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Magnesium in PDB 1u7p: X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily

Protein crystallography data

The structure of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily, PDB code: 1u7p was solved by E.Peisach, J.D.Selengut, 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) 76.58 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.524, 57.651, 76.621, 90.00, 91.97, 90.00
R / Rfree (%) 19 / 23.6

Other elements in 1u7p:

The structure of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily also contains other interesting chemical elements:

Tungsten (W) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily (pdb code 1u7p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily, PDB code: 1u7p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1u7p

Go back to Magnesium Binding Sites List in 1u7p
Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:25.5
occ:1.00
OD2 A:ASP11 2.2 19.7 1.0
OD1 A:ASP123 2.3 22.0 1.0
O A:HOH533 2.3 14.2 1.0
O A:ASP13 2.3 15.4 1.0
O A:HOH564 2.3 23.7 1.0
O1 A:WO4505 2.6 0.8 0.5
CG A:ASP11 3.1 17.5 1.0
CG A:ASP123 3.2 21.2 1.0
OD1 A:ASP11 3.4 18.4 1.0
C A:ASP13 3.4 17.4 1.0
OD2 A:ASP123 3.5 20.5 1.0
CB A:ASP13 4.0 17.6 1.0
W A:WO4505 4.0 0.1 0.5
CA A:ASP13 4.1 16.5 1.0
O A:HOH518 4.2 20.6 1.0
N A:ASP13 4.2 17.7 1.0
OD1 A:ASP122 4.2 16.4 1.0
OG1 A:THR15 4.3 17.4 1.0
O A:HOH571 4.3 29.5 1.0
O3 A:WO4505 4.4 0.8 0.5
CB A:TYR14 4.4 17.5 1.0
N A:TYR14 4.4 15.6 1.0
CB A:ASP11 4.5 18.1 1.0
N A:ASP123 4.6 16.4 1.0
CB A:ASP123 4.6 19.8 1.0
CG A:GLU124 4.6 21.5 1.0
O2 A:WO4505 4.6 0.0 0.5
O A:HOH547 4.7 31.5 1.0
CA A:TYR14 4.7 17.0 1.0
CG A:ASP122 4.8 17.2 1.0
C A:TYR14 4.8 18.5 1.0
C A:LEU12 4.9 16.1 1.0
OD2 A:ASP122 4.9 17.2 1.0
N A:GLU124 5.0 19.8 1.0
N A:THR15 5.0 17.9 1.0

Magnesium binding site 2 out of 4 in 1u7p

Go back to Magnesium Binding Sites List in 1u7p
Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:38.8
occ:1.00
OD2 B:ASP11 2.5 27.3 1.0
O B:HOH597 2.5 28.0 1.0
O B:ASP13 2.5 23.7 1.0
CB B:ASP123 2.9 23.8 1.0
N B:ASP123 3.2 22.1 1.0
CG B:ASP11 3.5 23.9 1.0
CA B:ASP123 3.5 24.1 1.0
OD1 B:ASP122 3.6 20.4 1.0
C B:ASP13 3.6 24.3 1.0
OG1 B:THR15 3.7 23.0 1.0
N B:GLU124 4.0 25.0 1.0
CB B:ASP11 4.0 22.5 1.0
CG B:ASP123 4.1 25.8 1.0
C B:ASP123 4.1 24.2 1.0
CG B:ASP122 4.2 20.4 1.0
CG B:GLU124 4.2 31.1 1.0
OD2 B:ASP123 4.3 26.8 1.0
O B:HOH605 4.3 37.6 1.0
CB B:TYR14 4.3 21.4 1.0
C B:ASP122 4.4 23.2 1.0
CB B:ASP13 4.4 22.2 1.0
CA B:ASP13 4.4 22.9 1.0
OD1 B:ASP11 4.5 24.2 1.0
N B:TYR14 4.5 22.8 1.0
C B:TYR14 4.6 21.1 1.0
OD2 B:ASP122 4.6 22.0 1.0
N B:ASP13 4.6 22.0 1.0
CA B:ASP122 4.7 20.2 1.0
CA B:TYR14 4.7 21.5 1.0
O B:TYR14 4.7 22.0 1.0
N B:THR15 4.8 21.5 1.0
CB B:THR15 4.9 21.5 1.0
O B:HOH549 4.9 24.5 1.0
CB B:GLU124 5.0 26.3 1.0

Magnesium binding site 3 out of 4 in 1u7p

Go back to Magnesium Binding Sites List in 1u7p
Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:26.3
occ:1.00
OD1 C:ASP123 2.2 25.8 1.0
O C:ASP13 2.3 24.3 1.0
OD2 C:ASP11 2.3 19.1 1.0
O C:HOH584 2.3 20.8 1.0
O C:HOH550 2.3 14.0 1.0
O3 C:WO4506 2.5 37.0 0.5
CG C:ASP123 3.1 25.5 1.0
CG C:ASP11 3.2 21.7 1.0
OD2 C:ASP123 3.4 22.9 1.0
C C:ASP13 3.4 22.9 1.0
OD1 C:ASP11 3.4 20.0 1.0
W C:WO4506 3.9 47.2 0.5
CB C:ASP13 4.0 22.5 1.0
CA C:ASP13 4.1 24.2 1.0
OG1 C:THR15 4.2 16.0 1.0
N C:ASP13 4.2 21.6 1.0
CB C:TYR14 4.2 21.3 1.0
OD1 C:ASP122 4.3 19.6 1.0
O C:HOH515 4.3 28.5 1.0
O C:HOH560 4.3 34.4 1.0
O1 C:WO4506 4.4 38.8 0.5
N C:TYR14 4.4 23.0 1.0
CB C:ASP123 4.5 23.5 1.0
CB C:ASP11 4.5 19.6 1.0
O4 C:WO4506 4.5 40.0 0.5
N C:ASP123 4.6 21.8 1.0
CA C:TYR14 4.7 21.0 1.0
CG C:GLU124 4.8 29.7 1.0
C C:TYR14 4.8 22.0 1.0
C C:LEU12 4.9 22.1 1.0
O2 C:WO4506 4.9 42.9 0.5
N C:THR15 4.9 20.2 1.0
CG C:ASP122 4.9 19.7 1.0
N C:GLU124 4.9 26.6 1.0
CA C:ASP123 5.0 23.3 1.0

Magnesium binding site 4 out of 4 in 1u7p

Go back to Magnesium Binding Sites List in 1u7p
Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:49.3
occ:1.00
OD2 D:ASP11 2.3 32.9 1.0
O D:HOH562 2.5 22.7 1.0
O D:ASP13 2.6 21.6 1.0
CB D:ASP123 2.8 28.6 1.0
N D:ASP123 3.1 22.8 1.0
CA D:ASP123 3.4 26.2 1.0
CG D:ASP11 3.4 27.9 1.0
OD1 D:ASP122 3.7 20.7 1.0
C D:ASP13 3.8 23.0 1.0
OG1 D:THR15 3.8 23.3 1.0
CG D:ASP123 3.8 34.8 1.0
OD1 D:ASP123 3.9 35.9 1.0
C D:ASP123 3.9 26.1 1.0
N D:GLU124 3.9 24.6 1.0
CB D:TYR14 4.2 21.9 1.0
CB D:ASP11 4.2 22.6 1.0
O D:HOH550 4.2 36.5 1.0
CG D:GLU124 4.2 30.2 1.0
CG D:ASP122 4.3 19.4 1.0
C D:ASP122 4.3 21.2 1.0
OD1 D:ASP11 4.4 30.9 1.0
CB D:ASP13 4.6 22.6 1.0
C D:TYR14 4.6 23.9 1.0
CA D:ASP13 4.6 21.8 1.0
N D:TYR14 4.6 22.2 1.0
CA D:TYR14 4.7 23.8 1.0
OD2 D:ASP122 4.7 18.7 1.0
CA D:ASP122 4.7 19.8 1.0
O D:TYR14 4.7 26.3 1.0
O D:ASP123 4.8 25.1 1.0
N D:ASP13 4.8 22.3 1.0
CB D:GLU124 4.9 27.4 1.0
OE1 D:GLU124 4.9 33.7 1.0
CA D:GLU124 5.0 25.3 1.0
N D:THR15 5.0 24.8 1.0
OD2 D:ASP123 5.0 35.5 1.0

Reference:

E.Peisach, J.D.Selengut, D.Dunaway-Mariano, K.N.Allen. X-Ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase Mdp-1 of the Haloacid Dehalogenase Superfamily Biochemistry V. 43 12770 2004.
ISSN: ISSN 0006-2960
PubMed: 15461449
DOI: 10.1021/BI0490688
Page generated: Mon Dec 14 06:52:40 2020

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