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Magnesium in PDB 2ik2: Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate

Enzymatic activity of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate

All present enzymatic activity of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate:
3.6.1.1;

Protein crystallography data

The structure of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate, PDB code: 2ik2 was solved by E.Oksanen, A.K.Ahonen, H.Tuominen, V.Tuominen, R.Lahti, A.Goldman, P.Heikinheimo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.578, 93.366, 69.797, 90.00, 99.86, 90.00
R / Rfree (%) 17.5 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate (pdb code 2ik2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate, PDB code: 2ik2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2ik2

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Magnesium binding site 1 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg287

b:28.1
occ:1.00
 O A:HOH325 1.7 17.7 1.0
O A:HOH326 2.0 18.5 1.0
OD1 A:ASP152 2.0 21.3 1.0
OD2 A:ASP120 2.2 15.4 1.0
OE1 A:GLU115 2.2 31.4 1.0
O A:HOH317 2.2 16.6 1.0
CG A:ASP120 2.9 16.0 1.0
CD A:GLU115 3.1 34.1 1.0
CG A:ASP152 3.3 21.1 1.0
OD1 A:ASP120 3.4 14.3 1.0
OE2 A:GLU115 3.4 35.7 1.0
O A:HOH320 3.5 17.4 1.0
O A:HOH509 3.7 39.9 1.0
OE1 A:GLU101 3.7 34.8 1.0
OD2 A:ASP152 3.9 16.9 1.0
CB A:ASP120 4.0 15.1 1.0
O4 A:PO4292 4.0 25.0 1.0
OE2 A:GLU101 4.0 29.2 1.0
O A:TRP153 4.1 17.7 1.0
NZ A:LYS154 4.1 13.1 1.0
CA A:ASP152 4.1 21.7 1.0
CB A:ASP152 4.3 20.8 1.0
N A:ASP120 4.3 15.4 1.0
CD A:GLU101 4.3 32.2 1.0
O A:PRO118 4.3 19.3 1.0
MG A:MG288 4.4 17.5 1.0
C A:ASP152 4.5 20.2 1.0
CG A:GLU115 4.5 35.3 1.0
N A:TRP153 4.5 19.8 1.0
O3 A:PO4292 4.6 16.8 1.0
O A:HOH533 4.7 40.2 1.0
CA A:ASP120 4.8 14.9 1.0
CB A:GLU115 4.8 34.4 1.0
P A:PO4292 4.8 32.9 1.0
CE A:LYS154 4.9 13.0 1.0
MG A:MG290 5.0 39.2 1.0

Magnesium binding site 2 out of 8 in 2ik2

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Magnesium binding site 2 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg288

b:17.5
occ:1.00
 OD1 A:ASP120 2.0 14.3 1.0
O3 A:PO4292 2.1 16.8 1.0
O A:HOH337 2.1 19.8 1.0
O A:HOH320 2.1 17.4 1.0
O A:HOH319 2.1 16.5 1.0
O A:HOH332 2.2 19.3 1.0
CG A:ASP120 3.0 16.0 1.0
P A:PO4292 3.4 32.9 1.0
OD2 A:ASP120 3.4 15.4 1.0
O1 A:PO4292 3.6 33.2 1.0
O A:HOH325 3.7 17.7 1.0
O A:HOH326 4.0 18.5 1.0
O A:HOH329 4.0 19.5 1.0
OH A:TYR93 4.0 15.6 1.0
O4 A:PO4292 4.2 25.0 1.0
O A:HOH535 4.2 43.0 1.0
OD2 A:ASP117 4.2 33.2 1.0
O A:HOH439 4.3 34.7 1.0
CB A:ASP120 4.3 15.1 1.0
O A:PRO118 4.3 19.3 1.0
OE1 A:GLU48 4.3 16.0 1.0
CE1 A:TYR93 4.4 12.0 1.0
MG A:MG287 4.4 28.1 1.0
O2 A:PO4292 4.6 34.1 1.0
CZ A:TYR93 4.7 11.9 1.0
CG A:ASP117 4.7 30.4 1.0
NZ A:LYS56 4.7 25.6 1.0
OE2 A:GLU48 4.7 16.2 1.0
CA A:ASP120 4.7 14.9 1.0
O A:GLY94 4.7 12.1 1.0
O A:HOH308 4.9 13.9 1.0
CB A:ALA95 5.0 16.2 1.0
CD A:GLU48 5.0 17.6 1.0

Magnesium binding site 3 out of 8 in 2ik2

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Magnesium binding site 3 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg289

b:41.0
occ:1.00
 O1 A:PO4292 2.1 33.2 1.0
O1 A:PO4291 2.2 33.8 1.0
O A:HOH414 2.2 33.2 1.0
O A:HOH535 2.2 43.0 1.0
OE2 A:GLU58 2.4 27.6 1.0
CD A:GLU58 3.2 26.2 1.0
OE1 A:GLU58 3.3 24.6 1.0
P A:PO4291 3.4 37.5 1.0
O3 A:PO4291 3.4 33.4 1.0
P A:PO4292 3.6 32.9 1.0
NZ A:LYS56 4.0 25.6 1.0
O2 A:PO4292 4.1 34.1 1.0
O2 A:PO4291 4.2 29.6 1.0
O A:HOH320 4.2 17.4 1.0
O4 A:PO4292 4.3 25.0 1.0
OD2 A:ASP117 4.3 33.2 1.0
O A:HOH337 4.3 19.8 1.0
O3 A:PO4292 4.4 16.8 1.0
O4 A:PO4291 4.5 37.1 1.0
NH1 A:ARG78 4.6 33.4 1.0
CG A:GLU58 4.6 21.6 1.0
CE A:LYS56 4.6 24.1 1.0
OD2 A:ASP71 4.7 29.3 1.0
O A:HOH439 5.0 34.7 1.0

Magnesium binding site 4 out of 8 in 2ik2

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Magnesium binding site 4 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg290

b:39.2
occ:1.00
 O A:HOH533 2.1 40.2 1.0
O3 A:PO4291 2.2 33.4 1.0
OD2 A:ASP152 2.4 16.9 1.0
O4 A:PO4292 2.4 25.0 1.0
OD2 A:ASP147 3.0 40.3 1.0
CG A:ASP152 3.3 21.1 1.0
O A:HOH326 3.4 18.5 1.0
CG A:ASP147 3.5 38.8 1.0
P A:PO4291 3.5 37.5 1.0
O A:HOH404 3.5 30.3 1.0
CB A:ASP147 3.6 36.7 1.0
P A:PO4292 3.7 32.9 1.0
OE2 A:GLU115 3.9 35.7 1.0
OD1 A:ASP152 3.9 21.3 1.0
OH A:TYR192 4.0 19.4 1.0
O2 A:PO4291 4.0 29.6 1.0
O2 A:PO4292 4.0 34.1 1.0
NZ A:LYS154 4.1 13.1 1.0
O1 A:PO4292 4.1 33.2 1.0
O4 A:PO4291 4.2 37.1 1.0
CB A:ASP152 4.4 20.8 1.0
OD1 A:ASP147 4.4 38.6 1.0
O1 A:PO4291 4.5 33.8 1.0
NZ A:LYS193 4.6 25.3 1.0
CD A:GLU115 4.9 34.1 1.0
OD2 A:ASP120 4.9 15.4 1.0
MG A:MG287 5.0 28.1 1.0
O3 A:PO4292 5.0 16.8 1.0

Magnesium binding site 5 out of 8 in 2ik2

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Magnesium binding site 5 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg287

b:22.0
occ:1.00
 OE1 B:GLU115 1.8 31.1 1.0
OD2 B:ASP120 2.0 14.2 1.0
O4 B:PO4291 2.1 28.6 1.0
OD1 B:ASP152 2.2 24.0 1.0
O B:HOH327 2.3 17.1 1.0
O B:HOH376 2.5 22.4 1.0
CD B:GLU115 2.9 33.8 1.0
CG B:ASP120 3.0 14.2 1.0
CG B:ASP152 3.1 21.2 1.0
OD1 B:ASP120 3.2 12.0 1.0
P B:PO4291 3.2 34.7 1.0
OD2 B:ASP152 3.3 23.9 1.0
OE2 B:GLU115 3.4 34.0 1.0
MG B:MG290 3.5 37.3 1.0
O3 B:PO4291 3.5 18.6 1.0
MG B:MG288 3.6 15.8 1.0
O2 B:PO4291 3.8 36.3 1.0
NZ B:LYS154 3.8 19.3 1.0
O B:HOH354 3.9 19.9 1.0
CG B:GLU115 4.2 31.5 1.0
CB B:ASP120 4.3 11.8 1.0
CB B:ASP152 4.3 18.7 1.0
OH B:TYR93 4.4 14.8 1.0
O B:HOH474 4.5 30.8 1.0
O1 B:PO4291 4.5 34.2 1.0
CB B:GLU115 4.6 28.6 1.0
O1 B:PO4292 4.6 42.9 1.0
OD2 B:ASP117 4.7 19.7 1.0
O B:HOH299 4.7 11.8 1.0
CB B:ASP117 4.7 15.1 1.0
O B:HOH564 4.8 39.3 1.0
CA B:ASP152 4.8 18.4 1.0
O B:PRO118 4.8 13.4 1.0

Magnesium binding site 6 out of 8 in 2ik2

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Magnesium binding site 6 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg288

b:15.8
occ:1.00
 OD1 B:ASP120 2.0 12.0 1.0
O B:HOH327 2.0 17.1 1.0
O B:HOH315 2.1 14.6 1.0
O B:HOH303 2.1 12.4 1.0
O3 B:PO4291 2.1 18.6 1.0
O B:HOH299 2.1 11.8 1.0
CG B:ASP120 3.1 14.2 1.0
P B:PO4291 3.2 34.7 1.0
O2 B:PO4291 3.4 36.3 1.0
OD2 B:ASP120 3.5 14.2 1.0
MG B:MG287 3.6 22.0 1.0
O4 B:PO4291 3.9 28.6 1.0
O B:HOH322 4.0 15.7 1.0
OH B:TYR93 4.0 14.8 1.0
OD2 B:ASP117 4.1 19.7 1.0
O B:PRO118 4.2 13.4 1.0
O B:HOH376 4.3 22.4 1.0
CB B:ASP120 4.3 11.8 1.0
OE1 B:GLU48 4.4 12.1 1.0
CG B:ASP117 4.4 17.5 1.0
O1 B:PO4291 4.5 34.2 1.0
CE2 B:TYR93 4.5 11.3 1.0
CB B:ASP117 4.5 15.1 1.0
NZ B:LYS56 4.6 19.5 1.0
O B:HOH374 4.6 21.9 1.0
CA B:ASP120 4.7 11.5 1.0
CZ B:TYR93 4.7 13.0 1.0
O B:GLY94 4.7 10.2 1.0
OE1 B:GLU115 4.8 31.1 1.0
OE2 B:GLU48 4.9 13.0 1.0
O B:HOH312 5.0 14.1 1.0
N B:ASP120 5.0 12.2 1.0

Magnesium binding site 7 out of 8 in 2ik2

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Magnesium binding site 7 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg289

b:44.3
occ:1.00
 O2 B:PO4291 1.9 36.3 1.0
O4 B:PO4292 1.9 43.2 1.0
O B:HOH564 2.2 39.3 1.0
OE2 B:GLU58 2.2 27.8 1.0
O B:HOH665 2.4 50.8 1.0
O B:HOH605 2.5 43.5 1.0
P B:PO4292 3.2 43.7 1.0
P B:PO4291 3.2 34.7 1.0
CD B:GLU58 3.3 24.2 1.0
O1 B:PO4292 3.3 42.9 1.0
O1 B:PO4291 3.4 34.2 1.0
OE1 B:GLU58 3.6 24.8 1.0
NZ B:LYS56 3.8 19.5 1.0
OD2 B:ASP117 4.0 19.7 1.0
O3 B:PO4292 4.1 39.4 1.0
O4 B:PO4291 4.1 28.6 1.0
CE B:LYS56 4.1 26.8 1.0
O B:HOH648 4.1 44.2 1.0
O B:HOH315 4.2 14.6 1.0
O2 B:PO4292 4.2 44.2 1.0
O3 B:PO4291 4.3 18.6 1.0
O B:HOH327 4.3 17.1 1.0
NH1 B:ARG78 4.4 33.8 1.0
CG B:GLU58 4.6 19.9 1.0
OE2 B:GLU115 4.7 34.0 1.0
MG B:MG290 4.9 37.3 1.0
CD B:LYS56 4.9 22.5 1.0

Magnesium binding site 8 out of 8 in 2ik2

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Magnesium binding site 8 out of 8 in the Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast Inorganic Pyrophosphatase Variant D115E with Magnesium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg290

b:37.3
occ:1.00
 OD2 B:ASP147 1.8 26.8 1.0
O1 B:PO4292 2.0 42.9 1.0
OE2 B:GLU115 2.1 34.0 1.0
O4 B:PO4291 2.2 28.6 1.0
O B:HOH474 2.4 30.8 1.0
OD2 B:ASP152 2.5 23.9 1.0
CG B:ASP147 3.0 26.7 1.0
CD B:GLU115 3.1 33.8 1.0
P B:PO4291 3.4 34.7 1.0
CG B:ASP152 3.4 21.2 1.0
OE1 B:GLU115 3.4 31.1 1.0
P B:PO4292 3.4 43.7 1.0
MG B:MG287 3.5 22.0 1.0
CB B:ASP147 3.6 24.6 1.0
O1 B:PO4291 3.6 34.2 1.0
OD1 B:ASP152 3.9 24.0 1.0
NZ B:LYS154 3.9 19.3 1.0
O B:HOH564 3.9 39.3 1.0
O2 B:PO4291 4.0 36.3 1.0
OD1 B:ASP147 4.0 25.4 1.0
O3 B:PO4292 4.0 39.4 1.0
OH B:TYR192 4.0 17.1 1.0
O2 B:PO4292 4.1 44.2 1.0
CB B:ASP152 4.4 18.7 1.0
O B:HOH594 4.4 41.3 1.0
O4 B:PO4292 4.4 43.2 1.0
CG B:GLU115 4.5 31.5 1.0
OD2 B:ASP120 4.5 14.2 1.0
O B:HOH613 4.5 43.8 1.0
O3 B:PO4291 4.6 18.6 1.0
NZ B:LYS193 4.8 23.8 1.0
O B:HOH327 4.8 17.1 1.0
MG B:MG289 4.9 44.3 1.0

Reference:

E.Oksanen, A.K.Ahonen, H.Tuominen, V.Tuominen, R.Lahti, A.Goldman, P.Heikinheimo. A Complete Structural Description of the Catalytic Cycle of Yeast Pyrophosphatase. Biochemistry V. 46 1228 2007.
ISSN: ISSN 0006-2960
PubMed: 17260952
DOI: 10.1021/BI0619977
Page generated: Wed Aug 14 00:11:13 2024

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