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Magnesium in PDB 2auu: Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride

Enzymatic activity of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride

All present enzymatic activity of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride:
3.6.1.1;

Protein crystallography data

The structure of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride, PDB code: 2auu was solved by V.R.Samygina, A.N.Popov, S.M.Avaeva, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.22
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 109.363, 109.363, 75.165, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18.4

Other elements in 2auu:

The structure of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride (pdb code 2auu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride, PDB code: 2auu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2auu

Go back to Magnesium Binding Sites List in 2auu
Magnesium binding site 1 out of 4 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:31.0
occ:1.00
 OD1 A:ASP65 1.9 41.0 1.0
O4 A:POP180 2.0 33.9 1.0
F A:F211 2.0 30.0 1.0
OD1 A:ASP102 2.1 40.8 1.0
OD2 A:ASP70 2.1 29.4 1.0
O A:HOH322 2.2 25.5 0.7
CG A:ASP102 2.9 37.7 1.0
CG A:ASP65 3.0 47.6 1.0
P2 A:POP180 3.1 29.4 1.0
CG A:ASP70 3.1 27.8 1.0
OD2 A:ASP102 3.1 35.5 1.0
O5 A:POP180 3.4 27.5 1.0
OD1 A:ASP70 3.4 28.6 1.0
MG A:MG202 3.5 29.9 1.0
OD2 A:ASP65 3.5 39.5 1.0
MG A:MG203 3.6 34.2 1.0
O A:HOH364 3.7 34.9 1.0
O6 A:POP180 3.8 33.0 1.0
NZ A:LYS104 3.9 31.3 1.0
OD2 A:ASP67 3.9 44.2 1.0
O A:HOH316 4.1 43.4 1.0
CB A:ASP65 4.2 47.8 1.0
CB A:ASP67 4.3 41.6 1.0
CB A:ASP102 4.4 37.5 1.0
O A:POP180 4.4 29.2 1.0
CB A:ASP70 4.5 28.1 1.0
CG A:ASP67 4.5 39.4 1.0
O A:HOH315 4.5 30.1 1.0
OH A:TYR55 4.5 26.4 1.0
O A:PRO68 4.7 36.2 1.0
O A:HOH355 4.7 33.2 1.0
O A:HOH353 4.7 29.7 1.0
O1 A:POP180 5.0 31.1 1.0
CA A:ASP102 5.0 38.5 1.0

Magnesium binding site 2 out of 4 in 2auu

Go back to Magnesium Binding Sites List in 2auu
Magnesium binding site 2 out of 4 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:29.9
occ:1.00
 F A:F211 1.9 30.0 1.0
O5 A:POP180 2.1 27.5 1.0
O A:HOH315 2.1 30.1 1.0
O A:HOH308 2.1 28.6 1.0
OD1 A:ASP70 2.1 28.6 1.0
O A:HOH353 2.1 29.7 1.0
CG A:ASP70 3.0 27.8 1.0
P2 A:POP180 3.1 29.4 1.0
OD2 A:ASP70 3.4 29.4 1.0
MG A:MG201 3.5 31.0 1.0
O6 A:POP180 3.6 33.0 1.0
O4 A:POP180 3.7 33.9 1.0
O A:HOH317 3.9 33.2 1.0
OD2 A:ASP67 3.9 44.2 1.0
OH A:TYR55 3.9 26.4 1.0
O A:HOH322 4.1 25.5 0.7
O A:PRO68 4.1 36.2 1.0
CB A:ASP67 4.2 41.6 1.0
CB A:ASP70 4.4 28.1 1.0
O A:HOH363 4.4 42.9 1.0
OE1 A:GLU20 4.4 24.6 1.0
O A:POP180 4.4 29.2 1.0
CG A:ASP67 4.4 39.4 1.0
CE2 A:TYR55 4.5 23.2 1.0
CZ A:TYR55 4.5 22.7 1.0
NZ A:LYS29 4.6 29.7 1.0
OD1 A:ASP65 4.8 41.0 1.0
O A:HOH307 4.9 25.7 1.0
CA A:ASP70 4.9 26.0 1.0
O A:GLY56 5.0 23.4 1.0

Magnesium binding site 3 out of 4 in 2auu

Go back to Magnesium Binding Sites List in 2auu
Magnesium binding site 3 out of 4 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:34.2
occ:1.00
 OD2 A:ASP97 2.0 34.1 1.0
O1 A:POP180 2.0 31.1 1.0
O A:HOH364 2.1 34.9 1.0
OD2 A:ASP102 2.1 35.5 1.0
O A:HOH355 2.1 33.2 1.0
O4 A:POP180 2.2 33.9 1.0
CG A:ASP97 3.0 39.9 1.0
P1 A:POP180 3.2 29.4 1.0
P2 A:POP180 3.2 29.4 1.0
CG A:ASP102 3.3 37.7 1.0
O A:POP180 3.3 29.2 1.0
OD1 A:ASP97 3.5 47.0 1.0
MG A:MG201 3.6 31.0 1.0
NZ A:LYS142 3.7 40.6 1.0
OD1 A:ASP65 3.9 41.0 1.0
O6 A:POP180 3.9 33.0 1.0
OD1 A:ASP102 3.9 40.8 1.0
O A:HOH378 4.0 32.3 1.0
NZ A:LYS104 4.0 31.3 1.0
O2 A:POP180 4.1 29.1 1.0
OH A:TYR141 4.1 29.2 1.0
O3 A:POP180 4.3 30.9 1.0
CB A:ASP102 4.3 37.5 1.0
CB A:ASP97 4.3 42.1 1.0
O5 A:POP180 4.5 27.5 1.0
OD2 A:ASP70 4.6 29.4 1.0
CE A:LYS104 4.8 27.5 1.0
MG A:MG204 4.9 32.9 1.0
F A:F211 4.9 30.0 1.0
CG A:ASP65 4.9 47.6 1.0
CE A:LYS142 4.9 32.3 1.0

Magnesium binding site 4 out of 4 in 2auu

Go back to Magnesium Binding Sites List in 2auu
Magnesium binding site 4 out of 4 in the Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inorganic Pyrophosphatase Complexed with Magnesium Pyrophosphate and Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:32.9
occ:1.00
 O3 A:POP180 2.0 30.9 1.0
O6 A:POP180 2.0 33.0 1.0
O A:HOH479 2.0 34.3 1.0
O A:HOH480 2.0 27.1 0.7
O A:HOH378 2.0 32.3 1.0
OE2 A:GLU31 2.1 30.7 1.0
CD A:GLU31 3.1 32.3 1.0
P1 A:POP180 3.2 29.4 1.0
P2 A:POP180 3.3 29.4 1.0
OE1 A:GLU31 3.4 32.3 1.0
O A:POP180 3.5 29.2 1.0
O1 A:POP180 3.6 31.1 1.0
OD2 A:ASP67 3.8 44.2 1.0
NZ A:LYS29 3.9 29.7 1.0
O A:HOH411 4.0 38.3 0.5
O A:HOH353 4.1 29.7 1.0
O A:HOH462 4.1 42.2 0.6
NH1 A:ARG43 4.2 32.6 1.0
O4 A:POP180 4.2 33.9 1.0
OD2 A:ASP42 4.2 36.9 1.0
O A:HOH414 4.3 49.2 1.0
O5 A:POP180 4.4 27.5 1.0
O2 A:POP180 4.4 29.1 1.0
CG A:GLU31 4.5 28.6 1.0
O A:HOH364 4.5 34.9 1.0
CG A:ASP42 4.6 32.1 1.0
O A:HOH471 4.6 37.9 0.5
CE A:LYS29 4.6 26.7 1.0
OD1 A:ASP42 4.8 40.7 1.0
MG A:MG203 4.9 34.2 1.0
F A:F211 4.9 30.0 1.0

Reference:

V.R.Samygina, V.M.Moiseev, E.V.Rodina, N.N.Vorobyeva, A.N.Popov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva, H.D.Bartunik. Reversible Inhibition of Escherichia Coli Inorganic Pyrophosphatase By Fluoride: Trapped Catalytic Intermediates in Cryo-Crystallographic Studies J.Mol.Biol. V. 366 1305 2007.
ISSN: ISSN 0022-2836
PubMed: 17196979
DOI: 10.1016/J.JMB.2006.11.082
Page generated: Tue Aug 13 21:36:50 2024

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