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Manganese in PDB 1wgi: 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: 1wgi was solved by P.Heikinheimo, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.300, 68.400, 161.900, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.1

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 1wgi

Go back to Manganese Binding Sites List in 1wgi
Manganese binding site 1 out of 4 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:19.9
occ:1.00
 O A:HOH291 2.3 19.6 1.0
O A:HOH290 2.3 11.1 1.0
OD1 A:ASP152 2.4 30.5 1.0
OD2 A:ASP120 2.5 16.1 1.0
OD2 A:ASP115 2.5 22.4 1.0
O A:HOH289 2.6 14.0 1.0
CG A:ASP120 3.2 12.1 1.0
CG A:ASP115 3.2 16.8 1.0
CG A:ASP152 3.4 21.0 1.0
OD1 A:ASP115 3.5 12.7 1.0
OD1 A:ASP120 3.8 13.6 1.0
OD2 A:ASP152 4.1 35.3 1.0
CA A:ASP152 4.1 22.4 1.0
O A:TRP153 4.1 9.9 1.0
CB A:ASP120 4.2 6.5 1.0
OE2 A:GLU101 4.2 27.6 1.0
O A:HOH295 4.3 19.1 1.0
CB A:ASP152 4.3 25.6 1.0
NZ A:LYS154 4.3 5.8 1.0
O A:HOH313 4.3 30.9 1.0
CB A:ASP115 4.4 15.3 1.0
C A:ASP152 4.5 21.9 1.0
N A:ASP120 4.5 16.0 1.0
O A:PRO118 4.6 5.2 1.0
N A:TRP153 4.6 14.2 1.0
CD A:GLU101 4.7 28.7 1.0
OE1 A:GLU101 4.9 27.4 1.0
MN A:MN288 4.9 23.3 1.0
CA A:ASP120 5.0 13.0 1.0

Manganese binding site 2 out of 4 in 1wgi

Go back to Manganese Binding Sites List in 1wgi
Manganese binding site 2 out of 4 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:23.3
occ:1.00
 OD1 A:ASP120 2.3 13.6 1.0
O A:HOH292 2.4 14.5 1.0
O A:HOH295 2.5 19.1 1.0
O A:HOH296 2.5 24.1 1.0
O A:HOH293 2.5 29.8 1.0
O A:HOH294 2.5 16.6 1.0
CG A:ASP120 3.3 12.1 1.0
OD2 A:ASP120 3.7 16.1 1.0
O A:HOH304 3.9 19.0 1.0
OE1 A:GLU48 4.1 11.6 1.0
OH A:TYR93 4.2 22.5 1.0
O A:HOH291 4.2 19.6 1.0
O A:HOH289 4.3 14.0 1.0
CE2 A:TYR93 4.3 18.6 1.0
O A:HOH367 4.4 24.4 1.0
O A:PRO118 4.5 5.2 1.0
CB A:ASP120 4.6 6.5 1.0
O A:HOH320 4.6 23.5 1.0
CZ A:TYR93 4.7 24.1 1.0
OE2 A:GLU48 4.7 20.0 1.0
O A:HOH348 4.8 32.3 1.0
OD2 A:ASP117 4.8 23.4 1.0
CD A:GLU48 4.8 15.1 1.0
CB A:ALA95 4.8 10.8 1.0
O A:GLY94 4.9 14.8 1.0
CA A:ASP120 4.9 13.0 1.0
CB A:ASP117 4.9 17.1 1.0
MN A:MN287 4.9 19.9 1.0
CG A:ASP117 5.0 17.5 1.0

Manganese binding site 3 out of 4 in 1wgi

Go back to Manganese Binding Sites List in 1wgi
Manganese binding site 3 out of 4 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
B:Mn287

b:21.2
occ:1.00
 O B:HOH290 2.3 8.2 1.0
OD1 B:ASP152 2.4 18.0 1.0
O B:HOH289 2.5 35.8 1.0
OD2 B:ASP115 2.5 28.3 1.0
OD2 B:ASP120 2.5 15.5 1.0
O B:HOH291 2.5 12.1 1.0
CG B:ASP115 3.2 17.3 1.0
CG B:ASP120 3.2 8.2 1.0
CG B:ASP152 3.4 22.5 1.0
OD1 B:ASP115 3.5 18.7 1.0
OD1 B:ASP120 3.7 15.1 1.0
OD2 B:ASP152 4.1 23.6 1.0
CA B:ASP152 4.2 18.1 1.0
CB B:ASP120 4.2 4.1 1.0
O B:HOH383 4.2 37.6 1.0
O B:TRP153 4.3 14.6 1.0
CB B:ASP152 4.3 18.9 1.0
OE2 B:GLU101 4.3 26.1 1.0
CB B:ASP115 4.4 19.1 1.0
NZ B:LYS154 4.4 9.4 1.0
O B:HOH294 4.5 22.4 1.0
C B:ASP152 4.6 16.5 1.0
N B:ASP120 4.6 10.4 1.0
O B:PRO118 4.6 13.0 1.0
MN B:MN288 4.7 26.0 1.0
CD B:GLU101 4.8 21.2 1.0
N B:TRP153 4.8 13.5 1.0
O B:HOH295 4.8 24.4 1.0
OE1 B:GLU101 5.0 22.9 1.0

Manganese binding site 4 out of 4 in 1wgi

Go back to Manganese Binding Sites List in 1wgi
Manganese binding site 4 out of 4 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
B:Mn288

b:26.0
occ:1.00
 OD1 B:ASP120 2.3 15.1 1.0
O B:HOH293 2.4 19.7 1.0
O B:HOH292 2.4 17.9 1.0
O B:HOH294 2.4 22.4 1.0
O B:HOH296 2.4 38.5 1.0
O B:HOH295 2.6 24.4 1.0
CG B:ASP120 3.3 8.2 1.0
OD2 B:ASP120 3.6 15.5 1.0
O B:HOH316 4.1 10.8 1.0
O B:HOH290 4.2 8.2 1.0
O B:HOH289 4.2 35.8 1.0
OH B:TYR93 4.2 14.9 1.0
OE1 B:GLU48 4.3 11.8 1.0
O B:HOH360 4.3 22.5 1.0
CE2 B:TYR93 4.4 13.2 1.0
O B:PRO118 4.4 13.0 1.0
CB B:ASP120 4.6 4.1 1.0
O B:HOH334 4.7 23.8 1.0
MN B:MN287 4.7 21.2 1.0
CZ B:TYR93 4.8 15.7 1.0
CB B:ASP117 4.8 19.4 1.0
OD2 B:ASP117 4.8 25.1 1.0
CA B:ASP120 4.9 7.9 1.0
OE2 B:GLU48 4.9 22.2 1.0
CG B:ASP117 4.9 23.8 1.0
CB B:ALA95 5.0 21.8 1.0
O B:GLY94 5.0 14.9 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 12:54:22 2024

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