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Manganese in PDB 8prk: 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: 8prk 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.700, 102.300, 117.000, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.5

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 8prk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 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: 8prk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 8prk

Go back to Manganese Binding Sites List in 8prk
Manganese binding site 1 out of 6 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:Mn2004

b:9.1
occ:1.00
 O2 A:PO43002 2.3 7.4 1.0
OD2 A:ASP147 2.4 10.0 1.0
OD2 A:ASP152 2.4 7.1 1.0
CG A:ASP152 3.2 10.8 1.0
CG A:ASP147 3.3 7.8 1.0
P A:PO43002 3.4 10.8 1.0
CB A:ASP147 3.6 8.2 1.0
OD1 A:ASP152 3.7 9.2 1.0
O3 A:PO43002 3.7 13.3 1.0
MN A:MN2001 3.8 9.0 1.0
NZ A:LYS154 3.9 5.9 1.0
OD2 A:ASP115 4.0 8.2 1.0
OH A:TYR192 4.1 12.8 1.0
O1 A:PO43002 4.3 18.5 1.0
O A:HOH4272 4.3 10.8 1.0
O4 A:PO43002 4.4 11.9 1.0
O A:HOH4041 4.4 7.5 1.0
CB A:ASP152 4.4 9.0 1.0
OD1 A:ASP147 4.5 7.8 1.0
O A:HOH4021 4.6 23.6 1.0
OD2 A:ASP120 4.8 8.0 1.0
NZ A:LYS193 4.8 14.3 1.0
CE A:LYS154 4.9 5.0 1.0
OH A:TYR93 4.9 7.1 1.0
O A:HOH4262 5.0 26.7 1.0

Manganese binding site 2 out of 6 in 8prk

Go back to Manganese Binding Sites List in 8prk
Manganese binding site 2 out of 6 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:9.6
occ:1.00
 OD1 A:ASP120 2.3 6.9 1.0
O A:HOH4004 2.4 4.3 1.0
O A:HOH4003 2.4 9.2 1.0
O4 A:PO43002 2.5 11.9 1.0
O A:HOH4002 2.5 13.1 1.0
O1 A:PO43002 2.5 18.5 1.0
P A:PO43002 2.9 10.8 1.0
CG A:ASP120 3.4 8.1 1.0
MN A:MN2001 3.8 9.0 1.0
O2 A:PO43002 3.8 7.4 1.0
OD2 A:ASP120 3.9 8.0 1.0
OH A:TYR93 3.9 7.1 1.0
O3 A:PO43002 3.9 13.3 1.0
O A:HOH4024 4.0 8.5 1.0
CE1 A:TYR93 4.1 5.3 1.0
OE1 A:GLU48 4.2 7.2 1.0
OD2 A:ASP117 4.3 12.7 1.0
O A:PRO118 4.4 7.3 1.0
O A:HOH4088 4.4 10.2 1.0
CZ A:TYR93 4.4 7.1 1.0
CB A:ASP117 4.4 7.8 1.0
CB A:ASP120 4.5 6.1 1.0
OE2 A:GLU48 4.5 9.7 1.0
O A:HOH4001 4.6 8.1 1.0
O A:GLY94 4.7 7.2 1.0
CG A:ASP117 4.7 11.7 1.0
NZ A:LYS56 4.8 16.2 1.0
CB A:ALA95 4.8 8.7 1.0
CD A:GLU48 4.8 8.2 1.0
CA A:ASP120 4.9 8.0 1.0

Manganese binding site 3 out of 6 in 8prk

Go back to Manganese Binding Sites List in 8prk
Manganese binding site 3 out of 6 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:Mn2001

b:9.0
occ:1.00
 OD1 A:ASP152 2.3 9.2 1.0
OD2 A:ASP120 2.4 8.0 1.0
O2 A:PO43002 2.4 7.4 1.0
OD2 A:ASP115 2.4 8.2 1.0
O A:HOH4001 2.4 8.1 1.0
O4 A:PO43002 2.5 11.9 1.0
P A:PO43002 2.9 10.8 1.0
CG A:ASP120 3.2 8.1 1.0
OD1 A:ASP120 3.2 6.9 1.0
CG A:ASP115 3.3 11.4 1.0
CG A:ASP152 3.3 10.8 1.0
OD1 A:ASP115 3.5 8.6 1.0
OD2 A:ASP152 3.7 7.1 1.0
MN A:MN2002 3.8 9.6 1.0
MN A:MN2004 3.8 9.1 1.0
O1 A:PO43002 3.8 18.5 1.0
O A:HOH4289 3.9 6.3 1.0
NZ A:LYS154 4.0 5.9 1.0
O3 A:PO43002 4.1 13.3 1.0
CB A:ASP117 4.1 7.8 1.0
OD2 A:ASP117 4.3 12.7 1.0
O A:HOH4004 4.5 4.3 1.0
O A:PRO118 4.5 7.3 1.0
OH A:TYR93 4.5 7.1 1.0
CB A:ASP152 4.5 9.0 1.0
CB A:ASP120 4.6 6.1 1.0
CB A:ASP115 4.6 8.4 1.0
CG A:ASP117 4.7 11.7 1.0
CA A:ASP152 4.8 9.6 1.0

Manganese binding site 4 out of 6 in 8prk

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Manganese binding site 4 out of 6 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
B:Mn2005

b:12.5
occ:1.00
 OD1 B:ASP1152 2.3 7.9 1.0
OD2 B:ASP1115 2.4 6.9 1.0
O4 B:PO43004 2.4 15.8 1.0
OD2 B:ASP1120 2.4 6.5 1.0
O B:HOH4008 2.4 7.8 1.0
O1 B:PO43004 2.5 11.9 1.0
P B:PO43004 2.9 16.0 1.0
CG B:ASP1120 3.2 6.7 1.0
CG B:ASP1115 3.2 9.9 1.0
OD1 B:ASP1120 3.3 8.6 1.0
CG B:ASP1152 3.3 8.7 1.0
OD1 B:ASP1115 3.5 9.3 1.0
MN B:MN2008 3.6 10.1 1.0
OD2 B:ASP1152 3.7 8.3 1.0
MN B:MN2006 3.7 8.9 1.0
O3 B:PO43004 3.9 11.4 1.0
NZ B:LYS1154 4.0 8.2 1.0
O B:HOH4052 4.0 7.3 1.0
O2 B:PO43004 4.1 12.9 1.0
CB B:ASP1117 4.2 9.9 1.0
OD2 B:ASP1117 4.3 12.2 1.0
CB B:ASP1115 4.5 8.2 1.0
O B:HOH4009 4.5 6.9 1.0
O B:PRO1118 4.5 6.0 1.0
OH B:TYR1093 4.5 14.7 1.0
CB B:ASP1152 4.6 7.2 1.0
CB B:ASP1120 4.6 5.9 1.0
CG B:ASP1117 4.8 12.2 1.0
CA B:ASP1152 4.9 7.4 1.0

Manganese binding site 5 out of 6 in 8prk

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Manganese binding site 5 out of 6 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:Mn2008

b:10.1
occ:1.00
 OD2 B:ASP1152 2.4 8.3 1.0
O1 B:PO43004 2.4 11.9 1.0
OD2 B:ASP1147 2.4 10.6 1.0
O B:HOH4012 2.5 10.2 1.0
CG B:ASP1152 3.3 8.7 1.0
CG B:ASP1147 3.4 8.3 1.0
P B:PO43004 3.6 16.0 1.0
OD1 B:ASP1152 3.6 7.9 1.0
MN B:MN2005 3.6 12.5 1.0
CB B:ASP1147 3.7 7.8 1.0
O2 B:PO43004 3.7 12.9 1.0
NZ B:LYS1154 3.8 8.2 1.0
OH B:TYR1192 4.0 12.1 1.0
OD2 B:ASP1115 4.1 6.9 1.0
O B:HOH4154 4.2 25.8 1.0
O B:HOH4062 4.3 10.7 1.0
O4 B:PO43004 4.4 15.8 1.0
O3 B:PO43004 4.4 11.4 1.0
O B:HOH4257 4.4 32.5 1.0
CB B:ASP1152 4.5 7.2 1.0
O B:HOH4047 4.5 14.7 1.0
OD1 B:ASP1147 4.5 9.6 1.0
NZ B:LYS1193 4.7 6.7 1.0
OD2 B:ASP1120 4.7 6.5 1.0
CE B:LYS1154 4.9 10.8 1.0
OH B:TYR1093 4.9 14.7 1.0

Manganese binding site 6 out of 6 in 8prk

Go back to Manganese Binding Sites List in 8prk
Manganese binding site 6 out of 6 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:8.9
occ:1.00
 OD1 B:ASP1120 2.3 8.6 1.0
O B:HOH4011 2.4 7.6 1.0
O B:HOH4010 2.4 9.0 1.0
O B:HOH4009 2.5 6.9 1.0
O4 B:PO43004 2.5 15.8 1.0
O3 B:PO43004 2.5 11.4 1.0
P B:PO43004 2.8 16.0 1.0
CG B:ASP1120 3.3 6.7 1.0
O1 B:PO43004 3.7 11.9 1.0
MN B:MN2005 3.7 12.5 1.0
OD2 B:ASP1120 3.9 6.5 1.0
OH B:TYR1093 3.9 14.7 1.0
O2 B:PO43004 3.9 12.9 1.0
O B:HOH4105 4.0 9.0 1.0
CE1 B:TYR1093 4.1 9.3 1.0
O B:HOH4216 4.1 21.0 1.0
OE1 B:GLU1048 4.2 11.4 1.0
O B:PRO1118 4.3 6.0 1.0
O B:HOH4098 4.3 10.8 1.0
OD2 B:ASP1117 4.3 12.2 1.0
CB B:ASP1120 4.4 5.9 1.0
CZ B:TYR1093 4.4 11.4 1.0
O B:HOH4008 4.5 7.8 1.0
CB B:ASP1117 4.5 9.9 1.0
OE2 B:GLU1048 4.6 12.0 1.0
O B:GLY1094 4.6 4.6 1.0
CB B:ALA1095 4.8 10.0 1.0
CG B:ASP1117 4.8 12.2 1.0
CD B:GLU1048 4.8 12.2 1.0
CA B:ASP1120 4.9 7.2 1.0
NZ B:LYS1056 5.0 18.4 1.0
O B:HOH4266 5.0 8.2 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: Sun Oct 6 13:35:01 2024

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