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Manganese in PDB 1wgj: Structure of Inorganic Pyrophosphatase

Enzymatic activity of Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1wgj was solved by P.Heikinheimo, J.Lehtonen, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.100, 103.800, 117.200, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Inorganic Pyrophosphatase (pdb code 1wgj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of Inorganic Pyrophosphatase, PDB code: 1wgj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1wgj

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Manganese binding site 1 out of 8 in the Structure of Inorganic Pyrophosphatase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn287

b:15.2
occ:1.00
 OD1 A:ASP152 2.3 9.9 1.0
O2 A:PO4292 2.3 6.5 1.0
OD2 A:ASP115 2.4 9.4 1.0
O A:HOH293 2.4 17.3 1.0
O A:HOH294 2.5 6.1 1.0
OD2 A:ASP120 2.5 6.2 1.0
CG A:ASP152 3.2 13.8 1.0
CG A:ASP115 3.2 13.0 1.0
CG A:ASP120 3.3 5.3 1.0
OD1 A:ASP120 3.3 6.5 1.0
P A:PO4292 3.4 10.5 1.0
OD2 A:ASP152 3.5 8.8 1.0
O4 A:PO4292 3.5 8.6 1.0
OD1 A:ASP115 3.5 9.6 1.0
MN A:MN288 3.6 16.3 1.0
O A:HOH301 3.8 14.1 1.0
MN A:MN290 3.8 11.5 1.0
O1 A:PO4292 3.9 9.8 1.0
O A:HOH316 4.0 9.6 1.0
NZ A:LYS154 4.0 5.0 1.0
CB A:ASP117 4.4 11.4 1.0
CB A:ASP115 4.5 8.9 1.0
CB A:ASP152 4.5 12.1 1.0
OH A:TYR93 4.5 7.3 1.0
OD2 A:ASP117 4.5 10.9 1.0
O3 A:PO4292 4.6 13.8 1.0
O A:PRO118 4.6 9.5 1.0
CB A:ASP120 4.7 7.8 1.0
O A:HOH298 4.9 16.1 1.0
O A:HOH302 4.9 6.8 1.0
O A:HOH423 4.9 19.1 1.0
CA A:ASP152 5.0 12.5 1.0
CG A:ASP117 5.0 11.9 1.0

Manganese binding site 2 out of 8 in 1wgj

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Manganese binding site 2 out of 8 in the Structure of Inorganic Pyrophosphatase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn288

b:16.3
occ:1.00
 OD1 A:ASP120 2.3 6.5 1.0
O4 A:PO4292 2.3 8.6 1.0
O A:HOH297 2.4 22.0 1.0
O A:HOH296 2.4 11.9 1.0
O A:HOH295 2.4 10.1 1.0
O A:HOH293 2.5 17.3 1.0
O1 A:PO4292 3.2 9.8 1.0
CG A:ASP120 3.3 5.3 1.0
P A:PO4292 3.3 10.5 1.0
MN A:MN287 3.6 15.2 1.0
O2 A:PO4292 3.7 6.5 1.0
OD2 A:ASP120 3.8 6.2 1.0
OH A:TYR93 4.1 7.3 1.0
O A:HOH312 4.1 15.2 1.0
O A:PRO118 4.2 9.5 1.0
OE1 A:GLU48 4.2 5.6 1.0
OD2 A:ASP117 4.3 10.9 1.0
CE2 A:TYR93 4.3 5.2 1.0
O A:HOH294 4.4 6.1 1.0
O3 A:PO4292 4.5 13.8 1.0
CB A:ASP120 4.5 7.8 1.0
CG A:ASP117 4.5 11.9 1.0
CB A:ASP117 4.5 11.4 1.0
O A:HOH349 4.6 8.7 1.0
CZ A:TYR93 4.6 7.0 1.0
OE2 A:GLU48 4.7 5.9 1.0
O A:GLY94 4.9 12.1 1.0
CB A:ALA95 4.9 11.1 1.0
CD A:GLU48 4.9 5.8 1.0
O A:HOH344 4.9 10.3 1.0
CA A:ASP120 4.9 11.5 1.0

Manganese binding site 3 out of 8 in 1wgj

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Manganese binding site 3 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn289

b:14.8
occ:1.00
 O1 A:PO4291 2.4 6.9 1.0
O1 A:PO4292 2.4 9.8 1.0
O A:HOH299 2.4 18.1 1.0
OE2 A:GLU58 2.5 12.3 1.0
O A:HOH300 2.5 12.4 1.0
O A:HOH298 2.5 16.1 1.0
CD A:GLU58 3.4 10.5 1.0
P A:PO4291 3.4 13.1 1.0
O4 A:PO4291 3.5 13.4 1.0
P A:PO4292 3.5 10.5 1.0
OE1 A:GLU58 3.6 15.6 1.0
NZ A:LYS56 3.8 8.2 1.0
O3 A:PO4292 4.1 13.8 1.0
O A:HOH295 4.1 10.1 1.0
O2 A:PO4292 4.1 6.5 1.0
O A:HOH423 4.2 19.1 1.0
OD2 A:ASP117 4.2 10.9 1.0
O A:HOH293 4.3 17.3 1.0
NH1 A:ARG78 4.3 12.2 1.0
O3 A:PO4291 4.4 12.5 1.0
O2 A:PO4291 4.5 14.1 1.0
OD2 A:ASP71 4.6 11.5 1.0
O4 A:PO4292 4.6 8.6 1.0
CE A:LYS56 4.6 13.9 1.0
CG A:GLU58 4.7 10.9 1.0
O A:HOH375 4.8 28.4 1.0
O A:HOH301 4.9 14.1 1.0
MN A:MN290 5.0 11.5 1.0

Manganese binding site 4 out of 8 in 1wgj

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Manganese binding site 4 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn290

b:11.5
occ:1.00
 O A:HOH301 2.3 14.1 1.0
O4 A:PO4291 2.3 13.4 1.0
OD2 A:ASP147 2.3 13.2 1.0
O2 A:PO4292 2.4 6.5 1.0
OD2 A:ASP152 2.4 8.8 1.0
O A:HOH302 2.4 6.8 1.0
P A:PO4292 3.3 10.5 1.0
CG A:ASP147 3.4 14.0 1.0
CG A:ASP152 3.4 13.8 1.0
O3 A:PO4292 3.5 13.8 1.0
P A:PO4291 3.5 13.1 1.0
MN A:MN287 3.8 15.2 1.0
CB A:ASP147 3.8 10.7 1.0
O3 A:PO4291 3.8 12.5 1.0
O A:HOH298 3.9 16.1 1.0
OD1 A:ASP152 4.0 9.9 1.0
O A:HOH351 4.0 21.4 1.0
OH A:TYR192 4.1 12.4 1.0
NZ A:LYS154 4.1 5.0 1.0
OD2 A:ASP115 4.2 9.4 1.0
O1 A:PO4292 4.2 9.8 1.0
O2 A:PO4291 4.3 14.1 1.0
O A:HOH331 4.4 12.0 1.0
O4 A:PO4292 4.4 8.6 1.0
O1 A:PO4291 4.5 6.9 1.0
OD1 A:ASP147 4.5 12.7 1.0
CB A:ASP152 4.6 12.1 1.0
OD2 A:ASP120 4.9 6.2 1.0
O A:HOH293 4.9 17.3 1.0
NZ A:LYS193 4.9 11.1 1.0
MN A:MN289 5.0 14.8 1.0

Manganese binding site 5 out of 8 in 1wgj

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Manganese binding site 5 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn287

b:10.7
occ:1.00
 OD1 B:ASP152 2.3 8.6 1.0
OD2 B:ASP115 2.4 8.3 1.0
OD2 B:ASP120 2.4 8.2 1.0
O2 B:PO4292 2.4 5.1 1.0
O B:HOH293 2.4 14.5 1.0
O B:HOH294 2.5 5.4 1.0
CG B:ASP152 3.2 9.5 1.0
CG B:ASP115 3.2 15.3 1.0
CG B:ASP120 3.3 11.4 1.0
OD2 B:ASP152 3.4 9.0 1.0
OD1 B:ASP120 3.5 10.4 1.0
O4 B:PO4292 3.5 6.2 1.0
OD1 B:ASP115 3.5 14.1 1.0
P B:PO4292 3.5 11.6 1.0
MN B:MN290 3.7 12.0 1.0
MN B:MN288 3.7 12.5 1.0
O B:HOH301 3.7 7.9 1.0
O1 B:PO4292 4.0 8.7 1.0
O B:HOH316 4.1 8.1 1.0
NZ B:LYS154 4.1 10.3 1.0
CB B:ASP115 4.5 13.8 1.0
CB B:ASP152 4.5 6.5 1.0
CB B:ASP117 4.6 11.4 1.0
CB B:ASP120 4.6 5.1 1.0
OD2 B:ASP117 4.7 13.8 1.0
O B:HOH295 4.7 11.8 1.0
OH B:TYR93 4.7 7.7 1.0
O B:PRO118 4.7 9.1 1.0
O3 B:PO4292 4.8 10.7 1.0
O B:HOH302 4.8 12.6 1.0
O B:HOH299 4.9 9.4 1.0
CA B:ASP152 4.9 8.8 1.0
O B:HOH337 5.0 13.0 1.0

Manganese binding site 6 out of 8 in 1wgj

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Manganese binding site 6 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn288

b:12.5
occ:1.00
 O4 B:PO4292 2.3 6.2 1.0
O B:HOH296 2.3 5.8 1.0
OD1 B:ASP120 2.3 10.4 1.0
O B:HOH297 2.4 2.7 1.0
O B:HOH295 2.4 11.8 1.0
O B:HOH293 2.5 14.5 1.0
O1 B:PO4292 3.2 8.7 1.0
P B:PO4292 3.3 11.6 1.0
CG B:ASP120 3.3 11.4 1.0
O2 B:PO4292 3.7 5.1 1.0
OD2 B:ASP120 3.7 8.2 1.0
MN B:MN287 3.7 10.7 1.0
O B:HOH359 3.8 7.8 1.0
OH B:TYR93 4.1 7.7 1.0
OE1 B:GLU48 4.2 9.0 1.0
OD2 B:ASP117 4.3 13.8 1.0
O B:PRO118 4.3 9.1 1.0
O B:HOH294 4.3 5.4 1.0
CE2 B:TYR93 4.4 4.2 1.0
O3 B:PO4292 4.5 10.7 1.0
CB B:ASP120 4.5 5.1 1.0
O B:HOH303 4.6 17.4 1.0
CG B:ASP117 4.6 12.4 1.0
CB B:ASP117 4.7 11.4 1.0
OE2 B:GLU48 4.7 9.8 1.0
CZ B:TYR93 4.7 7.7 1.0
O B:HOH353 4.7 9.0 1.0
O B:GLY94 4.7 4.6 1.0
CD B:GLU48 4.9 8.8 1.0
NZ B:LYS56 4.9 5.7 1.0
CA B:ASP120 4.9 6.9 1.0
O B:HOH300 5.0 24.7 1.0
CB B:ALA95 5.0 10.6 1.0

Manganese binding site 7 out of 8 in 1wgj

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Manganese binding site 7 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn289

b:15.0
occ:1.00
 O B:HOH300 2.3 24.7 1.0
O B:HOH299 2.3 9.4 1.0
OE2 B:GLU58 2.4 15.6 1.0
O1 B:PO4292 2.4 8.7 1.0
O2 B:PO4291 2.4 6.8 1.0
O B:HOH298 2.5 13.2 1.0
CD B:GLU58 3.3 14.1 1.0
P B:PO4291 3.4 10.0 1.0
O3 B:PO4291 3.4 7.0 1.0
OE1 B:GLU58 3.4 17.6 1.0
P B:PO4292 3.5 11.6 1.0
NZ B:LYS56 3.9 5.7 1.0
O B:HOH297 4.1 2.7 1.0
O2 B:PO4292 4.1 5.1 1.0
O3 B:PO4292 4.2 10.7 1.0
O B:HOH337 4.2 13.0 1.0
O1 B:PO4291 4.2 9.4 1.0
O B:HOH293 4.2 14.5 1.0
OD2 B:ASP117 4.3 13.8 1.0
O4 B:PO4291 4.4 8.9 1.0
NH1 B:ARG78 4.4 6.8 1.0
CG B:GLU58 4.6 10.7 1.0
O4 B:PO4292 4.6 6.2 1.0
CE B:LYS56 4.6 6.2 1.0
OD2 B:ASP71 4.8 16.6 1.0
O B:HOH415 4.8 46.0 1.0
O B:HOH301 4.9 7.9 1.0
MN B:MN290 5.0 12.0 1.0

Manganese binding site 8 out of 8 in 1wgj

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Manganese binding site 8 out of 8 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn290

b:12.0
occ:1.00
 OD2 B:ASP147 2.3 7.2 1.0
O B:HOH301 2.4 7.9 1.0
OD2 B:ASP152 2.4 9.0 1.0
O3 B:PO4291 2.4 7.0 1.0
O2 B:PO4292 2.4 5.1 1.0
O B:HOH302 2.6 12.6 1.0
CG B:ASP147 3.4 9.3 1.0
CG B:ASP152 3.4 9.5 1.0
P B:PO4292 3.4 11.6 1.0
P B:PO4291 3.5 10.0 1.0
MN B:MN287 3.7 10.7 1.0
O3 B:PO4292 3.7 10.7 1.0
CB B:ASP147 3.8 5.9 1.0
O B:HOH396 3.8 17.8 1.0
OD1 B:ASP152 3.8 8.6 1.0
O B:HOH299 3.9 9.4 1.0
O1 B:PO4291 4.0 9.4 1.0
OH B:TYR192 4.0 11.5 1.0
OD2 B:ASP115 4.1 8.3 1.0
NZ B:LYS154 4.2 10.3 1.0
O1 B:PO4292 4.2 8.7 1.0
O B:HOH329 4.2 13.3 1.0
O4 B:PO4291 4.3 8.9 1.0
OD1 B:ASP147 4.5 9.3 1.0
O4 B:PO4292 4.5 6.2 1.0
O2 B:PO4291 4.5 6.8 1.0
CB B:ASP152 4.6 6.5 1.0
NZ B:LYS193 4.7 8.3 1.0
O B:HOH293 4.8 14.5 1.0
OD2 B:ASP120 4.9 8.2 1.0
MN B:MN289 5.0 15.0 1.0

Reference:

P.Heikinheimo, J.Lehtonen, A.Baykov, R.Lahti, B.S.Cooperman, A.Goldman. The Structural Basis For Pyrophosphatase Catalysis. Structure V. 4 1491 1996.
ISSN: ISSN 0969-2126
PubMed: 8994974
DOI: 10.1016/S0969-2126(96)00155-4
Page generated: Sat Oct 5 12:54:41 2024

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