Magnesium in PDB 6iah: Phosphatase TT82 From Thermococcus Thioreducens

Protein crystallography data

The structure of Phosphatase TT82 From Thermococcus Thioreducens, PDB code: 6iah was solved by J.Brynda, I.K.Smatanova, P.Pachl, T.Prudnikova, R.J.Masters, P.Havlickova, B.Kascakova, V.Brinsa, M.Kuty, M.L.Pusey, J.D.Ng, P.M.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.87 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.330, 117.000, 33.830, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.6

Other elements in 6iah:

The structure of Phosphatase TT82 From Thermococcus Thioreducens also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phosphatase TT82 From Thermococcus Thioreducens (pdb code 6iah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Phosphatase TT82 From Thermococcus Thioreducens, PDB code: 6iah:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6iah

Go back to Magnesium Binding Sites List in 6iah
Magnesium binding site 1 out of 3 in the Phosphatase TT82 From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phosphatase TT82 From Thermococcus Thioreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.9
occ:1.00
OD2 A:ASP6 1.9 29.8 1.0
O A:HOH445 2.0 26.9 1.0
O A:HOH518 2.0 26.6 1.0
OD1 A:ASP199 2.0 24.4 1.0
O A:HOH418 2.1 25.1 1.0
O A:ASP8 2.1 29.3 1.0
CG A:ASP6 3.0 27.3 1.0
CG A:ASP199 3.1 28.3 1.0
C A:ASP8 3.3 27.6 1.0
OD2 A:ASP199 3.4 26.9 1.0
OD1 A:ASP6 3.5 27.7 1.0
OD2 A:ASP203 4.0 25.5 1.0
CA A:ASP8 4.1 24.7 1.0
CB A:ASP8 4.2 23.8 1.0
O A:HOH609 4.2 43.2 1.0
N A:ASP8 4.3 23.7 1.0
CB A:ASP6 4.3 25.9 1.0
O A:HOH620 4.3 42.0 1.0
N A:GLY9 4.3 27.1 1.0
CB A:ASP199 4.4 27.7 1.0
O A:HOH576 4.4 44.1 1.0
CA A:GLY9 4.5 27.3 1.0
CG2 A:THR200 4.6 30.3 1.0
N A:ASP199 4.7 24.1 1.0
CL A:CL305 4.8 31.4 1.0
O A:HOH463 4.8 23.5 1.0
CG A:ASP203 4.9 27.8 1.0
OG1 A:THR200 5.0 30.1 1.0

Magnesium binding site 2 out of 3 in 6iah

Go back to Magnesium Binding Sites List in 6iah
Magnesium binding site 2 out of 3 in the Phosphatase TT82 From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phosphatase TT82 From Thermococcus Thioreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:56.2
occ:1.00
O A:HOH432 2.8 46.5 1.0
OD1 A:ASP13 2.9 32.0 1.0
O A:HOH429 3.0 44.8 1.0
OE2 A:GLU16 3.0 53.0 1.0
OD2 A:ASP13 3.4 33.4 1.0
CG A:ASP13 3.5 31.4 1.0
OE1 A:GLU16 3.5 70.3 1.0
CD A:GLU16 3.7 58.9 1.0
O A:HOH549 4.3 49.5 1.0
CA A:ARG15 4.3 46.6 1.0
CG A:ARG15 4.5 50.1 1.0
N A:ARG15 4.7 44.6 1.0
CL A:CL307 4.9 42.5 1.0
CB A:ASP13 4.9 27.4 1.0

Magnesium binding site 3 out of 3 in 6iah

Go back to Magnesium Binding Sites List in 6iah
Magnesium binding site 3 out of 3 in the Phosphatase TT82 From Thermococcus Thioreducens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phosphatase TT82 From Thermococcus Thioreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:53.0
occ:1.00
O A:HOH612 2.1 49.6 1.0
O A:HOH415 2.2 50.2 1.0
O A:HOH405 2.3 45.1 1.0
OE2 A:GLU231 4.1 43.8 1.0
OE1 A:GLU231 4.2 44.0 1.0
CD A:GLU231 4.6 43.0 1.0
O A:HOH569 4.6 46.8 1.0

Reference:

P.Havlickova, V.Brinsa, J.Brynda, P.Pachl, T.Prudnikova, J.R.Mesters, B.Kascakova, M.Kuty, M.L.Pusey, J.D.Ng, P.Rezacova, I.Kuta Smatanova. A Novel Structurally Characterized Haloacid Dehalogenase Superfamily Phosphatase From Thermococcus Thioreducens with Diverse Substrate Specificity. Acta Crystallogr D Struct V. 75 743 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31373573
DOI: 10.1107/S2059798319009586
Page generated: Mon Dec 14 22:56:34 2020

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