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Manganese in PDB 117e: The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications

Enzymatic activity of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications

All present enzymatic activity of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications:
3.6.1.1;

Protein crystallography data

The structure of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications, PDB code: 117e was solved by V.Tuominen, P.Heikinheimo, T.Kajander, T.Torkkel, T.Hyytia, J.Kapyla, R.Lahti, B.S.Cooperman, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.400, 102.800, 116.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 24

Manganese Binding Sites:

The binding sites of Manganese atom in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications (pdb code 117e). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications, PDB code: 117e:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 117e

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Manganese binding site 1 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2001

b:7.7
occ:1.00
 OE2 A:GLU117 2.2 6.6 1.0
O4 A:PO43002 2.3 4.3 1.0
OD1 A:ASP152 2.3 5.1 1.0
OD2 A:ASP115 2.4 6.4 1.0
OD2 A:ASP120 2.5 10.4 1.0
O A:HOH4002 2.8 8.1 1.0
CD A:GLU117 3.1 10.2 1.0
CG A:ASP115 3.2 8.4 1.0
CG A:ASP120 3.2 7.0 1.0
OD1 A:ASP120 3.3 6.5 1.0
CG A:ASP152 3.3 8.0 1.0
OD1 A:ASP115 3.4 6.5 1.0
P A:PO43002 3.4 8.9 1.0
CG A:GLU117 3.5 10.0 1.0
O1 A:PO43002 3.5 11.9 1.0
MN A:MN2002 3.6 10.4 1.0
OD2 A:ASP152 3.6 7.8 1.0
O A:HOH4009 3.6 9.2 1.0
MN A:MN2004 3.7 6.8 1.0
NZ A:LYS154 4.0 4.0 1.0
OE1 A:GLU117 4.2 11.4 1.0
O A:HOH4034 4.2 4.7 1.0
O2 A:PO43002 4.3 11.6 1.0
CB A:ASP115 4.5 5.3 1.0
O A:HOH4006 4.5 16.5 1.0
O3 A:PO43002 4.6 6.8 1.0
CB A:ASP152 4.6 8.6 1.0
OH A:TYR93 4.6 9.2 1.0
O A:HOH4010 4.6 10.6 1.0
CB A:ASP120 4.6 7.5 1.0
O A:PRO118 4.7 5.1 1.0
O A:HOH4005 4.8 11.9 1.0
CA A:ASP152 5.0 8.8 1.0
CB A:GLU117 5.0 8.4 1.0

Manganese binding site 2 out of 8 in 117e

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Manganese binding site 2 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:10.4
occ:1.00
 O1 A:PO43002 2.0 11.9 1.0
OD1 A:ASP120 2.3 6.5 1.0
OE2 A:GLU117 2.4 6.6 1.0
O A:HOH4004 2.5 6.8 1.0
O A:HOH4005 2.5 11.9 1.0
O A:HOH4003 2.8 13.6 1.0
CD A:GLU117 3.1 10.2 1.0
CG A:ASP120 3.3 7.0 1.0
P A:PO43002 3.3 8.9 1.0
MN A:MN2001 3.6 7.7 1.0
OE1 A:GLU117 3.7 11.4 1.0
OD2 A:ASP120 3.7 10.4 1.0
O4 A:PO43002 3.7 4.3 1.0
CG A:GLU117 3.8 10.0 1.0
O2 A:PO43002 3.9 11.6 1.0
OH A:TYR93 4.1 9.2 1.0
O A:HOH4030 4.1 4.6 1.0
O A:PRO118 4.2 5.1 1.0
CE2 A:TYR93 4.3 7.5 1.0
OE1 A:GLU48 4.3 3.7 1.0
O A:HOH4002 4.4 8.1 1.0
O3 A:PO43002 4.5 6.8 1.0
CB A:ASP120 4.5 7.5 1.0
CZ A:TYR93 4.7 6.8 1.0
O A:HOH4116 4.7 16.1 1.0
CB A:GLU117 4.8 8.4 1.0
OE2 A:GLU48 4.8 7.2 1.0
O A:GLY94 4.8 4.8 1.0
CB A:ALA95 4.8 6.8 1.0
CA A:ASP120 4.9 6.7 1.0
NZ A:LYS56 4.9 12.5 1.0
O A:HOH4105 4.9 4.6 1.0

Manganese binding site 3 out of 8 in 117e

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Manganese binding site 3 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:18.5
occ:1.00
 O A:HOH4414 1.9 26.4 1.0
O1 A:PO43001 2.3 19.4 1.0
O A:HOH4006 2.5 16.5 1.0
O A:HOH4405 2.5 9.4 1.0
O A:HOH4008 2.7 13.7 1.0
P A:PO43001 3.3 14.6 1.0
O4 A:PO43001 3.6 12.5 1.0
O3 A:PO43001 3.8 19.2 1.0
NH1 A:ARG78 3.8 7.1 1.0
O2 A:PO43002 3.9 11.6 1.0
O A:HOH4157 3.9 14.9 1.0
OD2 A:ASP71 4.0 6.2 1.0
O A:HOH4119 4.1 13.9 1.0
O A:HOH4415 4.1 14.1 1.0
O A:HOH4182 4.3 10.4 1.0
O A:HOH4174 4.5 7.5 1.0
O2 A:PO43001 4.6 12.1 1.0
OE1 A:GLU58 4.9 10.6 1.0
CG A:ASP71 5.0 5.1 1.0
CZ A:ARG78 5.0 7.3 1.0

Manganese binding site 4 out of 8 in 117e

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Manganese binding site 4 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2004

b:6.8
occ:1.00
 O A:HOH4009 2.1 9.2 1.0
O4 A:PO43001 2.3 12.5 1.0
OD2 A:ASP147 2.3 4.6 1.0
O A:HOH4010 2.3 10.6 1.0
OD2 A:ASP152 2.4 7.8 1.0
O4 A:PO43002 2.4 4.3 1.0
CG A:ASP152 3.3 8.0 1.0
CG A:ASP147 3.3 5.4 1.0
P A:PO43002 3.6 8.9 1.0
O3 A:PO43002 3.6 6.8 1.0
O A:HOH4006 3.6 16.5 1.0
P A:PO43001 3.7 14.6 1.0
CB A:ASP147 3.7 4.8 1.0
MN A:MN2001 3.7 7.7 1.0
OD1 A:ASP152 3.7 5.1 1.0
OH A:TYR192 3.9 7.8 1.0
NZ A:LYS154 4.0 4.0 1.0
OD2 A:ASP115 4.1 6.4 1.0
O2 A:PO43001 4.1 12.1 1.0
O2 A:PO43002 4.2 11.6 1.0
O A:HOH4119 4.3 13.9 1.0
O3 A:PO43001 4.4 19.2 1.0
O A:HOH4049 4.4 6.6 1.0
CB A:ASP152 4.4 8.6 1.0
OD1 A:ASP147 4.4 5.0 1.0
OE2 A:GLU117 4.7 6.6 1.0
O1 A:PO43001 4.7 19.4 1.0
OD2 A:ASP120 4.8 10.4 1.0
O1 A:PO43002 4.8 11.9 1.0
NZ A:LYS193 4.8 4.4 1.0

Manganese binding site 5 out of 8 in 117e

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Manganese binding site 5 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2005

b:7.0
occ:1.00
 O4 B:PO43004 2.3 10.6 1.0
OD1 B:ASP1152 2.3 9.8 1.0
OD2 B:ASP1115 2.3 6.1 1.0
OE2 B:GLU1117 2.3 9.7 1.0
OD2 B:ASP1120 2.5 7.5 1.0
O B:HOH4012 2.7 8.9 1.0
OD1 B:ASP1120 3.2 5.4 1.0
CG B:ASP1115 3.2 6.8 1.0
CG B:ASP1120 3.2 7.2 1.0
CD B:GLU1117 3.2 8.7 1.0
CG B:ASP1152 3.3 9.7 1.0
P B:PO43004 3.3 6.7 1.0
O1 B:PO43004 3.4 8.4 1.0
OD1 B:ASP1115 3.5 6.5 1.0
OD2 B:ASP1152 3.6 11.0 1.0
CG B:GLU1117 3.6 8.6 1.0
MN B:MN2006 3.6 6.9 1.0
O B:HOH4019 3.7 8.1 1.0
MN B:MN2008 3.7 8.1 1.0
O2 B:PO43004 3.9 11.1 1.0
NZ B:LYS1154 4.0 2.2 1.0
O B:HOH4062 4.1 5.7 1.0
O B:HOH4017 4.2 7.6 1.0
OE1 B:GLU1117 4.3 10.8 1.0
CB B:ASP1115 4.5 5.5 1.0
CB B:ASP1152 4.6 8.2 1.0
O3 B:PO43004 4.6 4.4 1.0
O B:PRO1118 4.6 5.5 1.0
OH B:TYR1093 4.6 5.9 1.0
CB B:ASP1120 4.7 5.9 1.0
O B:HOH4013 4.7 4.8 1.0
MN B:MN2007 4.8 14.7 1.0
O B:HOH4416 4.9 11.3 1.0
CA B:ASP1152 5.0 8.2 1.0

Manganese binding site 6 out of 8 in 117e

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Manganese binding site 6 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2006

b:6.9
occ:1.00
 O1 B:PO43004 2.1 8.4 1.0
O B:HOH4015 2.2 6.8 1.0
O B:HOH4014 2.3 12.2 1.0
OD1 B:ASP1120 2.3 5.4 1.0
OE2 B:GLU1117 2.4 9.7 1.0
O B:HOH4013 2.6 4.8 1.0
CD B:GLU1117 3.2 8.7 1.0
CG B:ASP1120 3.3 7.2 1.0
P B:PO43004 3.4 6.7 1.0
MN B:MN2005 3.6 7.0 1.0
O2 B:PO43004 3.8 11.1 1.0
OH B:TYR1093 3.9 5.9 1.0
OD2 B:ASP1120 3.9 7.5 1.0
OE1 B:GLU1117 3.9 10.8 1.0
O4 B:PO43004 3.9 10.6 1.0
CG B:GLU1117 4.0 8.6 1.0
CE1 B:TYR1093 4.1 5.4 1.0
O B:HOH4130 4.2 6.5 1.0
O B:PRO1118 4.3 5.5 1.0
MN B:MN2007 4.4 14.7 1.0
O B:HOH4117 4.4 12.5 1.0
OE1 B:GLU1048 4.4 6.4 1.0
CB B:ASP1120 4.4 5.9 1.0
CZ B:TYR1093 4.5 4.1 1.0
O B:HOH4012 4.5 8.9 1.0
O3 B:PO43004 4.6 4.4 1.0
OE1 B:GLU1058 4.6 16.4 1.0
O B:GLY1094 4.8 4.2 1.0
OE2 B:GLU1048 4.8 8.5 1.0
CB B:ALA1095 4.8 6.7 1.0
CA B:ASP1120 4.9 7.0 1.0
NZ B:LYS1056 5.0 12.5 1.0

Manganese binding site 7 out of 8 in 117e

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Manganese binding site 7 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2007

b:14.7
occ:1.00
 O2 B:PO43004 2.1 11.1 1.0
O B:HOH4417 2.1 15.3 1.0
OE1 B:GLU1117 2.4 10.8 1.0
O B:HOH4017 2.5 7.6 1.0
OE1 B:GLU1058 2.6 16.4 1.0
O B:HOH4016 2.7 7.9 1.0
OE2 B:GLU1117 3.1 9.7 1.0
CD B:GLU1117 3.1 8.7 1.0
O B:HOH4015 3.5 6.8 1.0
P B:PO43004 3.5 6.7 1.0
CD B:GLU1058 3.6 19.2 1.0
OE2 B:GLU1058 3.8 22.0 1.0
NZ B:LYS1056 3.9 12.5 1.0
O1 B:PO43004 4.0 8.4 1.0
O B:HOH4412 4.0 14.7 1.0
O B:HOH4416 4.1 11.3 1.0
O4 B:PO43004 4.3 10.6 1.0
CE B:LYS1056 4.3 13.4 1.0
MN B:MN2006 4.4 6.9 1.0
O3 B:PO43004 4.5 4.4 1.0
CG B:GLU1117 4.6 8.6 1.0
O B:HOH4821 4.7 27.6 1.0
OD2 B:ASP1115 4.7 6.1 1.0
O B:HOH4407 4.8 13.7 1.0
MN B:MN2005 4.8 7.0 1.0
O B:HOH4409 4.9 12.2 1.0
O B:HOH4822 4.9 30.7 1.0
CG B:GLU1058 5.0 15.8 1.0

Manganese binding site 8 out of 8 in 117e

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Manganese binding site 8 out of 8 in the The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The R78K and D117E Active Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2008

b:8.1
occ:1.00
 O4 B:PO43004 2.1 10.6 1.0
O B:HOH4416 2.2 11.3 1.0
OD2 B:ASP1147 2.3 5.4 1.0
O B:HOH4019 2.3 8.1 1.0
OD2 B:ASP1152 2.3 11.0 1.0
O B:HOH4020 2.7 6.4 1.0
P B:PO43004 3.2 6.7 1.0
CG B:ASP1152 3.2 9.7 1.0
CG B:ASP1147 3.3 4.0 1.0
O3 B:PO43004 3.3 4.4 1.0
O2 B:PO43004 3.6 11.1 1.0
CB B:ASP1147 3.6 4.6 1.0
MN B:MN2005 3.7 7.0 1.0
OD1 B:ASP1152 3.7 9.8 1.0
O B:HOH4017 3.8 7.6 1.0
NZ B:LYS1154 3.9 2.2 1.0
O B:HOH4409 4.0 12.2 1.0
OH B:TYR1192 4.0 8.7 1.0
OD2 B:ASP1115 4.1 6.1 1.0
CB B:ASP1152 4.4 8.2 1.0
OD1 B:ASP1147 4.4 7.7 1.0
O B:HOH4075 4.4 5.7 1.0
O B:HOH4209 4.4 15.7 1.0
O1 B:PO43004 4.5 8.4 1.0
NZ B:LYS1193 4.7 6.5 1.0
OD2 B:ASP1120 4.7 7.5 1.0
OE2 B:GLU1117 4.9 9.7 1.0
CE B:LYS1154 5.0 6.5 1.0
CG B:ASP1115 5.0 6.8 1.0

Reference:

V.Tuominen, P.Heikinheimo, T.Kajander, T.Torkkel, T.Hyytia, J.Kapyla, R.Lahti, B.S.Cooperman, A.Goldman. The R78K and D117E Active-Site Variants of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications. J.Mol.Biol. V. 284 1565 1998.
ISSN: ISSN 0022-2836
PubMed: 9878371
DOI: 10.1006/JMBI.1998.2266
Page generated: Sat Oct 5 09:42:10 2024

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