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Magnesium in PDB 1obw: Structure of Inorganic Pyrophosphatase

Enzymatic activity of Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1obw was solved by V.Yu.Oganessyan, E.H.Harutyunyan, S.M.Avaeva, N.N.Oganessyan, T.Mather, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.300, 110.300, 78.200, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 1obw

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Magnesium binding site 1 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg176

b:34.8
occ:1.00
 OD1 A:ASP102 2.0 30.4 1.0
OD2 A:ASP65 2.0 38.6 1.0
O A:HOH202 2.0 36.8 1.0
O A:HOH198 2.1 35.0 1.0
O A:HOH200 2.2 33.0 1.0
OD2 A:ASP70 2.2 28.6 1.0
CG A:ASP65 3.0 39.6 1.0
CG A:ASP102 3.1 35.6 1.0
CG A:ASP70 3.2 27.3 1.0
OD1 A:ASP65 3.4 32.5 1.0
OD1 A:ASP70 3.8 29.9 1.0
OD2 A:ASP102 3.8 33.9 1.0
NZ A:LYS104 3.9 26.2 1.0
O A:HOH225 3.9 33.8 1.0
CA A:ASP102 4.1 31.9 1.0
CB A:ASP102 4.1 27.8 1.0
CB A:ASP65 4.3 35.5 1.0
CB A:ASP70 4.3 25.2 1.0
C A:ASP102 4.4 33.1 1.0
O A:HOH265 4.4 45.4 1.0
O A:ALA103 4.4 27.4 1.0
OG A:SER63 4.4 42.2 1.0
O A:PRO68 4.5 26.5 1.0
O A:HOH208 4.7 37.3 1.0
O A:ASP102 4.8 32.2 1.0
N A:ASP70 4.8 23.2 1.0
N A:ALA103 4.8 28.8 1.0
CE A:LYS104 4.9 24.3 1.0
MG A:MG178 5.0 36.4 0.5

Magnesium binding site 2 out of 7 in 1obw

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Magnesium binding site 2 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg177

b:27.5
occ:1.00
 O A:HOH209 2.1 25.5 1.0
O A:HOH203 2.1 27.8 1.0
O A:HOH201 2.2 26.8 1.0
OD1 A:ASN24 3.9 28.5 1.0
O A:ASN24 4.1 24.7 1.0
O A:ALA25 4.2 22.5 1.0
C A:ALA25 4.5 23.6 1.0
OD1 A:ASP26 4.5 28.2 1.0
C A:ASN24 4.6 24.9 1.0
CG A:ASN24 4.6 31.3 1.0
O A:HOH234 4.8 58.4 1.0
ND2 A:ASN24 4.9 32.3 1.0
N A:ASP26 4.9 21.5 1.0
N A:ALA25 5.0 23.9 1.0

Magnesium binding site 3 out of 7 in 1obw

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Magnesium binding site 3 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg178

b:36.4
occ:0.50
 O A:HOH225 2.0 33.8 1.0
O A:HOH224 2.0 31.7 1.0
OD1 A:ASP70 2.1 29.9 1.0
O A:HOH213 2.1 29.7 1.0
O A:HOH242 2.2 51.1 1.0
O A:HOH217 2.7 42.1 1.0
CG A:ASP70 3.2 27.3 1.0
OD2 A:ASP70 3.9 28.6 1.0
O A:PRO68 4.1 26.5 1.0
OH A:TYR55 4.2 27.9 1.0
OE1 A:GLU20 4.3 25.1 1.0
O A:HOH202 4.3 36.8 1.0
CB A:ASP70 4.4 25.2 1.0
O A:HOH200 4.4 33.0 1.0
CB A:TYR57 4.6 21.7 1.0
CE2 A:TYR55 4.7 25.5 1.0
CA A:ASP70 4.7 23.8 1.0
CB A:ASP67 4.7 42.8 1.0
O A:HOH211 4.8 40.5 1.0
CZ A:TYR55 4.8 26.5 1.0
O A:GLY56 4.9 19.7 1.0
OE2 A:GLU20 4.9 24.3 1.0
MG A:MG176 5.0 34.8 1.0

Magnesium binding site 4 out of 7 in 1obw

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Magnesium binding site 4 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg176

b:35.3
occ:1.00
 O B:HOH253 1.9 38.0 1.0
OD1 B:ASP102 2.0 39.9 1.0
O B:HOH242 2.1 42.2 1.0
OD2 B:ASP65 2.1 37.1 1.0
O B:HOH209 2.1 31.4 1.0
OD2 B:ASP70 2.1 30.5 1.0
CG B:ASP102 3.1 40.1 1.0
CG B:ASP70 3.2 28.9 1.0
CG B:ASP65 3.2 41.3 1.0
OD1 B:ASP65 3.6 34.8 1.0
OD1 B:ASP70 3.8 28.8 1.0
O B:HOH233 3.9 37.9 1.0
OD2 B:ASP102 3.9 40.8 1.0
NZ B:LYS104 4.0 28.0 1.0
CA B:ASP102 4.1 37.0 1.0
CB B:ASP102 4.1 39.0 1.0
CB B:ASP70 4.3 24.6 1.0
O B:ALA103 4.4 30.9 1.0
O B:HOH232 4.4 47.7 1.0
CB B:ASP65 4.5 41.9 1.0
OG B:SER63 4.5 46.9 1.0
C B:ASP102 4.5 36.4 1.0
O B:PRO68 4.6 27.8 1.0
N B:ASP70 4.7 22.4 1.0
MG B:MG177 4.9 33.1 0.5
O B:ASP102 4.9 36.6 1.0
CE B:LYS104 4.9 30.9 1.0
N B:ALA103 5.0 32.6 1.0
CB B:ASP67 5.0 39.4 1.0

Magnesium binding site 5 out of 7 in 1obw

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Magnesium binding site 5 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg177

b:33.1
occ:0.50
 O B:HOH233 2.0 37.9 1.0
OD1 B:ASP70 2.1 28.8 1.0
O B:HOH211 2.1 34.2 1.0
O B:HOH206 2.2 38.2 1.0
O B:HOH237 2.3 50.7 1.0
O B:HOH239 2.3 39.1 1.0
CG B:ASP70 3.1 28.9 1.0
OD2 B:ASP70 3.7 30.5 1.0
OH B:TYR55 3.9 28.8 1.0
O B:HOH253 4.1 38.0 1.0
CB B:ASP70 4.2 24.6 1.0
O B:PRO68 4.3 27.8 1.0
OE1 B:GLU20 4.4 26.4 1.0
CE2 B:TYR55 4.5 26.3 1.0
O B:HOH209 4.5 31.4 1.0
OD2 B:ASP67 4.5 55.6 1.0
CZ B:TYR55 4.6 30.0 1.0
CB B:ASP67 4.7 39.4 1.0
CA B:ASP70 4.7 24.6 1.0
CB B:TYR57 4.8 23.1 1.0
MG B:MG176 4.9 35.3 1.0

Magnesium binding site 6 out of 7 in 1obw

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Magnesium binding site 6 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg176

b:30.3
occ:0.50
 O C:HOH232 2.1 28.9 1.0
O C:HOH200 2.1 27.0 1.0
O C:HOH187 2.2 30.0 1.0
OD1 C:ASN24 3.8 27.0 1.0
O C:ALA25 4.1 24.8 1.0
O C:ASN24 4.2 26.9 1.0
C C:ALA25 4.5 24.8 1.0
OD1 C:ASP26 4.6 29.3 1.0
C C:ASN24 4.6 25.1 1.0
CG C:ASN24 4.6 31.3 1.0
N C:ASP26 5.0 23.2 1.0

Magnesium binding site 7 out of 7 in 1obw

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Magnesium binding site 7 out of 7 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg177

b:29.9
occ:0.70
 O C:HOH218 1.7 41.6 0.7
O C:HOH254 1.8 40.9 1.0
O C:HOH195 2.0 36.8 1.0
OD2 C:ASP65 2.1 45.7 1.0
OD1 C:ASP102 2.1 47.0 1.0
OD2 C:ASP70 2.2 31.7 1.0
CG C:ASP70 3.1 33.2 1.0
CG C:ASP65 3.1 44.5 1.0
CG C:ASP102 3.2 47.8 1.0
OD1 C:ASP65 3.4 38.7 1.0
OD1 C:ASP70 3.6 33.2 1.0
OD2 C:ASP102 4.0 51.8 1.0
O C:HOH222 4.0 39.8 1.0
NZ C:LYS104 4.0 33.1 1.0
O C:HOH227 4.1 50.6 1.0
CB C:ASP102 4.2 44.8 1.0
CB C:ASP70 4.2 24.1 1.0
CA C:ASP102 4.3 44.7 1.0
CB C:ASP65 4.4 41.7 1.0
OG C:SER63 4.5 46.3 1.0
O C:ALA103 4.5 36.7 1.0
O C:PRO68 4.5 26.7 1.0
C C:ASP102 4.7 42.6 1.0
N C:ASP70 4.8 25.5 1.0
CB C:ASP67 4.9 42.2 1.0
OD2 C:ASP67 5.0 60.1 1.0
CE C:LYS104 5.0 26.5 1.0

Reference:

E.H.Harutyunyan, V.Y.Oganessyan, N.N.Oganessyan, S.M.Avaeva, T.I.Nazarova, N.N.Vorobyeva, S.A.Kurilova, R.Huber, T.Mather. Crystal Structure of Holo Inorganic Pyrophosphatase From Escherichia Coli at 1.9 A Resolution. Mechanism of Hydrolysis. Biochemistry V. 36 7754 1997.
ISSN: ISSN 0006-2960
PubMed: 9201917
DOI: 10.1021/BI962637U
Page generated: Tue Aug 13 10:36:03 2024

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