Atomistry » Manganese » PDB 1w2c-1xie » 1wgj
Atomistry »
  Manganese »
    PDB 1w2c-1xie »
      1wgj »

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

Go back to Manganese Binding Sites List in 1wgj
Manganese binding site 1 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 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

Go back to Manganese Binding Sites List in 1wgj
Manganese binding site 2 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 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

Go back to Manganese Binding Sites List in 1wgj
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

Go back to Manganese Binding Sites List in 1wgj
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

Go back to Manganese Binding Sites List in 1wgj
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

Go back to Manganese Binding Sites List in 1wgj
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

Go back to Manganese Binding Sites List in 1wgj
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

Go back to Manganese Binding Sites List in 1wgj
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy