Atomistry » Manganese » PDB 8kfj-8q1k » 8prk
Atomistry »
  Manganese »
    PDB 8kfj-8q1k »
      8prk »

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

Go back to Manganese Binding Sites List in 8prk
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

Go back to Manganese Binding Sites List in 8prk
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy