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Manganese in PDB 2au9: Inorganic Pyrophosphatase Complexed with Substrate

Enzymatic activity of Inorganic Pyrophosphatase Complexed with Substrate

All present enzymatic activity of Inorganic Pyrophosphatase Complexed with Substrate:
3.6.1.1;

Protein crystallography data

The structure of Inorganic Pyrophosphatase Complexed with Substrate, PDB code: 2au9 was solved by V.R.Samygina, A.N.Popov, S.M.Avaeva, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 110.247, 110.247, 74.612, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 18.2

Other elements in 2au9:

The structure of Inorganic Pyrophosphatase Complexed with Substrate also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Inorganic Pyrophosphatase Complexed with Substrate (pdb code 2au9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Inorganic Pyrophosphatase Complexed with Substrate, PDB code: 2au9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 2au9

Go back to Manganese Binding Sites List in 2au9
Manganese binding site 1 out of 5 in the Inorganic Pyrophosphatase Complexed with Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Inorganic Pyrophosphatase Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:22.1
occ:1.00
 OD2 A:ASP70 2.2 20.9 1.0
F A:F211 2.2 25.4 1.0
O A:HOH322 2.2 24.6 1.0
OD1 A:ASP102 2.2 25.0 1.0
OD1 A:ASP65 2.2 25.8 1.0
O4 A:POP180 2.2 22.4 1.0
CG A:ASP70 3.0 22.1 1.0
CG A:ASP102 3.1 22.8 1.0
CG A:ASP65 3.1 25.9 1.0
P2 A:POP180 3.2 21.7 1.0
OD2 A:ASP102 3.3 23.7 1.0
OD1 A:ASP70 3.3 21.1 1.0
OD2 A:ASP65 3.5 26.8 1.0
O5 A:POP180 3.5 21.4 1.0
MN A:MN202 3.7 20.4 1.0
MN A:MN203 3.7 22.5 1.0
O A:HOH364 3.8 26.6 1.0
O6 A:POP180 3.9 21.9 1.0
O A:HOH316 3.9 24.5 1.0
OD2 A:ASP67 4.0 32.3 1.0
NZ A:LYS104 4.0 25.0 1.0
CB A:ASP65 4.4 31.2 1.0
CB A:ASP67 4.4 27.8 1.0
CB A:ASP70 4.4 20.3 1.0
CB A:ASP102 4.5 26.2 1.0
OH A:TYR55 4.6 21.6 1.0
O A:PRO68 4.6 23.5 1.0
O A:HOH315 4.6 23.1 1.0
O A:POP180 4.6 23.0 1.0
CG A:ASP67 4.6 29.8 1.0
O A:HOH353 5.0 26.8 1.0
CA A:ASP102 5.0 27.9 1.0

Manganese binding site 2 out of 5 in 2au9

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Manganese binding site 2 out of 5 in the Inorganic Pyrophosphatase Complexed with Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Inorganic Pyrophosphatase Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:20.4
occ:1.00
 O A:HOH315 2.1 23.1 1.0
O A:HOH308 2.1 20.5 1.0
F A:F211 2.1 25.4 1.0
OD1 A:ASP70 2.2 21.1 1.0
O5 A:POP180 2.2 21.4 1.0
O A:HOH353 2.3 26.8 1.0
CG A:ASP70 3.2 22.1 1.0
P2 A:POP180 3.2 21.7 1.0
O6 A:POP180 3.6 21.9 1.0
OD2 A:ASP70 3.6 20.9 1.0
MN A:MN201 3.7 22.1 1.0
O4 A:POP180 3.9 22.4 1.0
O A:HOH317 3.9 29.8 1.0
OH A:TYR55 4.0 21.6 1.0
OD2 A:ASP67 4.0 32.3 1.0
O A:PRO68 4.1 23.5 1.0
O A:HOH322 4.2 24.6 1.0
O A:HOH357 4.3 35.6 1.0
OE1 A:GLU20 4.3 20.0 1.0
CB A:ASP67 4.4 27.8 1.0
CE2 A:TYR55 4.4 18.1 1.0
CB A:ASP70 4.4 20.3 1.0
NZ A:LYS29 4.4 20.3 1.0
O A:POP180 4.5 23.0 1.0
CZ A:TYR55 4.5 18.4 1.0
CG A:ASP67 4.6 29.8 1.0
O A:GLY56 4.7 18.2 1.0
CA A:ASP70 4.8 19.4 1.0
CB A:TYR57 4.9 20.0 1.0
O A:HOH307 4.9 19.3 1.0

Manganese binding site 3 out of 5 in 2au9

Go back to Manganese Binding Sites List in 2au9
Manganese binding site 3 out of 5 in the Inorganic Pyrophosphatase Complexed with Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Inorganic Pyrophosphatase Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:22.5
occ:1.00
 OD2 A:ASP102 2.1 23.7 1.0
O1 A:POP180 2.1 22.6 1.0
OD2 A:ASP97 2.2 28.2 1.0
O4 A:POP180 2.2 22.4 1.0
O A:HOH364 2.2 26.6 1.0
CL A:CL208 2.3 31.6 0.7
CG A:ASP97 3.1 26.8 1.0
CG A:ASP102 3.2 22.8 1.0
P2 A:POP180 3.3 21.7 1.0
P1 A:POP180 3.3 23.3 1.0
O A:POP180 3.3 23.0 1.0
OD1 A:ASP97 3.4 27.0 1.0
MN A:MN201 3.7 22.1 1.0
OD1 A:ASP102 3.8 25.0 1.0
OD1 A:ASP65 3.9 25.8 1.0
NZ A:LYS142 3.9 25.3 1.0
O6 A:POP180 4.0 21.9 1.0
O A:HOH378 4.0 25.9 1.0
NZ A:LYS104 4.1 25.0 1.0
O2 A:POP180 4.2 23.8 1.0
OH A:TYR141 4.3 24.1 1.0
CB A:ASP102 4.3 26.2 1.0
CB A:ASP97 4.4 26.1 1.0
O3 A:POP180 4.4 23.6 1.0
O5 A:POP180 4.5 21.4 1.0
OD2 A:ASP70 4.6 20.9 1.0
F A:F211 4.8 25.4 1.0
CE A:LYS104 4.9 24.3 1.0
CE A:MET95 4.9 33.2 0.8
O A:HOH350 4.9 23.7 1.0
CG A:ASP65 5.0 25.9 1.0

Manganese binding site 4 out of 5 in 2au9

Go back to Manganese Binding Sites List in 2au9
Manganese binding site 4 out of 5 in the Inorganic Pyrophosphatase Complexed with Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Inorganic Pyrophosphatase Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:23.8
occ:1.00
 O A:HOH479 2.1 29.2 1.0
O3 A:POP180 2.1 23.6 1.0
O6 A:POP180 2.2 21.9 1.0
O A:HOH480 2.2 23.1 0.8
OE2 A:GLU31 2.3 24.7 1.0
O A:HOH378 2.3 25.9 1.0
CD A:GLU31 3.3 28.6 1.0
P1 A:POP180 3.3 23.3 1.0
P2 A:POP180 3.4 21.7 1.0
OE1 A:GLU31 3.5 26.9 1.0
O A:POP180 3.5 23.0 1.0
O1 A:POP180 3.7 22.6 1.0
OD2 A:ASP67 3.9 32.3 1.0
O A:HOH358 4.0 29.9 1.0
NZ A:LYS29 4.0 20.3 1.0
O A:HOH353 4.1 26.8 1.0
O A:HOH446 4.2 34.2 0.5
O A:HOH399 4.3 33.6 0.5
O4 A:POP180 4.3 22.4 1.0
NH1 A:ARG43 4.3 24.1 1.0
OD2 A:ASP42 4.4 27.2 1.0
O5 A:POP180 4.5 21.4 1.0
OD1 A:ASP42 4.5 32.1 1.0
CG A:ASP42 4.6 23.9 1.0
O2 A:POP180 4.6 23.8 1.0
CE A:LYS29 4.6 19.4 1.0
CG A:GLU31 4.6 20.9 1.0
O A:HOH364 4.7 26.6 1.0
F A:F211 4.8 25.4 1.0

Manganese binding site 5 out of 5 in 2au9

Go back to Manganese Binding Sites List in 2au9
Manganese binding site 5 out of 5 in the Inorganic Pyrophosphatase Complexed with Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Inorganic Pyrophosphatase Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn205

b:31.5
occ:0.50
 O A:HOH371 2.6 13.7 0.3
OD1 A:ASN24 2.8 18.3 0.5
CD2 A:PHE50 3.5 16.5 1.0
CG A:ASN24 3.9 19.1 0.5
CE2 A:PHE50 3.9 18.0 1.0
O A:HOH472 4.0 18.0 1.0
CG A:PHE50 4.2 15.7 1.0
O A:ASN24 4.3 18.2 1.0
ND2 A:ASN24 4.4 18.8 0.5
NA A:NA207 4.4 17.9 1.0
CB A:PHE50 4.6 15.2 1.0
CZ A:PHE50 4.7 19.2 1.0
C A:ASN24 4.7 15.7 1.0
CA A:ASN24 5.0 16.1 1.0

Reference:

V.R.Samygina, V.M.Moiseev, E.V.Rodina, N.N.Vorobyeva, A.N.Popov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva, H.D.Bartunik. Reversible Inhibition of Escherichia Coli Inorganic Pyrophosphatase By Fluoride: Trapped Catalytic Intermediates in Cryo-Crystallographic Studies J.Mol.Biol. V. 366 1305 2007.
ISSN: ISSN 0022-2836
PubMed: 17196979
DOI: 10.1016/J.JMB.2006.11.082
Page generated: Sat Oct 5 13:29:21 2024

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