Atomistry » Magnesium » PDB 2gqr-2haw » 2haw
Atomistry »
  Magnesium »
    PDB 2gqr-2haw »
      2haw »

Magnesium in PDB 2haw: Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp

Enzymatic activity of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp

All present enzymatic activity of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp, PDB code: 2haw was solved by I.P.Fabrichniy, L.Lehtio, E.Oksanen, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.011, 115.867, 147.874, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.6

Other elements in 2haw:

The structure of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp (pdb code 2haw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp, PDB code: 2haw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 1 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:32.8
occ:1.00
 O1 A:2PN2001 1.9 29.7 0.8
F A:F3001 2.0 35.4 1.0
OD1 A:ASP75 2.1 38.5 1.0
OD1 A:ASP13 2.1 39.2 1.0
NE2 A:HIS9 2.3 35.4 1.0
OD2 A:ASP13 2.5 37.7 1.0
CG A:ASP13 2.7 42.4 1.0
CG A:ASP75 3.0 38.8 1.0
P1 A:2PN2001 3.1 34.3 0.8
OD2 A:ASP75 3.2 36.4 1.0
CE1 A:HIS9 3.3 38.5 1.0
CD2 A:HIS9 3.3 35.8 1.0
MG A:MG1004 3.3 42.5 0.8
MG A:MG1002 3.5 33.7 1.0
O3 A:2PN2001 3.5 32.5 0.8
O2 A:2PN2001 3.6 32.7 0.8
OG1 A:THR16 4.1 36.3 1.0
O A:HOH6042 4.1 41.7 1.0
NZ A:LYS205 4.1 38.2 1.0
O4 A:SO44003 4.2 28.6 0.1
CB A:ASP13 4.2 39.3 1.0
ND1 A:HIS9 4.4 37.0 1.0
CB A:ASP75 4.4 34.6 1.0
N A:THR16 4.4 40.1 1.0
CB A:ASP15 4.4 37.6 1.0
CG A:HIS9 4.4 33.1 1.0
CB A:THR16 4.4 35.5 1.0
O A:ASP75 4.5 38.2 1.0
CE A:LYS205 4.6 38.9 1.0
N1 A:2PN2001 4.6 30.5 0.8
CE1 A:HIS98 4.7 38.1 1.0
OD2 A:ASP15 4.7 40.5 1.0
O A:HOH6007 4.8 37.4 1.0
OD1 A:ASP149 4.8 42.3 1.0
MG A:MG1003 4.9 35.7 0.8
OD2 A:ASP149 5.0 42.2 1.0
NE2 A:HIS98 5.0 40.9 1.0
CA A:THR16 5.0 37.0 1.0

Magnesium binding site 2 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 2 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:33.7
occ:1.00
 O2 A:2PN2001 2.0 32.7 0.8
F A:F3001 2.0 35.4 1.0
OD2 A:ASP149 2.1 42.2 1.0
OD2 A:ASP75 2.2 36.4 1.0
OD2 A:ASP15 2.2 40.5 1.0
NE2 A:HIS97 2.3 36.5 1.0
CE1 A:HIS97 3.0 41.1 1.0
CG A:ASP149 3.2 45.2 1.0
CG A:ASP75 3.2 38.8 1.0
CG A:ASP15 3.2 42.4 1.0
P1 A:2PN2001 3.3 34.3 0.8
O1 A:2PN2001 3.4 29.7 0.8
CB A:ASP15 3.5 37.6 1.0
CD2 A:HIS97 3.5 38.0 1.0
MG A:MG1001 3.5 32.8 1.0
OD1 A:ASP149 3.5 42.3 1.0
OD1 A:ASP75 3.6 38.5 1.0
MG A:MG1004 3.8 42.5 0.8
O3 A:2PN2001 4.0 32.5 0.8
OG1 A:THR119 4.1 38.9 1.0
CE1 A:HIS98 4.2 38.1 1.0
ND1 A:HIS97 4.2 39.3 1.0
O A:HOH6031 4.3 38.1 1.0
O4 A:SO44003 4.4 28.6 0.1
OD1 A:ASP15 4.4 39.0 1.0
N A:THR119 4.4 36.3 1.0
CB A:ASP75 4.5 34.6 1.0
CB A:ASP149 4.5 39.4 1.0
NZ A:LYS296 4.5 41.4 1.0
CG A:HIS97 4.5 34.3 1.0
CA A:CYS118 4.7 38.6 1.0
NE2 A:HIS98 4.8 40.9 1.0
N1 A:2PN2001 4.8 30.5 0.8
OD1 A:ASP13 4.9 39.2 1.0
CA A:ASP15 4.9 41.2 1.0

Magnesium binding site 3 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 3 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:35.7
occ:0.85
 O3 A:2PN2001 1.9 32.5 0.8
O A:HOH6042 2.0 41.7 1.0
O2 A:SO44003 2.1 29.4 0.1
O A:HOH6119 2.1 37.7 1.0
O6 A:2PN2001 2.1 34.4 0.8
O A:HOH6088 2.2 40.6 1.0
O A:HOH6044 2.3 41.1 1.0
P1 A:2PN2001 3.2 34.3 0.8
S A:SO44003 3.3 29.9 0.1
MG A:MG1004 3.3 42.5 0.8
P2 A:2PN2001 3.4 33.1 0.8
N1 A:2PN2001 3.4 30.5 0.8
O4 A:SO44003 3.6 28.6 0.1
O A:HOH6019 3.7 34.6 1.0
NH2 A:ARG295 3.8 38.9 1.0
O A:HOH6031 3.9 38.1 1.0
OD1 A:ASP13 3.9 39.2 1.0
O A:HOH6038 3.9 47.9 1.0
O3 A:SO44003 3.9 30.6 0.1
O1 A:2PN2001 4.0 29.7 0.8
OD2 A:ASP203 4.1 39.2 1.0
O5 A:2PN2001 4.2 31.7 0.8
OD1 A:ASP203 4.3 42.9 1.0
OE1 A:GLN218 4.4 41.3 1.0
O1 A:SO44003 4.4 30.0 0.1
O2 A:2PN2001 4.5 32.7 0.8
O4 A:2PN2001 4.6 33.2 0.8
O A:HOH6054 4.6 47.9 1.0
O A:HOH6074 4.6 47.2 1.0
CG A:ASP203 4.7 41.9 1.0
CZ A:ARG295 4.9 39.8 1.0
MG A:MG1001 4.9 32.8 1.0
OD1 A:ASP149 4.9 42.3 1.0
F A:F3001 5.0 35.4 1.0
O A:HOH6093 5.0 50.3 1.0

Magnesium binding site 4 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 4 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:42.5
occ:0.85
 OD1 A:ASP149 2.2 42.3 1.0
O3 A:2PN2001 2.2 32.5 0.8
F A:F3001 2.4 35.4 1.0
O A:HOH6044 2.5 41.1 1.0
O A:HOH6007 2.5 37.4 1.0
OD1 A:ASP13 2.5 39.2 1.0
CG A:ASP13 3.1 42.4 1.0
CG A:ASP149 3.2 45.2 1.0
P1 A:2PN2001 3.3 34.3 0.8
MG A:MG1001 3.3 32.8 1.0
MG A:MG1003 3.3 35.7 0.8
O A:HOH6042 3.6 41.7 1.0
OD2 A:ASP149 3.6 42.2 1.0
O1 A:2PN2001 3.6 29.7 0.8
O2 A:2PN2001 3.7 32.7 0.8
OD2 A:ASP13 3.7 37.7 1.0
MG A:MG1002 3.8 33.7 1.0
CB A:ASP13 3.9 39.3 1.0
O A:HOH6031 3.9 38.1 1.0
CB A:ASP15 4.1 37.6 1.0
O A:HOH6088 4.2 40.6 1.0
CB A:ASP149 4.3 39.4 1.0
CA A:ASP149 4.4 39.2 1.0
O A:HOH6074 4.4 47.2 1.0
OG A:SER148 4.5 39.1 1.0
O A:HOH6038 4.6 47.9 1.0
O4 A:SO44003 4.7 28.6 0.1
N A:ASP15 4.7 37.1 1.0
N A:ASP149 4.7 39.4 1.0
O2 A:SO44003 4.8 29.4 0.1
N1 A:2PN2001 4.9 30.5 0.8
OD1 A:ASP75 4.9 38.5 1.0

Magnesium binding site 5 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 5 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:27.4
occ:1.00
 O1 B:2PN2002 1.9 23.7 0.8
F B:F3002 2.0 27.8 1.0
OD1 B:ASP75 2.0 37.6 1.0
OD1 B:ASP13 2.2 36.0 1.0
NE2 B:HIS9 2.3 36.6 1.0
OD2 B:ASP13 2.5 37.5 1.0
CG B:ASP13 2.7 39.7 1.0
CG B:ASP75 3.0 39.3 1.0
P1 B:2PN2002 3.1 31.5 0.8
CD2 B:HIS9 3.2 36.2 1.0
OD2 B:ASP75 3.3 36.3 1.0
MG B:MG1008 3.3 33.6 0.8
CE1 B:HIS9 3.3 35.5 1.0
MG B:MG1006 3.4 27.1 1.0
O3 B:2PN2002 3.5 28.8 0.8
O2 B:2PN2002 3.8 26.9 0.8
OG1 B:THR16 4.0 38.0 1.0
O B:HOH5135 4.1 32.3 1.0
CB B:ASP13 4.2 38.6 1.0
NZ B:LYS205 4.2 40.7 1.0
CB B:ASP75 4.3 37.0 1.0
CB B:THR16 4.4 36.6 1.0
N B:THR16 4.4 36.8 1.0
CB B:ASP15 4.4 36.5 1.0
CG B:HIS9 4.4 34.2 1.0
ND1 B:HIS9 4.4 36.3 1.0
O B:ASP75 4.5 37.4 1.0
N1 B:2PN2002 4.6 28.5 0.8
O2 B:SO44004 4.6 32.8 0.1
OD1 B:ASP15 4.6 38.4 1.0
CE B:LYS205 4.7 37.2 1.0
OD1 B:ASP149 4.7 42.8 1.0
O B:HOH5015 4.8 30.8 1.0
CE1 B:HIS98 4.8 38.3 1.0
CA B:THR16 4.9 35.5 1.0
OD2 B:ASP149 5.0 41.2 1.0
MG B:MG1007 5.0 32.2 0.8
N B:ASP13 5.0 40.3 1.0

Magnesium binding site 6 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 6 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:27.1
occ:1.00
 F B:F3002 1.9 27.8 1.0
OD2 B:ASP75 2.1 36.3 1.0
O2 B:2PN2002 2.1 26.9 0.8
OD2 B:ASP149 2.2 41.2 1.0
OD1 B:ASP15 2.2 38.4 1.0
NE2 B:HIS97 2.3 38.4 1.0
CG B:ASP75 3.1 39.3 1.0
CE1 B:HIS97 3.1 38.0 1.0
P1 B:2PN2002 3.2 31.5 0.8
CG B:ASP149 3.2 40.4 1.0
CG B:ASP15 3.3 40.5 1.0
MG B:MG1005 3.4 27.4 1.0
OD1 B:ASP75 3.4 37.6 1.0
OD1 B:ASP149 3.5 42.8 1.0
CD2 B:HIS97 3.5 37.7 1.0
O1 B:2PN2002 3.5 23.7 0.8
CB B:ASP15 3.5 36.5 1.0
MG B:MG1008 3.8 33.6 0.8
O3 B:2PN2002 3.9 28.8 0.8
OG1 B:THR119 4.1 39.0 1.0
CE1 B:HIS98 4.2 38.3 1.0
CB B:ASP75 4.3 37.0 1.0
ND1 B:HIS97 4.4 38.3 1.0
O B:HOH5061 4.4 37.7 1.0
OD2 B:ASP15 4.4 38.8 1.0
N B:THR119 4.4 37.1 1.0
N1 B:2PN2002 4.5 28.5 0.8
CG B:HIS97 4.6 36.7 1.0
CB B:ASP149 4.6 37.7 1.0
NZ B:LYS296 4.6 44.0 1.0
O2 B:SO44004 4.7 32.8 0.1
NE2 B:HIS98 4.7 40.5 1.0
OD1 B:ASP13 4.8 36.0 1.0
CA B:CYS118 4.8 38.4 1.0
OD2 B:ASP13 5.0 37.5 1.0
CA B:ASP15 5.0 35.9 1.0

Magnesium binding site 7 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 7 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1007

b:32.2
occ:0.85
 O3 B:2PN2002 2.0 28.8 0.8
O6 B:2PN2002 2.0 27.2 0.8
O B:HOH5135 2.1 32.3 1.0
O B:HOH5063 2.2 33.4 1.0
O B:HOH5171 2.2 37.6 1.0
O B:HOH5093 2.3 37.0 1.0
O3 B:SO44004 2.4 31.9 0.1
P1 B:2PN2002 3.2 31.5 0.8
P2 B:2PN2002 3.3 28.2 0.8
MG B:MG1008 3.3 33.6 0.8
N1 B:2PN2002 3.5 28.5 0.8
S B:SO44004 3.6 32.2 0.1
O2 B:SO44004 3.6 32.8 0.1
NH2 B:ARG295 3.7 38.5 1.0
O B:HOH5048 3.8 32.9 1.0
O B:HOH5061 3.8 37.7 1.0
OD1 B:ASP13 3.9 36.0 1.0
O B:HOH5134 3.9 45.0 1.0
O1 B:2PN2002 4.0 23.7 0.8
OD2 B:ASP203 4.1 46.4 1.0
O5 B:2PN2002 4.1 28.1 0.8
OD1 B:ASP203 4.3 43.1 1.0
O4 B:2PN2002 4.4 29.9 0.8
O B:HOH5124 4.5 42.2 1.0
O4 B:SO44004 4.5 31.4 0.1
OE1 B:GLN218 4.5 43.4 1.0
O B:HOH5074 4.5 39.0 1.0
O2 B:2PN2002 4.5 26.9 0.8
O1 B:SO44004 4.5 32.4 0.1
CG B:ASP203 4.6 44.6 1.0
CZ B:ARG295 4.8 41.8 1.0
F B:F3002 4.9 27.8 1.0
MG B:MG1005 5.0 27.4 1.0
OD1 B:ASP149 5.0 42.8 1.0

Magnesium binding site 8 out of 8 in 2haw

Go back to Magnesium Binding Sites List in 2haw
Magnesium binding site 8 out of 8 in the Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Family II Inorganic Pyrophosphatase in Complex with Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1008

b:33.6
occ:0.85
 O3 B:2PN2002 2.2 28.8 0.8
OD1 B:ASP149 2.3 42.8 1.0
O B:HOH5093 2.3 37.0 1.0
F B:F3002 2.3 27.8 1.0
OD1 B:ASP13 2.4 36.0 1.0
O B:HOH5015 2.6 30.8 1.0
CG B:ASP13 3.0 39.7 1.0
P1 B:2PN2002 3.2 31.5 0.8
MG B:MG1005 3.3 27.4 1.0
CG B:ASP149 3.3 40.4 1.0
MG B:MG1007 3.3 32.2 0.8
O1 B:2PN2002 3.6 23.7 0.8
O B:HOH5135 3.6 32.3 1.0
OD2 B:ASP13 3.7 37.5 1.0
OD2 B:ASP149 3.7 41.2 1.0
O2 B:2PN2002 3.7 26.9 0.8
CB B:ASP13 3.8 38.6 1.0
O B:HOH5061 3.8 37.7 1.0
MG B:MG1006 3.8 27.1 1.0
O B:HOH5074 4.2 39.0 1.0
O B:HOH5171 4.2 37.6 1.0
CB B:ASP15 4.3 36.5 1.0
CB B:ASP149 4.5 37.7 1.0
CA B:ASP149 4.5 40.3 1.0
O B:HOH5134 4.5 45.0 1.0
OG B:SER148 4.6 39.4 1.0
N1 B:2PN2002 4.7 28.5 0.8
N B:ASP15 4.8 36.1 1.0
O2 B:SO44004 4.9 32.8 0.1
N B:ASP149 4.9 37.7 1.0
OD1 B:ASP75 4.9 37.6 1.0
O6 B:2PN2002 5.0 27.2 0.8

Reference:

I.P.Fabrichniy, L.Lehtio, M.Tammenkoski, A.B.Zyryanov, E.Oksanen, A.A.Baykov, R.Lahti, A.Goldman. A Trimetal Site and Substrate Distortion in A Family II Inorganic Pyrophosphatase J.Biol.Chem. V. 282 1422 2007.
ISSN: ISSN 0021-9258
PubMed: 17095506
DOI: 10.1074/JBC.M513161200
Page generated: Tue Aug 13 23:44:18 2024

Last articles

Na in 5DB8
Na in 5DB7
Na in 5DB6
Na in 5D9T
Na in 5CXP
Na in 5D8G
Na in 5D7Z
Na in 5D77
Na in 5CZZ
Na in 5D61
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy