Phosphorus 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

Phosphorus Binding Sites:

The binding sites of Phosphorus 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 Phosphorus atom.
In total 3 binding sites of Phosphorus 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 Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 117e

Go back to Phosphorus Binding Sites List in 117e
Phosphorus binding site 1 out of 3 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 Phosphorus with other atoms in the P 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:P3001

b:14.6
occ:1.00
 P A:PO43001 0.0 14.6 1.0
O3 A:PO43001 1.5 19.2 1.0
O2 A:PO43001 1.5 12.1 1.0
O1 A:PO43001 1.5 19.4 1.0
O4 A:PO43001 1.5 12.5 1.0
NH2 A:ARG78 3.3 4.7 1.0
MN A:MN2003 3.3 18.5 1.0
NH1 A:ARG78 3.4 7.1 1.0
O A:HOH4006 3.6 16.5 1.0
NZ A:LYS193 3.6 4.4 1.0
OH A:TYR192 3.7 7.8 1.0
O3 A:PO43002 3.7 6.8 1.0
O A:HOH4119 3.7 13.9 1.0
O A:HOH4182 3.7 10.4 1.0
MN A:MN2004 3.7 6.8 1.0
O2 A:PO43002 3.8 11.6 1.0
CZ A:ARG78 3.8 7.3 1.0
OD2 A:ASP147 3.9 4.6 1.0
O A:HOH4414 3.9 26.4 1.0
O A:HOH4405 4.1 9.4 1.0
O A:HOH4010 4.1 10.6 1.0
P A:PO43002 4.2 8.9 1.0
O4 A:PO43002 4.3 4.3 1.0
CE A:LYS56 4.4 11.9 1.0
CE A:LYS193 4.5 2.3 1.0
CZ A:TYR192 4.6 5.7 1.0
O A:HOH4009 4.7 9.2 1.0
CE2 A:TYR192 4.7 5.7 1.0
CD A:LYS193 4.8 3.5 1.0
NZ A:LYS56 4.9 12.5 1.0

Phosphorus binding site 2 out of 3 in 117e

Go back to Phosphorus Binding Sites List in 117e
Phosphorus binding site 2 out of 3 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 Phosphorus with other atoms in the P 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:P3002

b:8.9
occ:1.00
 P A:PO43002 0.0 8.9 1.0
O1 A:PO43002 1.5 11.9 1.0
O3 A:PO43002 1.5 6.8 1.0
O2 A:PO43002 1.5 11.6 1.0
O4 A:PO43002 1.5 4.3 1.0
OE2 A:GLU117 2.9 6.6 1.0
MN A:MN2002 3.3 10.4 1.0
NZ A:LYS56 3.3 12.5 1.0
O4 A:PO43001 3.4 12.5 1.0
MN A:MN2001 3.4 7.7 1.0
O A:HOH4401 3.5 20.4 1.0
O A:HOH4010 3.5 10.6 1.0
MN A:MN2004 3.6 6.8 1.0
O3 A:PO43001 3.6 19.2 1.0
OH A:TYR93 3.6 9.2 1.0
O A:HOH4006 3.8 16.5 1.0
CD A:GLU117 3.9 10.2 1.0
O A:HOH4405 4.1 9.4 1.0
OD2 A:ASP120 4.1 10.4 1.0
O A:HOH4003 4.1 13.6 1.0
P A:PO43001 4.2 14.6 1.0
OE1 A:GLU117 4.2 11.4 1.0
CE A:LYS56 4.2 11.9 1.0
CE2 A:TYR93 4.4 7.5 1.0
CZ A:TYR93 4.5 6.8 1.0
OD1 A:ASP120 4.5 6.5 1.0
NZ A:LYS154 4.5 4.0 1.0
CG A:ASP120 4.6 7.0 1.0
O A:HOH4009 4.6 9.2 1.0
OD2 A:ASP115 4.8 6.4 1.0
OD2 A:ASP152 4.9 7.8 1.0
O A:HOH4004 4.9 6.8 1.0
O A:HOH4105 5.0 4.6 1.0

Phosphorus binding site 3 out of 3 in 117e

Go back to Phosphorus Binding Sites List in 117e
Phosphorus binding site 3 out of 3 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 Phosphorus with other atoms in the P 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
B:P3004

b:6.7
occ:1.00
 P B:PO43004 0.0 6.7 1.0
O1 B:PO43004 1.5 8.4 1.0
O3 B:PO43004 1.5 4.4 1.0
O2 B:PO43004 1.5 11.1 1.0
O4 B:PO43004 1.5 10.6 1.0
O B:HOH4416 3.0 11.3 1.0
MN B:MN2008 3.2 8.1 1.0
OE2 B:GLU1117 3.2 9.7 1.0
OH B:TYR1093 3.3 5.9 1.0
MN B:MN2005 3.3 7.0 1.0
MN B:MN2006 3.4 6.9 1.0
O B:HOH4056 3.5 11.1 1.0
MN B:MN2007 3.5 14.7 1.0
O B:HOH4020 3.6 6.4 1.0
NZ B:LYS1056 3.6 12.5 1.0
O B:HOH4409 3.7 12.2 1.0
O B:HOH4017 3.9 7.6 1.0
OD2 B:ASP1120 4.0 7.5 1.0
NZ B:LYS1154 4.1 2.2 1.0
O B:HOH4015 4.1 6.8 1.0
CZ B:TYR1093 4.2 4.1 1.0
OD1 B:ASP1120 4.3 5.4 1.0
CD B:GLU1117 4.3 8.7 1.0
CG B:ASP1120 4.4 7.2 1.0
OD2 B:ASP1152 4.4 11.0 1.0
CE1 B:TYR1093 4.5 5.4 1.0
O B:HOH4019 4.5 8.1 1.0
O B:HOH4016 4.6 7.9 1.0
OE1 B:GLU1117 4.6 10.8 1.0
OD2 B:ASP1115 4.7 6.1 1.0
OD1 B:ASP1152 4.8 9.8 1.0
CE B:LYS1056 4.9 13.4 1.0
OE1 B:GLU1058 4.9 16.4 1.0
O B:HOH4117 4.9 12.5 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: Fri Sep 25 11:11:55 2020

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