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Manganese in PDB 1e6a: Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase

Enzymatic activity of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase

All present enzymatic activity of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase, PDB code: 1e6a was solved by P.Heikinheimo, V.Tuominen, A.-K.Ahonen, A.Teplyakov, B.S.Cooperman, A.A.Baykov, R.Lahti, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.770, 102.340, 115.630, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.2

Other elements in 1e6a:

The structure of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase (pdb code 1e6a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase, PDB code: 1e6a:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1e6a

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Manganese binding site 1 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2001

b:6.8
occ:1.00
 F A:F4001 2.1 5.1 1.0
OD1 A:ASP152 2.2 6.1 1.0
OD2 A:ASP115 2.2 3.8 1.0
OD2 A:ASP120 2.3 3.9 1.0
O5 A:POP3001 2.3 7.4 1.0
O A:HOH2334 2.5 4.3 1.0
CG A:ASP120 3.1 3.8 1.0
CG A:ASP152 3.1 8.2 1.0
CG A:ASP115 3.2 7.9 1.0
P2 A:POP3001 3.3 7.2 1.0
OD1 A:ASP120 3.3 6.8 1.0
NA A:NA4740 3.3 20.3 0.6
OD2 A:ASP152 3.4 6.6 1.0
O4 A:POP3001 3.5 5.5 1.0
OD1 A:ASP115 3.5 5.3 1.0
MN A:MN2002 3.6 7.1 1.0
MN A:MN2004 3.7 7.0 1.0
O A:HOH2341 3.8 3.2 1.0
O6 A:POP3001 3.9 9.5 1.0
O A:HOH2156 4.1 4.4 1.0
NZ A:LYS154 4.2 3.9 1.0
OD2 A:ASP117 4.3 9.2 0.4
CB A:ASP117 4.3 7.0 0.4
CB A:ASP117 4.4 5.2 0.6
CB A:ASP152 4.5 5.3 1.0
CB A:ASP120 4.5 3.5 1.0
CB A:ASP115 4.5 5.5 1.0
O A:PRO118 4.5 6.2 0.6
O A:PRO118 4.6 6.6 0.5
O A:HOH2336 4.6 2.2 1.0
O A:POP3001 4.6 9.4 1.0
O A:HOH2342 4.6 4.9 1.0
OH A:TYR93 4.6 5.6 1.0
CG A:ASP117 4.8 8.5 0.4
CA A:ASP152 4.9 5.8 1.0
OD2 A:ASP117 5.0 11.2 0.6

Manganese binding site 2 out of 8 in 1e6a

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Manganese binding site 2 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:7.1
occ:1.00
 F A:F4001 2.1 5.1 1.0
O A:HOH2337 2.2 4.5 1.0
OD1 A:ASP120 2.2 6.8 1.0
O A:HOH2336 2.2 2.2 1.0
O4 A:POP3001 2.2 5.5 1.0
O A:HOH2335 2.3 10.8 1.0
P2 A:POP3001 3.2 7.2 1.0
CG A:ASP120 3.3 3.8 1.0
O6 A:POP3001 3.4 9.5 1.0
MN A:MN2001 3.6 6.8 1.0
OD2 A:ASP120 3.7 3.9 1.0
O5 A:POP3001 3.9 7.4 1.0
O A:HOH2080 3.9 6.3 1.0
OH A:TYR93 4.1 5.6 1.0
OD2 A:ASP117 4.1 9.2 0.4
O A:PRO118 4.2 6.6 0.5
O A:PRO118 4.3 6.2 0.6
CB A:ASP117 4.3 7.0 0.4
NA A:NA4740 4.4 20.3 0.6
CB A:ASP117 4.4 5.2 0.6
CE2 A:TYR93 4.4 4.4 1.0
OE1 A:GLU48 4.4 7.3 1.0
O A:HOH2334 4.5 4.3 1.0
O A:HOH2096 4.5 9.6 1.0
CB A:ASP120 4.5 3.5 1.0
NZ A:LYS56 4.5 10.1 1.0
O A:POP3001 4.6 9.4 1.0
CG A:ASP117 4.6 8.5 0.4
CZ A:TYR93 4.7 5.5 1.0
CG A:ASP117 4.7 7.8 0.6
OD2 A:ASP117 4.7 11.2 0.6
O A:GLY94 4.8 6.6 1.0
CA A:ASP120 4.9 4.8 1.0
OE2 A:GLU48 4.9 6.6 1.0
O A:HOH2091 4.9 6.4 1.0

Manganese binding site 3 out of 8 in 1e6a

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Manganese binding site 3 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:13.0
occ:1.00
 O3 A:POP3001 2.1 10.1 1.0
O A:HOH2339 2.2 8.0 1.0
O6 A:POP3001 2.2 9.5 1.0
O A:HOH2340 2.3 16.6 1.0
OE2 A:GLU58 2.3 9.6 0.6
O A:HOH2338 2.4 11.0 1.0
P1 A:POP3001 3.2 12.6 1.0
O A:POP3001 3.4 9.4 1.0
NA A:NA4740 3.4 20.3 0.6
CD A:GLU58 3.4 9.3 0.6
P2 A:POP3001 3.4 7.2 1.0
OE1 A:GLU58 3.4 11.0 0.4
O1 A:POP3001 3.7 11.5 1.0
OE1 A:GLU58 3.8 17.4 0.6
NH1 A:ARG78 4.0 6.9 1.0
NZ A:LYS56 4.1 10.1 1.0
O A:HOH2343 4.1 24.4 1.0
O5 A:POP3001 4.1 7.4 1.0
OD2 A:ASP117 4.2 9.2 0.4
CD A:GLU58 4.2 12.5 0.4
O A:HOH2335 4.3 10.8 1.0
OE2 A:GLU58 4.3 14.6 0.4
OD2 A:ASP71 4.3 6.0 1.0
O A:HOH2165 4.3 16.7 1.0
OD2 A:ASP117 4.4 11.2 0.6
O2 A:POP3001 4.5 9.2 1.0
CE A:LYS56 4.5 9.8 1.0
O4 A:POP3001 4.6 5.5 1.0
O A:HOH2093 4.6 27.3 1.0
CG A:GLU58 4.7 10.5 0.6
F A:F4001 4.9 5.1 1.0
CG A:ASP71 5.0 5.1 1.0

Manganese binding site 4 out of 8 in 1e6a

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Manganese binding site 4 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2004

b:7.0
occ:1.00
 O5 A:POP3001 2.2 7.4 1.0
OD2 A:ASP147 2.2 11.4 1.0
O1 A:POP3001 2.3 11.5 1.0
O A:HOH2341 2.3 3.2 1.0
OD2 A:ASP152 2.3 6.6 1.0
O A:HOH2342 2.3 4.9 1.0
CG A:ASP152 3.2 8.2 1.0
P1 A:POP3001 3.3 12.6 1.0
CG A:ASP147 3.3 5.4 1.0
O A:POP3001 3.3 9.4 1.0
P2 A:POP3001 3.4 7.2 1.0
MN A:MN2001 3.7 6.8 1.0
CB A:ASP147 3.7 7.0 1.0
OD1 A:ASP152 3.7 6.1 1.0
OH A:TYR192 3.9 11.8 1.0
OD2 A:ASP115 3.9 3.8 1.0
O A:HOH2339 4.1 8.0 1.0
O2 A:POP3001 4.1 9.2 1.0
NZ A:LYS193 4.2 11.2 1.0
NZ A:LYS154 4.2 3.9 1.0
O6 A:POP3001 4.3 9.5 1.0
NA A:NA4740 4.3 20.3 0.6
CB A:ASP152 4.4 5.3 1.0
OD1 A:ASP147 4.4 8.7 1.0
O A:HOH2199 4.4 5.5 1.0
O4 A:POP3001 4.4 5.5 1.0
O3 A:POP3001 4.4 10.1 1.0
OD2 A:ASP120 4.5 3.9 1.0
O A:HOH2196 4.5 14.5 1.0
F A:F4001 4.9 5.1 1.0
OH A:TYR93 4.9 5.6 1.0
CE A:LYS193 5.0 9.6 1.0

Manganese binding site 5 out of 8 in 1e6a

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Manganese binding site 5 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2005

b:5.0
occ:1.00
 F B:F4010 2.1 7.9 1.0
O4 B:PO43004 2.2 6.9 0.2
O B:HOH2294 2.2 3.4 1.0
OD1 B:ASP1152 2.2 5.1 1.0
OD2 B:ASP1120 2.2 4.2 1.0
O3 B:POP3002 2.3 5.4 0.8
OD2 B:ASP1115 2.3 6.6 1.0
CG B:ASP1120 3.1 4.6 1.0
CG B:ASP1152 3.1 8.2 1.0
CG B:ASP1115 3.2 8.5 1.0
OD1 B:ASP1120 3.2 4.0 1.0
P1 B:POP3002 3.2 9.1 0.8
P B:PO43004 3.3 9.3 0.2
O1 B:PO43004 3.3 6.6 0.2
O2 B:POP3002 3.4 5.8 0.8
OD2 B:ASP1152 3.4 7.7 1.0
OD1 B:ASP1115 3.6 8.6 1.0
MN B:MN2006 3.6 6.4 1.0
O B:HOH2301 3.7 2.4 1.0
MN B:MN2008 3.7 6.1 1.0
O1 B:POP3002 3.8 10.8 0.8
O3 B:PO43004 3.9 8.8 0.2
NZ B:LYS1154 4.0 4.3 1.0
O B:HOH2102 4.1 2.2 1.0
OD2 B:ASP1117 4.1 11.2 0.6
CB B:ASP1117 4.2 7.2 0.6
CB B:ASP1117 4.4 7.4 0.4
CB B:ASP1152 4.5 4.3 1.0
CB B:ASP1120 4.5 3.8 1.0
CB B:ASP1115 4.5 8.0 1.0
OH B:TYR1093 4.5 8.4 1.0
O2 B:PO43004 4.5 6.3 0.2
O B:POP3002 4.6 8.8 0.8
O B:PRO1118 4.6 6.2 1.0
O B:HOH2295 4.6 5.6 1.0
CG B:ASP1117 4.7 6.9 0.6
OD2 B:ASP1117 4.7 13.5 0.4
O B:HOH2302 4.8 4.8 1.0
CA B:ASP1152 4.9 5.7 1.0
O4 B:PO43003 5.0 13.2 0.2

Manganese binding site 6 out of 8 in 1e6a

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Manganese binding site 6 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2006

b:6.4
occ:1.00
 O1 B:PO43004 2.1 6.6 0.2
F B:F4010 2.2 7.9 1.0
O B:HOH2296 2.2 4.0 1.0
OD1 B:ASP1120 2.2 4.0 1.0
O B:HOH2295 2.2 5.6 1.0
O B:HOH2297 2.3 2.2 1.0
O2 B:POP3002 2.3 5.8 0.8
P B:PO43004 3.2 9.3 0.2
P1 B:POP3002 3.2 9.1 0.8
CG B:ASP1120 3.3 4.6 1.0
O1 B:POP3002 3.4 10.8 0.8
O3 B:PO43004 3.4 8.8 0.2
MN B:MN2005 3.6 5.0 1.0
OD2 B:ASP1120 3.7 4.2 1.0
O B:HOH2044 3.9 4.2 1.0
O4 B:PO43004 3.9 6.9 0.2
O3 B:POP3002 3.9 5.4 0.8
OH B:TYR1093 4.1 8.4 1.0
OD2 B:ASP1117 4.1 11.2 0.6
O B:HOH2294 4.2 3.4 1.0
O B:PRO1118 4.3 6.2 1.0
CE2 B:TYR1093 4.3 5.9 1.0
CB B:ASP1117 4.3 7.4 0.4
OE1 B:GLU1048 4.4 7.3 1.0
CB B:ASP1117 4.4 7.2 0.6
CB B:ASP1120 4.5 3.8 1.0
O2 B:PO43004 4.5 6.3 0.2
O B:HOH2053 4.5 11.1 1.0
O B:POP3002 4.6 8.8 0.8
CZ B:TYR1093 4.6 5.5 1.0
NZ B:LYS1056 4.7 11.7 1.0
CG B:ASP1117 4.7 8.5 0.4
OD2 B:ASP1117 4.7 13.5 0.4
CG B:ASP1117 4.7 6.9 0.6
O B:HOH2051 4.7 6.6 1.0
O B:GLY1094 4.8 4.6 1.0
CA B:ASP1120 4.9 3.8 1.0
OE2 B:GLU1048 4.9 6.3 1.0
CB B:ALA1095 4.9 4.5 1.0

Manganese binding site 7 out of 8 in 1e6a

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Manganese binding site 7 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2007

b:9.8
occ:0.89
 O3 B:PO43003 2.0 12.0 0.2
O5 B:POP3002 2.1 11.6 0.8
O B:HOH2299 2.2 8.4 1.0
O3 B:PO43004 2.3 8.8 0.2
OE2 B:GLU1058 2.3 18.2 1.0
O1 B:POP3002 2.3 10.8 0.8
O B:HOH2300 2.5 10.1 1.0
O B:HOH2298 2.5 12.4 1.0
CD B:GLU1058 3.2 19.5 1.0
P B:PO43003 3.2 7.2 0.2
P2 B:POP3002 3.3 12.2 0.8
P1 B:POP3002 3.5 9.1 0.8
OE1 B:GLU1058 3.5 19.6 1.0
P B:PO43004 3.6 9.3 0.2
O4 B:PO43003 3.6 13.2 0.2
O6 B:POP3002 3.6 7.3 0.8
O B:POP3002 3.7 8.8 0.8
O2 B:PO43004 3.9 6.3 0.2
NZ B:LYS1056 4.0 11.7 1.0
OD2 B:ASP1117 4.0 11.2 0.6
NH1 B:ARG1078 4.0 12.1 1.0
O B:HOH2303 4.1 28.3 0.8
O2 B:PO43003 4.1 12.5 0.2
O B:HOH2297 4.1 2.2 1.0
OD2 B:ASP1117 4.2 13.5 0.4
O B:HOH2115 4.3 14.5 1.0
O3 B:POP3002 4.3 5.4 0.8
O4 B:PO43004 4.3 6.9 0.2
O B:HOH2305 4.3 14.9 1.0
O1 B:PO43003 4.4 12.7 0.2
O B:HOH2003 4.4 27.0 1.0
CE B:LYS1056 4.5 11.2 1.0
O B:HOH2002 4.5 20.4 1.0
CG B:GLU1058 4.6 11.7 1.0
OD2 B:ASP1071 4.6 12.5 1.0
O2 B:POP3002 4.6 5.8 0.8
O4 B:POP3002 4.6 7.2 0.8
O1 B:PO43004 4.7 6.6 0.2
F B:F4010 4.7 7.9 1.0
O B:HOH2055 4.7 25.4 1.0
O B:HOH2001 5.0 27.5 1.0

Manganese binding site 8 out of 8 in 1e6a

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Manganese binding site 8 out of 8 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2008

b:6.1
occ:1.00
 O4 B:PO43003 2.2 13.2 0.2
O3 B:POP3002 2.2 5.4 0.8
OD2 B:ASP1147 2.2 7.3 1.0
O4 B:PO43004 2.2 6.9 0.2
O B:HOH2301 2.2 2.4 1.0
O6 B:POP3002 2.2 7.3 0.8
OD2 B:ASP1152 2.2 7.7 1.0
O B:HOH2302 2.5 4.8 1.0
CG B:ASP1152 3.2 8.2 1.0
CG B:ASP1147 3.2 6.4 1.0
P1 B:POP3002 3.3 9.1 0.8
P B:PO43004 3.3 9.3 0.2
O B:POP3002 3.3 8.8 0.8
P2 B:POP3002 3.4 12.2 0.8
O2 B:PO43004 3.4 6.3 0.2
CB B:ASP1147 3.6 6.0 1.0
P B:PO43003 3.6 7.2 0.2
MN B:MN2005 3.7 5.0 1.0
OD1 B:ASP1152 3.7 5.1 1.0
OH B:TYR1192 3.9 6.9 1.0
O1 B:PO43003 3.9 12.7 0.2
OD2 B:ASP1115 4.0 6.6 1.0
O B:HOH2300 4.1 10.1 1.0
O1 B:POP3002 4.1 10.8 0.8
O3 B:PO43004 4.1 8.8 0.2
O4 B:POP3002 4.1 7.2 0.8
NZ B:LYS1154 4.2 4.3 1.0
NZ B:LYS1193 4.3 5.8 1.0
OD1 B:ASP1147 4.3 6.7 1.0
CB B:ASP1152 4.3 4.3 1.0
O B:HOH2161 4.4 8.0 1.0
O2 B:POP3002 4.4 5.8 0.8
O3 B:PO43003 4.5 12.0 0.2
O1 B:PO43004 4.5 6.6 0.2
O5 B:POP3002 4.5 11.6 0.8
O2 B:PO43003 4.6 12.5 0.2
OD2 B:ASP1120 4.6 4.2 1.0
O B:HOH2155 4.7 14.9 1.0
F B:F4010 4.9 7.9 1.0
OH B:TYR1093 5.0 8.4 1.0

Reference:

P.Heikinheimo, V.Tuominen, A.K.Ahonen, A.Teplyakov, B.S.Cooperman, A.A.Baykov, R.Lahti, A.Goldman. Toward A Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase. Proc. Natl. Acad. Sci. V. 98 3121 2001U.S.A..
ISSN: ISSN 0027-8424
PubMed: 11248042
DOI: 10.1073/PNAS.061612498
Page generated: Sat Oct 5 10:09:16 2024

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