASP125 3.5 12.7 1.0
OD2 A:ASP32 3.5 15.7 1.0
O A:HOH227 3.8 15.2 1.0
CA A:ASP34 3.9 12.7 1.0
CB A:ASP34 4.0 13.3 1.0
N A:ASP34 4.1 13.2 1.0
OD2 A:ASP129 4.1 15.9 1.0
O A:HOH301 4.1 24.9 1.0
CB A:ASP125 4.3 12.0 1.0
O A:HOH238 4.3 19.3 1.0
N A:GLY35 4.3 11.7 1.0
CB A:ASP32 4.4 15.3 1.0
O A:HOH406 4.5 40.9 1.0
N A:ASP125 4.6 12.4 1.0
CA A:GLY35 4.6 12.3 1.0
CB A:ASP126 4.8 14.3 1.0
N A:ASP126 4.8 12.9 1.0
CA A:ASP125 4.8 12.8 1.0
C A:VAL33 4.8 12.6 1.0
CG2 A:VAL36 4.9 14.0 1.0
CG A:ASP129 5.0 17.2 1.0
C A:ASP125 5.0 12.8 1.0
OD1 A:ASP129 5.0 16.0 1.0

Magnesium binding site 2 out of 8 in 2r8e

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Magnesium binding site 2 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:13.4
occ:1.00
 OD1 B:ASP32 2.0 13.8 1.0
O B:HOH353 2.0 15.2 1.0
OD2 B:ASP125 2.0 13.8 1.0
O B:ASP34 2.1 12.9 1.0
O B:HOH351 2.1 14.4 1.0
O B:HOH352 2.1 16.7 1.0
CG B:ASP32 3.1 14.7 1.0
CG B:ASP125 3.1 13.2 1.0
C B:ASP34 3.2 12.2 1.0
OD2 B:ASP32 3.5 15.6 1.0
OD1 B:ASP125 3.5 13.1 1.0
O B:HOH229 3.8 14.9 1.0
CA B:ASP34 3.9 13.0 1.0
CB B:ASP34 4.0 13.8 1.0
N B:ASP34 4.0 13.6 1.0
OD2 B:ASP129 4.1 15.4 1.0
CB B:ASP125 4.3 11.5 1.0
N B:GLY35 4.3 12.0 1.0
CB B:ASP32 4.4 15.4 1.0
O B:HOH226 4.4 18.6 1.0
O B:HOH336 4.4 27.4 1.0
N B:ASP125 4.6 12.3 1.0
O B:HOH413 4.6 41.4 1.0
CA B:GLY35 4.6 11.8 1.0
O B:HOH274 4.7 30.0 1.0
CB B:ASP126 4.8 13.9 1.0
N B:ASP126 4.8 12.9 1.0
CA B:ASP125 4.8 12.7 1.0
C B:VAL33 4.8 13.0 1.0
CG2 B:VAL36 4.9 14.2 1.0
CG B:ASP129 5.0 16.5 1.0
OD1 B:ASP129 5.0 16.5 1.0
C B:ASP125 5.0 13.0 1.0

Magnesium binding site 3 out of 8 in 2r8e

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Magnesium binding site 3 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:12.8
occ:1.00
 O C:HOH356 2.0 15.0 1.0
OD1 C:ASP32 2.0 14.3 1.0
OD2 C:ASP125 2.0 14.0 1.0
O C:ASP34 2.1 13.0 1.0
O C:HOH355 2.1 14.7 1.0
O C:HOH474 2.1 20.0 1.0
CG C:ASP125 3.1 13.9 1.0
CG C:ASP32 3.1 14.1 1.0
C C:ASP34 3.2 12.6 1.0
OD2 C:ASP32 3.5 15.9 1.0
OD1 C:ASP125 3.5 13.8 1.0
O C:HOH235 3.8 15.7 1.0
CA C:ASP34 3.9 12.9 1.0
CB C:ASP34 4.0 13.9 1.0
N C:ASP34 4.0 14.0 1.0
OD2 C:ASP129 4.1 15.9 1.0
O C:HOH315 4.1 26.8 1.0
CB C:ASP125 4.3 11.8 1.0
N C:GLY35 4.3 11.9 1.0
CB C:ASP32 4.4 14.6 1.0
O C:HOH228 4.4 20.0 1.0
O C:HOH370 4.4 27.9 1.0
O C:HOH350 4.5 41.7 1.0
N C:ASP125 4.6 12.8 1.0
O C:HOH389 4.6 35.3 1.0
CA C:GLY35 4.6 12.2 1.0
CB C:ASP126 4.8 14.1 1.0
N C:ASP126 4.8 13.0 1.0
C C:VAL33 4.8 13.3 1.0
CA C:ASP125 4.8 13.3 1.0
CG2 C:VAL36 4.9 13.9 1.0
CG C:ASP129 5.0 16.9 1.0
C C:ASP125 5.0 13.3 1.0
OD1 C:ASP129 5.0 16.6 1.0

Magnesium binding site 4 out of 8 in 2r8e

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Magnesium binding site 4 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:13.3
occ:1.00
 O D:HOH368 2.0 15.0 1.0
OD2 D:ASP125 2.0 13.9 1.0
OD1 D:ASP32 2.0 13.9 1.0
O D:ASP34 2.1 13.2 1.0
O D:HOH367 2.1 14.8 1.0
O D:HOH366 2.1 17.2 1.0
CG D:ASP125 3.0 13.4 1.0
CG D:ASP32 3.1 14.3 1.0
C D:ASP34 3.2 12.9 1.0
OD2 D:ASP32 3.5 15.8 1.0
OD1 D:ASP125 3.5 13.0 1.0
O D:HOH229 3.8 15.2 1.0
CA D:ASP34 3.9 12.9 1.0
CB D:ASP34 4.0 13.9 1.0
N D:ASP34 4.1 13.4 1.0
OD2 D:ASP129 4.1 15.8 1.0
O D:HOH312 4.1 25.6 1.0
CB D:ASP125 4.3 11.6 1.0
N D:GLY35 4.3 12.1 1.0
O D:HOH237 4.4 18.8 1.0
CB D:ASP32 4.4 15.2 1.0
O D:HOH385 4.4 27.6 1.0
N D:ASP125 4.6 12.1 1.0
CA D:GLY35 4.6 12.5 1.0
O D:HOH407 4.7 33.3 1.0
CB D:ASP126 4.8 14.2 1.0
N D:ASP126 4.8 13.2 1.0
CA D:ASP125 4.8 12.3 1.0
C D:VAL33 4.8 12.9 1.0
CG2 D:VAL36 4.9 14.2 1.0
CG D:ASP129 4.9 16.7 1.0
C D:ASP125 5.0 13.0 1.0
OD1 D:ASP129 5.0 16.1 1.0

Magnesium binding site 5 out of 8 in 2r8e

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Magnesium binding site 5 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg205

b:14.0
occ:1.00
 OD1 E:ASP32 2.0 15.4 1.0
OD2 E:ASP125 2.0 13.6 1.0
O E:HOH472 2.1 15.6 1.0
O E:ASP34 2.1 14.1 1.0
O E:HOH473 2.1 13.9 1.0
O G:HOH478 2.2 16.5 1.0
CG E:ASP125 3.1 13.2 1.0
CG E:ASP32 3.1 14.9 1.0
C E:ASP34 3.3 13.7 1.0
OD1 E:ASP125 3.4 14.4 1.0
OD2 E:ASP32 3.6 15.1 1.0
CA E:ASP34 4.1 13.8 1.0
OD2 E:ASP129 4.1 14.6 1.0
N E:ASP34 4.2 14.0 1.0
O E:HOH337 4.2 15.8 1.0
OG G:SER187 4.3 16.3 1.0
N E:GLY35 4.3 13.3 1.0
CB E:ASP34 4.3 14.5 1.0
CB E:ASP32 4.3 14.6 1.0
CB E:ASP125 4.4 12.8 1.0
CL E:CL306 4.4 17.4 1.0
CA E:GLY35 4.5 12.9 1.0
CB G:SER187 4.6 18.1 1.0
CB E:ASP126 4.7 13.7 1.0
CG2 G:VAL56 4.7 15.4 1.0
N E:ASP125 4.7 12.4 1.0
N E:ASP126 4.7 13.2 1.0
O G:SER187 4.9 17.8 1.0
C E:VAL33 4.9 14.2 1.0
CA E:ASP125 4.9 12.9 1.0
C E:GLY35 4.9 12.6 1.0
CG2 E:VAL36 5.0 13.3 1.0

Magnesium binding site 6 out of 8 in 2r8e

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Magnesium binding site 6 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg206

b:13.7
occ:1.00
 OD1 F:ASP32 2.0 15.1 1.0
OD2 F:ASP125 2.0 13.2 1.0
O F:ASP34 2.1 14.2 1.0
O H:HOH488 2.1 15.7 1.0
O F:HOH478 2.1 14.2 1.0
O H:HOH489 2.2 16.1 1.0
CG F:ASP125 3.0 12.5 1.0
CG F:ASP32 3.1 14.6 1.0
C F:ASP34 3.3 13.6 1.0
OD1 F:ASP125 3.4 13.6 1.0
OD2 F:ASP32 3.6 15.0 1.0
CA F:ASP34 4.1 13.6 1.0
OD2 F:ASP129 4.1 15.0 1.0
N F:ASP34 4.2 14.2 1.0
O F:HOH335 4.2 16.2 1.0
OG H:SER187 4.3 16.2 1.0
N F:GLY35 4.3 13.5 1.0
CB F:ASP32 4.3 14.0 1.0
CB F:ASP34 4.3 14.2 1.0
CB F:ASP125 4.4 12.9 1.0
CL F:CL305 4.4 17.1 1.0
CA F:GLY35 4.5 12.5 1.0
CB H:SER187 4.6 17.4 1.0
CG2 H:VAL56 4.7 15.0 1.0
CB F:ASP126 4.7 14.3 1.0
N F:ASP125 4.7 12.1 1.0
N F:ASP126 4.7 13.4 1.0
O H:SER187 4.9 17.3 1.0
C F:VAL33 4.9 13.9 1.0
CA F:ASP125 4.9 12.7 1.0
C F:GLY35 4.9 12.2 1.0
CG2 F:VAL36 5.0 12.6 1.0

Magnesium binding site 7 out of 8 in 2r8e

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Magnesium binding site 7 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg207

b:13.8
occ:1.00
 OD1 G:ASP32 2.0 15.2 1.0
OD2 G:ASP125 2.1 13.4 1.0
O G:HOH480 2.1 15.6 1.0
O G:ASP34 2.1 14.6 1.0
O G:HOH479 2.1 14.2 1.0
O F:HOH479 2.2 15.7 1.0
CG G:ASP125 3.1 13.1 1.0
CG G:ASP32 3.1 14.2 1.0
C G:ASP34 3.3 13.8 1.0
OD1 G:ASP125 3.4 14.0 1.0
OD2 G:ASP32 3.6 14.8 1.0
OD2 G:ASP129 4.1 14.7 1.0
CA G:ASP34 4.1 13.8 1.0
N G:ASP34 4.2 14.1 1.0
O G:HOH325 4.2 15.8 1.0
OG F:SER187 4.3 16.3 1.0
CB G:ASP32 4.3 14.3 1.0
N G:GLY35 4.3 13.4 1.0
CB G:ASP34 4.4 14.5 1.0
CB G:ASP125 4.4 13.1 1.0
CL G:CL307 4.4 17.1 1.0
CA G:GLY35 4.5 12.7 1.0
CB F:SER187 4.6 17.6 1.0
CG2 F:VAL56 4.7 15.2 1.0
CB G:ASP126 4.7 13.9 1.0
N G:ASP125 4.7 12.3 1.0
N G:ASP126 4.8 13.3 1.0
O F:SER187 4.8 17.9 1.0
C G:VAL33 4.9 13.8 1.0
CA G:ASP125 4.9 13.0 1.0
C G:GLY35 5.0 12.4 1.0
CG2 G:VAL36 5.0 13.1 1.0

Magnesium binding site 8 out of 8 in 2r8e

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Magnesium binding site 8 out of 8 in the Crystal Structure of Yrbi From Escherichia Coli in Complex with Mg


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 Yrbi From Escherichia Coli in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg208

b:13.6
occ:1.00
 OD1 H:ASP32 2.0 15.7 1.0
O H:HOH490 2.0 15.7 1.0
OD2 H:ASP125 2.1 13.9 1.0
O H:ASP34 2.1 14.1 1.0
O H:HOH491 2.1 14.3 1.0
O E:HOH474 2.2 15.8 1.0
CG H:ASP125 3.1 12.9 1.0
CG H:ASP32 3.1 14.1 1.0
C H:ASP34 3.3 13.1 1.0
OD1 H:ASP125 3.4 14.0 1.0
OD2 H:ASP32 3.6 15.4 1.0
CA H:ASP34 4.1 13.7 1.0
OD2 H:ASP129 4.1 14.4 1.0
N H:ASP34 4.2 13.7 1.0
O H:HOH344 4.2 16.4 1.0
OG E:SER187 4.3 16.0 1.0
N H:GLY35 4.3 13.4 1.0
CB H:ASP34 4.3 14.0 1.0
CB H:ASP32 4.3 14.0 1.0
CB H:ASP125 4.4 13.0 1.0
CL H:CL308 4.4 17.4 1.0
CA H:GLY35 4.5 12.7 1.0
CB E:SER187 4.6 17.9 1.0
CG2 E:VAL56 4.7 15.6 1.0
CB H:ASP126 4.7 14.0 1.0
N H:ASP126 4.7 13.3 1.0
N H:ASP125 4.7 12.6 1.0
O E:SER187 4.9 17.7 1.0
C H:VAL33 4.9 13.9 1.0
CG2 H:VAL36 4.9 13.5 1.0
CA H:ASP125 4.9 13.1 1.0
C H:GLY35 5.0 12.1 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: Sun Aug 10 13:43:10 2025

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