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Manganese in PDB 2au6: Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase

Enzymatic activity of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase

All present enzymatic activity of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase, PDB code: 2au6 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 / 1.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 110.805, 110.805, 73.576, 90.00, 90.00, 120.00
R / Rfree (%) 12.5 / 15.7

Other elements in 2au6:

The structure of Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase (pdb code 2au6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase, PDB code: 2au6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 1 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:11.2
occ:1.00
 OD1 A:ASP102 2.1 14.1 1.0
F A:F211 2.1 13.2 0.4
OD2 A:ASP70 2.1 11.7 1.0
OD1 A:ASP65 2.2 13.5 1.0
O A:HOH322 2.2 14.2 1.0
O3 A:PO4180 2.2 11.3 0.6
O4 A:POP182 2.2 13.8 0.5
O4 A:PO4180 2.2 11.1 0.6
P A:PO4180 2.8 12.4 0.6
CG A:ASP102 3.0 12.8 1.0
CG A:ASP70 3.1 11.3 1.0
CG A:ASP65 3.1 15.2 1.0
P2 A:POP182 3.2 11.2 0.5
OD2 A:ASP102 3.3 14.2 1.0
OD1 A:ASP70 3.4 11.6 1.0
OD2 A:ASP65 3.5 16.6 1.0
O5 A:POP182 3.6 11.1 0.5
O2 A:PO4180 3.7 11.3 0.6
MN A:MN202 3.7 11.2 1.0
MN A:MN203 3.8 12.0 1.0
O A:HOH364 3.8 14.1 1.0
NZ A:LYS104 3.9 20.7 1.0
O A:HOH316 3.9 12.3 1.0
O1 A:PO4180 4.0 13.1 0.6
OD2 A:ASP67 4.1 18.5 0.6
O6 A:POP182 4.1 13.8 0.5
CB A:ASP65 4.4 17.9 1.0
O A:HOH553 4.4 13.8 0.4
CB A:ASP102 4.4 12.7 1.0
CB A:ASP70 4.4 10.9 1.0
CB A:ASP67 4.5 17.8 0.6
O A:PRO68 4.6 11.3 1.0
OH A:TYR55 4.6 12.5 1.0
O A:POP182 4.6 13.9 0.5
O A:HOH315 4.6 12.0 1.0
CG A:ASP67 4.7 16.5 0.6
CA A:ASP102 4.9 12.8 1.0

Manganese binding site 2 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 2 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:11.2
occ:1.00
 OD1 A:ASP70 2.1 11.6 1.0
O A:HOH308 2.2 13.3 1.0
O5 A:POP182 2.2 11.1 0.5
O A:HOH315 2.2 12.0 1.0
O4 A:PO4180 2.2 11.1 0.6
O A:HOH352 2.2 13.1 0.5
O A:HOH353 2.3 12.3 0.5
F A:F211 2.3 13.2 0.4
O2 A:PO4180 2.4 11.3 0.6
P A:PO4180 2.8 12.4 0.6
CG A:ASP70 3.1 11.3 1.0
P2 A:POP182 3.2 11.2 0.5
OD2 A:ASP70 3.6 11.7 1.0
MN A:MN201 3.7 11.2 1.0
O1 A:PO4180 3.8 13.1 0.6
O6 A:POP182 3.8 13.8 0.5
OH A:TYR55 3.9 12.5 1.0
O3 A:PO4180 3.9 11.3 0.6
O A:HOH553 3.9 13.8 0.4
O4 A:POP182 4.0 13.8 0.5
O A:HOH317 4.0 22.9 1.0
O A:PRO68 4.1 11.3 1.0
O A:HOH322 4.2 14.2 1.0
OD2 A:ASP67 4.2 18.5 0.6
OE1 A:GLU20 4.2 14.2 1.0
O A:HOH357 4.3 31.1 1.0
CE2 A:TYR55 4.3 11.1 1.0
NZ A:LYS29 4.3 15.7 1.0
CB A:ASP70 4.4 10.9 1.0
CZ A:TYR55 4.5 11.0 1.0
CB A:ASP67 4.5 17.8 0.6
O A:POP182 4.6 13.9 0.5
O A:GLY56 4.7 10.3 1.0
O A:HOH307 4.8 14.5 1.0
CG A:ASP67 4.8 16.5 0.6
CB A:ASP67 4.8 18.9 0.4
OE2 A:GLU31 4.8 29.2 1.0
CA A:ASP70 4.8 10.0 1.0
CB A:TYR57 5.0 10.7 1.0

Manganese binding site 3 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 3 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:12.0
occ:1.00
 O1 A:POP182 2.1 14.5 0.5
OD2 A:ASP97 2.1 17.8 1.0
OD2 A:ASP102 2.1 14.2 1.0
O4 A:POP182 2.1 13.8 0.5
O3 A:PO4180 2.2 11.3 0.6
O A:HOH515 2.2 21.8 0.8
O A:HOH364 2.2 14.1 1.0
CL A:CL208 2.5 14.5 0.6
CG A:ASP97 3.1 14.9 1.0
O A:POP182 3.2 13.9 0.5
P1 A:POP182 3.2 14.6 0.5
CG A:ASP102 3.2 12.8 1.0
P2 A:POP182 3.3 11.2 0.5
P A:PO4180 3.5 12.4 0.6
OD1 A:ASP97 3.6 15.6 1.0
O1 A:PO4180 3.7 13.1 0.6
MN A:MN201 3.8 11.2 1.0
OD1 A:ASP102 3.8 14.1 1.0
NZ A:LYS104 3.8 20.7 1.0
O6 A:POP182 3.9 13.8 0.5
OD1 A:ASP65 4.0 13.5 1.0
NZ A:LYS142 4.1 17.8 1.0
O2 A:POP182 4.1 13.5 0.5
O A:HOH378 4.1 24.0 1.0
OH A:TYR141 4.2 13.1 0.4
CB A:ASP97 4.2 15.1 1.0
O3 A:POP182 4.3 14.3 0.5
O4 A:PO4180 4.3 11.1 0.6
CB A:ASP102 4.4 12.7 1.0
O5 A:POP182 4.5 11.1 0.5
O2 A:PO4180 4.5 11.3 0.6
OH A:TYR141 4.6 17.1 0.6
O A:HOH550 4.7 36.1 1.0
OD2 A:ASP70 4.7 11.7 1.0
O A:HOH350 4.7 16.9 1.0
O A:HOH532 4.8 32.9 0.8
F A:F211 4.9 13.2 0.4
CE A:LYS104 4.9 15.6 1.0
MN A:MN204 4.9 13.7 0.5

Manganese binding site 4 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 4 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:13.7
occ:0.45
 MN A:MN204 0.0 13.7 0.5
MN A:MN204 1.1 16.9 0.6
O A:HOH358 1.4 20.7 0.7
O6 A:POP182 2.0 13.8 0.5
O3 A:POP182 2.2 14.3 0.5
O A:HOH480 2.2 17.7 0.5
O1 A:PO4180 2.2 13.1 0.6
O A:HOH378 2.3 24.0 1.0
OE2 A:GLU31 2.4 29.2 1.0
O A:HOH479 2.4 27.2 0.8
O A:HOH553 3.2 13.8 0.4
O A:HOH515 3.2 21.8 0.8
P1 A:POP182 3.3 14.6 0.5
CD A:GLU31 3.4 16.8 1.0
P2 A:POP182 3.4 11.2 0.5
O A:POP182 3.6 13.9 0.5
OE1 A:GLU31 3.7 19.2 1.0
O1 A:POP182 3.7 14.5 0.5
P A:PO4180 3.7 12.4 0.6
O A:HOH532 3.8 32.9 0.8
OD2 A:ASP67 3.9 18.5 0.6
NZ A:LYS29 3.9 15.7 1.0
OD2 A:ASP42 4.0 30.8 1.0
O A:HOH550 4.0 36.1 1.0
O A:HOH401 4.2 27.2 0.5
O4 A:PO4180 4.3 11.1 0.6
O A:HOH451 4.3 29.4 0.5
O A:HOH402 4.3 35.2 0.6
O4 A:POP182 4.3 13.8 0.5
O A:HOH353 4.3 12.3 0.5
NH1 A:ARG43 4.3 45.8 1.0
O5 A:POP182 4.4 11.1 0.5
CG A:ASP42 4.5 20.6 1.0
CE A:LYS29 4.5 18.4 1.0
O3 A:PO4180 4.5 11.3 0.6
O2 A:PO4180 4.6 11.3 0.6
O2 A:POP182 4.6 13.5 0.5
OD1 A:ASP42 4.6 27.8 1.0
O A:HOH364 4.7 14.1 1.0
CG A:GLU31 4.7 14.8 1.0
F A:F211 4.8 13.2 0.4
O A:HOH452 4.8 31.4 0.6
MN A:MN203 4.9 12.0 1.0

Manganese binding site 5 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 5 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:16.9
occ:0.55
 MN A:MN204 0.0 16.9 0.6
MN A:MN204 1.1 13.7 0.5
O A:HOH479 1.9 27.2 0.8
O6 A:POP182 1.9 13.8 0.5
O A:HOH553 2.2 13.8 0.4
OE2 A:GLU31 2.2 29.2 1.0
O1 A:PO4180 2.2 13.1 0.6
O A:HOH378 2.4 24.0 1.0
O A:HOH358 2.4 20.7 0.7
O A:HOH480 2.9 17.7 0.5
OD2 A:ASP67 2.9 18.5 0.6
CD A:GLU31 3.1 16.8 1.0
O3 A:POP182 3.1 14.3 0.5
OE1 A:GLU31 3.3 19.2 1.0
P2 A:POP182 3.4 11.2 0.5
P A:PO4180 3.5 12.4 0.6
O4 A:PO4180 3.7 11.1 0.6
O A:HOH353 3.7 12.3 0.5
O A:HOH515 3.8 21.8 0.8
OD2 A:ASP67 4.0 23.7 0.4
O A:POP182 4.0 13.9 0.5
P1 A:POP182 4.0 14.6 0.5
CG A:ASP67 4.1 16.5 0.6
F A:F211 4.1 13.2 0.4
NZ A:LYS29 4.2 15.7 1.0
O A:HOH451 4.2 29.4 0.5
O4 A:POP182 4.2 13.8 0.5
O A:HOH452 4.2 31.4 0.6
O5 A:POP182 4.3 11.1 0.5
O1 A:POP182 4.3 14.5 0.5
O A:HOH357 4.4 31.1 1.0
O3 A:PO4180 4.4 11.3 0.6
O2 A:PO4180 4.4 11.3 0.6
O A:HOH352 4.5 13.1 0.5
CG A:GLU31 4.5 14.8 1.0
OD1 A:ASP67 4.5 16.6 0.6
O A:HOH364 4.6 14.1 1.0
O A:HOH402 4.7 35.2 0.6
OD2 A:ASP42 4.7 30.8 1.0
O A:HOH532 4.7 32.9 0.8
O A:HOH550 4.8 36.1 1.0
O A:HOH401 4.9 27.2 0.5
CG A:ASP42 4.9 20.6 1.0
OD1 A:ASP42 4.9 27.8 1.0

Manganese binding site 6 out of 6 in 2au6

Go back to Manganese Binding Sites List in 2au6
Manganese binding site 6 out of 6 in the Crystal Structure of Catalytic Intermediate 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 Crystal Structure of Catalytic Intermediate of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn205

b:33.9
occ:0.25
 O A:HOH477 1.7 20.9 0.4
O A:HOH588 2.0 19.8 0.6
O A:HOH587 2.1 42.6 1.0
NA A:NA207 2.5 26.5 0.8
O A:HOH371 3.7 17.7 0.3
O A:ASN24 3.8 28.3 1.0
OD1 A:ASN24 3.9 15.9 0.3
O A:HOH355 4.1 32.5 0.5
O A:ALA25 4.1 18.4 1.0
C A:ASN24 4.4 22.2 1.0
O A:HOH324 4.4 40.6 0.7
C A:ALA25 4.4 14.2 1.0
CG A:ASN24 4.4 16.4 0.3
OD1 A:ASP26 4.5 20.8 1.0
ND2 A:ASN24 4.6 18.2 0.3
N A:ALA25 4.8 17.7 1.0
O A:HOH310 4.8 36.6 1.0
N A:ASP26 4.9 14.3 1.0
CA A:ALA25 4.9 14.9 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 13:28:28 2024

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