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Magnesium in PDB 2iw4: Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp

Enzymatic activity of Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp

All present enzymatic activity of Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp, PDB code: 2iw4 was solved by I.P.Fabrichniy, L.Lehtio, E.Oksanen, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.908, 115.249, 148.060, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.5

Other elements in 2iw4:

The structure of Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp also contains other interesting chemical elements:

Manganese (Mn) 3 atoms
Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp (pdb code 2iw4). 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 Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp, PDB code: 2iw4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2iw4

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Magnesium binding site 1 out of 4 in the Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp


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 Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1311

b:21.9
occ:1.00
 O2 A:2PN1315 1.9 19.1 1.0
O A:HOH2013 2.0 19.4 1.0
O A:HOH2198 2.0 24.6 1.0
O5 A:2PN1315 2.1 22.9 1.0
O A:HOH2199 2.1 25.4 1.0
O A:HOH2131 2.1 17.1 1.0
MG A:MG1312 3.1 39.7 1.0
P1 A:2PN1315 3.2 23.1 1.0
P2 A:2PN1315 3.3 23.3 1.0
N1 A:2PN1315 3.6 21.9 1.0
O A:HOH2146 3.6 20.5 1.0
O A:HOH2196 3.6 26.3 1.0
NH2 A:ARG295 3.8 28.0 1.0
OD1 A:ASP13 3.9 35.4 1.0
O A:HOH2106 3.9 26.1 1.0
O3 A:2PN1315 3.9 20.4 1.0
O4 A:2PN1315 4.1 22.8 1.0
OD2 A:ASP203 4.2 33.8 1.0
O1 A:2PN1315 4.4 23.8 1.0
OD1 A:ASP203 4.4 33.7 1.0
OD1 A:ASP149 4.5 32.6 1.0
OE1 A:GLN218 4.5 36.0 1.0
O A:HOH2195 4.5 26.1 1.0
O A:HOH2014 4.5 31.6 1.0
O6 A:2PN1315 4.5 20.6 1.0
CG A:ASP203 4.8 32.6 1.0
O A:HOH2147 4.8 28.7 1.0
CZ A:ARG295 4.9 31.0 1.0
FE A:FE1309 4.9 42.5 0.9
MN A:MN1313 4.9 42.5 0.1
CG A:ASP13 5.0 32.5 1.0

Magnesium binding site 2 out of 4 in 2iw4

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Magnesium binding site 2 out of 4 in the Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp


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 Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1312

b:39.7
occ:1.00
 O A:HOH2195 2.1 26.1 1.0
OD1 A:ASP149 2.1 32.6 1.0
O A:HOH2199 2.2 25.4 1.0
O2 A:2PN1315 2.4 19.1 1.0
O A:HOH2105 2.6 24.4 1.0
OD1 A:ASP13 2.6 35.4 1.0
MG A:MG1311 3.1 21.9 1.0
CG A:ASP13 3.1 32.5 1.0
CG A:ASP149 3.2 33.8 1.0
P1 A:2PN1315 3.4 23.1 1.0
FE A:FE1309 3.5 42.5 0.9
MN A:MN1313 3.5 42.5 0.1
O A:HOH2013 3.5 19.4 1.0
OD2 A:ASP13 3.7 32.8 1.0
OD2 A:ASP149 3.8 34.2 1.0
CB A:ASP13 3.8 31.1 1.0
O3 A:2PN1315 3.8 20.4 1.0
O A:HOH2196 3.9 26.3 1.0
O1 A:2PN1315 3.9 23.8 1.0
FE A:FE1310 4.0 42.1 0.7
MN A:MN1314 4.0 42.1 0.3
O A:HOH2198 4.0 24.6 1.0
O A:HOH2014 4.2 31.6 1.0
CB A:ASP15 4.3 32.6 1.0
CA A:ASP149 4.3 32.3 1.0
CB A:ASP149 4.4 31.8 1.0
O A:HOH2106 4.5 26.1 1.0
OG A:SER148 4.5 30.3 1.0
N A:ASP149 4.7 32.1 1.0
O A:HOH2131 4.8 17.1 1.0
N1 A:2PN1315 4.8 21.9 1.0
N A:ASP15 4.8 32.7 1.0
O5 A:2PN1315 4.9 22.9 1.0

Magnesium binding site 3 out of 4 in 2iw4

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Magnesium binding site 3 out of 4 in the Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp


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 Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1313

b:23.4
occ:1.00
 O5 B:2PN1318 1.9 22.2 1.0
O2 B:2PN1318 2.0 19.0 1.0
O B:HOH2285 2.0 21.1 1.0
O B:HOH2023 2.1 22.9 1.0
O B:HOH2219 2.1 20.3 1.0
O B:HOH2286 2.2 17.1 1.0
P1 B:2PN1318 3.2 20.5 1.0
P2 B:2PN1318 3.2 22.1 1.0
MG B:MG1314 3.4 33.0 1.0
N1 B:2PN1318 3.5 21.1 1.0
O B:HOH2284 3.7 20.4 1.0
O B:HOH2234 3.7 20.9 1.0
NH2 B:ARG295 3.7 29.7 1.0
OD1 B:ASP13 3.8 33.2 1.0
O3 B:2PN1318 3.8 17.7 1.0
O B:HOH2188 4.1 28.0 1.0
OD2 B:ASP203 4.1 31.1 1.0
O4 B:2PN1318 4.1 23.8 1.0
O6 B:2PN1318 4.3 21.4 1.0
O1 B:2PN1318 4.4 20.9 1.0
OD1 B:ASP203 4.4 30.0 1.0
OE1 B:GLN218 4.5 29.2 1.0
O B:HOH2026 4.5 33.1 1.0
O B:HOH2235 4.6 30.7 1.0
CG B:ASP203 4.7 31.1 1.0
OD1 B:ASP149 4.7 33.9 1.0
O B:HOH2283 4.8 15.4 1.0
CZ B:ARG295 4.8 32.9 1.0
FE B:FE1311 4.9 37.9 1.0
CG B:ASP13 4.9 31.2 1.0
NZ B:LYS205 5.0 23.5 1.0

Magnesium binding site 4 out of 4 in 2iw4

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Magnesium binding site 4 out of 4 in the Crystal Structure of Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp


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 Basillus Subtilis Family II Inorganic Pyrophosphatase Mutant, H98Q, in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1314

b:33.0
occ:1.00
 OD1 B:ASP149 2.1 33.9 1.0
O B:HOH2283 2.3 15.4 1.0
O B:HOH2285 2.4 21.1 1.0
O2 B:2PN1318 2.4 19.0 1.0
O B:HOH2187 2.4 19.4 1.0
OD1 B:ASP13 2.5 33.2 1.0
CG B:ASP13 3.0 31.2 1.0
CG B:ASP149 3.2 31.6 1.0
FE B:FE1311 3.3 37.9 1.0
MG B:MG1313 3.4 23.4 1.0
P1 B:2PN1318 3.4 20.5 1.0
OD2 B:ASP13 3.5 30.3 1.0
O B:HOH2023 3.6 22.9 1.0
OD2 B:ASP149 3.7 30.8 1.0
CB B:ASP13 3.7 30.4 1.0
O3 B:2PN1318 3.8 17.7 1.0
O B:HOH2284 3.9 20.4 1.0
FE B:FE1312 3.9 36.5 0.8
MN B:MN1317 3.9 36.5 0.2
O1 B:2PN1318 3.9 20.9 1.0
O B:HOH2026 4.0 33.1 1.0
CB B:ASP15 4.1 32.6 1.0
O B:HOH2286 4.3 17.1 1.0
CB B:ASP149 4.4 30.1 1.0
CA B:ASP149 4.4 31.0 1.0
OG B:SER148 4.5 30.9 1.0
N B:ASP15 4.6 30.5 1.0
O B:HOH2188 4.7 28.0 1.0
N B:ASP149 4.8 30.8 1.0
OD1 B:ASP75 5.0 32.8 1.0
N1 B:2PN1318 5.0 21.1 1.0
O5 B:2PN1318 5.0 22.2 1.0
O B:HOH2219 5.0 20.3 1.0

Reference:

I.P.Fabrichniy, L.Lehtio, M.Tammenkoski, A.B.Zyryanov, E.Oksanen, A.A.Baykov, R.Lahti, A.Goldman. A Trimetal Site and Substrate Distortion in A Family II Inorganic Pyrophosphatase. J.Biol.Chem. V. 282 1422 2007.
ISSN: ISSN 0021-9258
PubMed: 17095506
DOI: 10.1074/JBC.M513161200
Page generated: Wed Aug 14 00:19:27 2024

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