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Magnesium in PDB 5eq9: Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+, PDB code: 5eq9 was solved by M.Ruszkowski, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.25 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.885, 89.802, 92.593, 90.00, 97.07, 90.00
R / Rfree (%) 11.6 / 15.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+ (pdb code 5eq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+, PDB code: 5eq9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5eq9

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Magnesium binding site 1 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+


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 Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:25.1
occ:0.70
OD1 A:ASP270 2.1 12.9 1.0
OD2 A:ASP146 2.2 17.9 1.0
CA A:ASP270 2.7 10.8 1.0
CG A:ASP270 2.9 18.4 1.0
CG A:ASP146 3.0 13.1 1.0
OD1 A:ASP149 3.1 11.9 1.0
N A:ASP270 3.1 8.3 1.0
CB A:ASP270 3.1 15.8 1.0
O A:TYR269 3.2 11.6 1.0
CB A:ASP146 3.3 11.7 1.0
C A:TYR269 3.4 9.6 1.0
O A:HOH527 3.5 29.4 0.5
CD1 A:TYR269 3.6 12.7 1.0
CG A:ASP149 3.6 8.4 1.0
CB A:ASP149 3.7 8.3 1.0
CD1 A:LEU164 3.8 8.3 1.0
OD2 A:ASP270 4.1 19.5 1.0
C A:ASP270 4.1 8.5 1.0
OD1 A:ASP146 4.2 16.2 1.0
CE1 A:TYR269 4.3 14.6 1.0
O A:HOH527 4.3 19.0 0.5
CA A:ASP149 4.3 7.9 1.0
O A:ASP270 4.5 10.7 1.0
O A:HOH553 4.5 34.5 1.0
CA A:TYR269 4.6 9.3 1.0
CG A:TYR269 4.6 10.8 1.0
CB A:TYR269 4.6 11.2 1.0
OD2 A:ASP149 4.6 9.0 1.0
CA A:ASP146 4.8 10.3 1.0
CG A:LEU164 4.9 8.4 1.0

Magnesium binding site 2 out of 4 in 5eq9

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Magnesium binding site 2 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+


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 Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:27.5
occ:0.70
OD2 B:ASP146 2.1 22.2 1.0
OD1 B:ASP270 2.2 12.8 1.0
CG B:ASP146 2.8 14.6 1.0
CA B:ASP270 2.9 9.4 1.0
CG B:ASP270 3.1 16.5 1.0
OD1 B:ASP149 3.1 11.8 1.0
CB B:ASP146 3.1 12.6 1.0
N B:ASP270 3.2 7.8 1.0
O B:TYR269 3.2 11.5 1.0
CB B:ASP270 3.3 14.3 1.0
O B:HOH503 3.3 22.8 0.5
C B:TYR269 3.4 8.2 1.0
CD1 B:TYR269 3.6 14.8 1.0
CG B:ASP149 3.6 8.1 1.0
CB B:ASP149 3.7 7.8 1.0
CD1 B:LEU164 3.8 9.0 1.0
OD1 B:ASP146 4.0 18.1 1.0
C B:ASP270 4.2 8.5 1.0
OD2 B:ASP270 4.3 18.0 1.0
O B:HOH503 4.3 20.1 0.5
CE1 B:TYR269 4.3 17.6 1.0
CA B:ASP149 4.3 7.2 1.0
O B:ASP270 4.5 10.9 1.0
CA B:TYR269 4.6 9.6 1.0
CG B:TYR269 4.6 12.0 1.0
O B:HOH626 4.6 28.4 1.0
CB B:TYR269 4.6 12.2 1.0
CA B:ASP146 4.6 9.1 1.0
OD2 B:ASP149 4.6 8.6 1.0
CG B:LEU164 4.8 7.7 1.0
N B:ASP149 5.0 7.8 1.0

Magnesium binding site 3 out of 4 in 5eq9

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Magnesium binding site 3 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+


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 Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:36.8
occ:0.70
OD2 C:ASP146 2.0 30.3 1.0
OD1 C:ASP270 2.1 14.8 1.0
CA C:ASP270 2.6 11.6 1.0
OD1 C:ASP149 2.8 14.7 1.0
CG C:ASP270 2.9 17.9 1.0
CG C:ASP146 3.0 18.0 1.0
CB C:ASP270 3.1 15.2 1.0
N C:ASP270 3.1 11.1 1.0
O C:HOH534 3.3 18.3 0.5
O C:TYR269 3.3 11.6 1.0
C C:TYR269 3.4 11.2 1.0
CB C:ASP146 3.4 14.4 1.0
CG C:ASP149 3.5 10.3 1.0
CB C:ASP149 3.7 10.4 1.0
CD1 C:TYR269 3.8 21.1 1.0
CD1 C:LEU164 3.8 9.3 1.0
C C:ASP270 3.9 10.0 1.0
OD1 C:ASP146 4.1 22.9 1.0
OD2 C:ASP270 4.2 19.1 1.0
O C:ASP270 4.3 12.3 1.0
CA C:ASP149 4.4 9.5 1.0
CE1 C:TYR269 4.4 32.1 1.0
OD2 C:ASP149 4.5 10.8 1.0
O C:HOH595 4.5 32.8 1.0
O C:HOH534 4.5 26.0 0.5
CA C:TYR269 4.6 11.7 1.0
CG C:TYR269 4.7 16.9 1.0
CB C:TYR269 4.8 15.8 1.0
CG C:LEU164 4.9 9.0 1.0
CA C:ASP146 4.9 11.9 1.0
O C:HOH606 5.0 11.3 1.0

Magnesium binding site 4 out of 4 in 5eq9

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Magnesium binding site 4 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+


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 Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) in Complex with L-Histidinol Phosphate and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:29.1
occ:0.70
OD2 D:ASP146 2.1 22.2 1.0
OD1 D:ASP270 2.1 16.1 1.0
CA D:ASP270 2.7 12.6 1.0
CG D:ASP270 2.8 20.6 1.0
CG D:ASP146 3.0 15.8 1.0
OD1 D:ASP149 3.0 13.9 1.0
CB D:ASP270 3.1 18.4 1.0
N D:ASP270 3.1 12.2 1.0
O D:TYR269 3.2 14.6 1.0
CB D:ASP146 3.3 13.7 1.0
C D:TYR269 3.3 12.9 1.0
O D:HOH577 3.4 24.8 0.5
CG D:ASP149 3.6 11.3 1.0
CD1 D:TYR269 3.6 18.7 1.0
CB D:ASP149 3.7 10.3 1.0
CD1 D:LEU164 3.8 10.6 1.0
C D:ASP270 4.0 11.4 1.0
OD2 D:ASP270 4.1 24.4 1.0
OD1 D:ASP146 4.2 17.3 1.0
CA D:ASP149 4.3 9.3 1.0
CE1 D:TYR269 4.3 21.5 1.0
O D:HOH577 4.4 25.7 0.5
O D:ASP270 4.4 12.3 1.0
O D:HOH551 4.5 34.7 1.0
CA D:TYR269 4.5 13.6 1.0
CG D:TYR269 4.6 17.2 1.0
OD2 D:ASP149 4.6 11.2 1.0
CB D:TYR269 4.7 17.4 1.0
CA D:ASP146 4.8 10.7 1.0
CG D:LEU164 4.8 8.7 1.0
N D:ASP149 5.0 9.1 1.0

Reference:

M.Ruszkowski, Z.Dauter. Structural Studies of Medicago Truncatula Histidinol Phosphate Phosphatase From Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. J.Biol.Chem. V. 291 9960 2016.
ISSN: ESSN 1083-351X
PubMed: 26994138
DOI: 10.1074/JBC.M115.708727
Page generated: Sun Sep 29 03:53:23 2024

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