Atomistry » Manganese » PDB 2a7a-2axt » 2au9
Atomistry »
  Manganese »
    PDB 2a7a-2axt »
      2au9 »

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

Go back to Manganese Binding Sites List in 2au9
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy