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Manganese in PDB 2au7: The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase

Enzymatic activity of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase

All present enzymatic activity of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase, PDB code: 2au7 was solved by V.R.Samygina, 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 / 1.05
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 110.985, 110.985, 73.054, 90.00, 90.00, 120.00
R / Rfree (%) 12.3 / 15.3

Other elements in 2au7:

The structure of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase (pdb code 2au7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase, PDB code: 2au7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 2au7

Go back to Manganese Binding Sites List in 2au7
Manganese binding site 1 out of 5 in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:10.1
occ:1.00
 OD1 A:ASP102 2.1 12.2 1.0
OD2 A:ASP70 2.2 10.3 1.0
OD1 A:ASP65 2.2 12.0 1.0
O A:HOH322 2.2 11.5 1.0
O4 A:PO4180 2.2 10.5 1.0
O3 A:PO4180 2.3 10.3 1.0
P A:PO4180 2.8 10.2 1.0
CG A:ASP102 3.1 10.6 1.0
CG A:ASP70 3.1 9.5 1.0
CG A:ASP65 3.2 13.3 1.0
OD1 A:ASP70 3.4 10.3 1.0
OD2 A:ASP102 3.5 11.0 1.0
OD2 A:ASP65 3.6 13.6 1.0
O2 A:PO4180 3.7 10.5 1.0
O A:HOH364 3.7 11.5 1.0
MN A:MN202 3.8 9.9 1.0
NZ A:LYS104 3.8 13.6 1.0
MN A:MN203 3.8 10.5 1.0
O A:HOH314 3.9 10.7 1.0
OD2 A:ASP67 4.1 11.9 0.6
O1 A:PO4180 4.1 10.6 1.0
CB A:ASP67 4.4 15.5 0.6
CB A:ASP102 4.4 11.5 1.0
CB A:ASP65 4.4 13.6 1.0
CB A:ASP70 4.5 10.1 1.0
O A:HOH500 4.5 13.0 0.4
O A:PRO68 4.5 10.1 1.0
OH A:TYR55 4.6 11.0 1.0
O A:HOH315 4.6 10.9 1.0
CG A:ASP67 4.6 12.8 0.6
CA A:ASP102 4.8 10.8 1.0
CB A:ASP67 5.0 17.4 0.4

Manganese binding site 2 out of 5 in 2au7

Go back to Manganese Binding Sites List in 2au7
Manganese binding site 2 out of 5 in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:9.9
occ:1.00
 OD1 A:ASP70 2.1 10.3 1.0
O A:HOH308 2.1 11.1 1.0
O A:HOH352 2.2 13.2 1.0
O A:HOH315 2.2 10.9 1.0
O4 A:PO4180 2.3 10.5 1.0
O2 A:PO4180 2.3 10.5 1.0
P A:PO4180 2.9 10.2 1.0
CG A:ASP70 3.1 9.5 1.0
OD2 A:ASP70 3.6 10.3 1.0
MN A:MN201 3.8 10.1 1.0
O1 A:PO4180 3.9 10.6 1.0
OH A:TYR55 3.9 11.0 1.0
O A:HOH316 3.9 15.9 1.0
O3 A:PO4180 4.0 10.3 1.0
O A:HOH500 4.0 13.0 0.4
OD2 A:ASP67 4.1 11.9 0.6
O A:PRO68 4.1 10.1 1.0
OE1 A:GLU20 4.2 14.5 1.0
O A:HOH322 4.2 11.5 1.0
CE2 A:TYR55 4.2 9.4 1.0
CB A:ASP70 4.4 10.1 1.0
CZ A:TYR55 4.4 9.5 1.0
OE2 A:GLU31 4.4 14.3 0.7
CB A:ASP67 4.5 15.5 0.6
O A:HOH306 4.5 23.4 1.0
O A:HOH348 4.5 29.9 0.5
NZ A:LYS29 4.6 21.7 1.0
O A:GLY56 4.7 8.8 1.0
CB A:ASP67 4.7 17.4 0.4
CG A:ASP67 4.7 12.8 0.6
CA A:ASP70 4.8 9.2 1.0
O A:HOH600 4.9 13.0 0.3
CB A:TYR57 5.0 8.9 1.0

Manganese binding site 3 out of 5 in 2au7

Go back to Manganese Binding Sites List in 2au7
Manganese binding site 3 out of 5 in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:10.5
occ:1.00
 OD2 A:ASP102 2.1 11.0 1.0
OD2 A:ASP97 2.1 12.0 1.0
O3 A:PO4180 2.2 10.3 1.0
O A:HOH416 2.2 12.3 1.0
O A:HOH364 2.3 11.5 1.0
CL A:CL208 2.5 12.4 1.0
CG A:ASP97 3.1 11.4 1.0
CG A:ASP102 3.2 10.6 1.0
P A:PO4180 3.4 10.2 1.0
OD1 A:ASP97 3.6 12.5 1.0
O1 A:PO4180 3.6 10.6 1.0
OD1 A:ASP102 3.7 12.2 1.0
NZ A:LYS104 3.7 13.6 1.0
MN A:MN201 3.8 10.1 1.0
OD1 A:ASP65 4.0 12.0 1.0
NZ A:LYS142 4.2 11.3 0.5
CB A:ASP97 4.2 11.8 1.0
O A:HOH349 4.3 28.7 1.0
O A:HOH378 4.3 16.9 1.0
O4 A:PO4180 4.4 10.5 1.0
CB A:ASP102 4.4 11.5 1.0
O2 A:PO4180 4.5 10.5 1.0
NZ A:LYS142 4.5 18.2 0.5
OH A:TYR141 4.6 14.5 1.0
O A:HOH343 4.7 14.8 1.0
CE A:LYS142 4.7 13.2 0.5
CE A:LYS104 4.8 12.3 1.0
OD2 A:ASP70 4.9 10.3 1.0

Manganese binding site 4 out of 5 in 2au7

Go back to Manganese Binding Sites List in 2au7
Manganese binding site 4 out of 5 in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:16.9
occ:0.80
 O A:HOH500 2.0 13.0 0.4
O1 A:PO4180 2.2 10.6 1.0
O A:HOH497 2.2 19.1 1.0
OE2 A:GLU31 2.2 14.3 0.7
O A:HOH377 2.3 27.6 1.0
O A:HOH600 2.4 13.0 0.3
O A:HOH378 2.5 16.9 1.0
OD2 A:ASP67 2.6 11.9 0.6
CD A:GLU31 3.2 14.3 0.7
P A:PO4180 3.4 10.2 1.0
OE1 A:GLU31 3.5 16.1 0.7
O4 A:PO4180 3.7 10.5 1.0
OD2 A:ASP42 3.7 26.4 0.7
NZ A:LYS29 3.8 21.7 1.0
O A:HOH416 3.8 12.3 1.0
CG A:ASP67 3.8 12.8 0.6
OE1 A:GLU31 4.0 28.7 0.3
O A:HOH429 4.1 30.6 0.5
OD2 A:ASP67 4.2 22.6 0.4
O A:HOH352 4.2 13.2 1.0
OD1 A:ASP67 4.3 12.3 0.6
O A:HOH430 4.3 17.7 0.5
O A:HOH528 4.3 18.9 1.0
O3 A:PO4180 4.4 10.3 1.0
O2 A:PO4180 4.4 10.5 1.0
O A:HOH387 4.5 23.6 0.5
OD2 A:ASP42 4.5 19.5 0.3
O A:HOH364 4.5 11.5 1.0
O A:HOH349 4.5 28.7 1.0
CE A:LYS29 4.5 18.9 1.0
CG A:GLU31 4.6 14.2 0.7
OD1 A:ASP42 4.6 33.2 0.3
O A:HOH348 4.6 29.9 0.5
CG A:ASP42 4.7 21.4 0.7
CG A:ASP42 4.8 25.6 0.3
OD1 A:ASP42 4.9 22.5 0.7

Manganese binding site 5 out of 5 in 2au7

Go back to Manganese Binding Sites List in 2au7
Manganese binding site 5 out of 5 in the The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The R43Q Active Site Variant of E.Coli Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn205

b:20.4
occ:0.25
 O A:HOH607 1.7 35.6 0.5
O A:HOH564 1.9 28.0 0.7
O A:HOH519 2.1 22.3 1.0
O A:HOH517 2.1 15.4 0.9
OD1 A:ASN24 3.9 12.8 0.4
O A:ALA25 4.0 11.4 1.0
O A:HOH602 4.0 27.5 0.7
O A:HOH309 4.0 23.2 0.7
O A:ASN24 4.1 16.7 0.4
ND2 A:ASN24 4.2 12.7 0.4
O A:ASN24 4.2 11.1 0.6
CG A:ASN24 4.3 16.2 0.4
C A:ALA25 4.4 10.0 1.0
OD1 A:ASP26 4.4 12.1 1.0
C A:ASN24 4.5 14.1 0.4
OD1 A:ASN24 4.5 25.3 0.6
C A:ASN24 4.6 9.7 0.6
O A:HOH345 4.7 38.7 0.5
N A:ALA25 4.8 11.8 1.0
N A:ASP26 4.9 9.9 1.0
CA A:ALA25 4.9 10.4 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 13:28:43 2024

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