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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy