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Magnesium in PDB 4z71: Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions

Enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions, PDB code: 4z71 was solved by A.C.Pratt, T.Biswas, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.70 / 1.85
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.695, 101.695, 81.154, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions (pdb code 4z71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions, PDB code: 4z71:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4z71

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Magnesium binding site 1 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:29.7
occ:1.00
 OD1 A:ASP57 2.2 25.5 1.0
O A:HOH616 2.2 30.1 1.0
O A:HOH602 2.2 29.4 1.0
OD2 A:ASP52 2.2 31.9 1.0
O A:HOH719 2.2 30.3 1.0
O A:HOH624 2.2 30.3 1.0
CG A:ASP57 3.1 23.2 1.0
CG A:ASP52 3.2 33.5 1.0
OD2 A:ASP57 3.4 24.0 1.0
OD1 A:ASP52 3.5 33.1 1.0
O A:HOH680 3.9 30.1 1.0
O A:PRO55 4.0 22.3 1.0
O A:HOH635 4.3 26.9 1.0
N A:ASP57 4.3 20.4 1.0
CB A:ASP57 4.4 21.9 1.0
OD2 A:ASP89 4.4 33.4 1.0
CB A:ASP54 4.4 30.4 1.0
CB A:ASP52 4.5 34.1 1.0
O A:ASP90 4.5 22.8 1.0
CG A:ASP89 4.7 32.9 1.0
OD2 A:ASP54 4.7 31.8 1.0
OD1 A:ASP89 4.7 33.2 1.0
CA A:ASP57 4.9 20.7 1.0

Magnesium binding site 2 out of 6 in 4z71

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Magnesium binding site 2 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:47.8
occ:1.00
 O A:HOH754 2.2 46.5 1.0
O A:HOH787 2.2 49.0 1.0
O A:HOH611 2.2 47.3 1.0
OD2 A:ASP89 3.4 33.4 1.0
O A:HOH602 3.8 29.4 1.0
OD2 A:ASP52 3.9 31.9 1.0
O A:GLY88 4.1 34.4 1.0
CB A:ASP52 4.2 34.1 1.0
CG A:ASP89 4.2 32.9 1.0
CB A:ASP89 4.4 32.2 1.0
CG A:ASP52 4.5 33.5 1.0
OD2 A:ASP84 4.5 37.5 1.0
CB A:HIS86 4.7 47.5 1.0
OD1 A:ASP84 4.8 37.2 1.0

Magnesium binding site 3 out of 6 in 4z71

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Magnesium binding site 3 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:42.9
occ:1.00
 O A:HOH601 2.2 43.5 1.0
O A:LYS133 2.2 42.1 1.0
O A:HOH659 2.2 41.0 1.0
O A:HOH743 2.5 45.7 1.0
C A:LYS133 3.2 41.2 1.0
O A:LYS127 3.7 20.8 1.0
O A:ASP128 3.9 21.6 1.0
CB A:LYS133 4.0 40.5 1.0
CA A:ASP128 4.0 21.0 1.0
CA A:LYS133 4.0 40.3 1.0
N A:PHE134 4.1 41.8 1.0
O A:GLU130 4.2 27.7 1.0
CA A:PHE134 4.2 42.2 1.0
C A:ASP128 4.3 21.6 1.0
N A:LYS133 4.3 38.8 1.0
C A:LYS127 4.4 20.9 1.0
OD1 A:ASP128 4.5 20.7 1.0
N A:ASP128 4.6 20.8 1.0
CB A:PHE134 4.7 43.1 1.0

Magnesium binding site 4 out of 6 in 4z71

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Magnesium binding site 4 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:30.2
occ:1.00
 O B:HOH602 2.2 29.5 1.0
OD2 B:ASP52 2.2 32.1 1.0
O B:HOH657 2.2 30.9 1.0
OD1 B:ASP57 2.2 25.6 1.0
O B:HOH606 2.2 29.8 1.0
OD1 B:ASP89 2.2 32.0 1.0
CG B:ASP57 3.0 23.1 1.0
CG B:ASP52 3.3 33.0 1.0
OD2 B:ASP57 3.3 23.9 1.0
CG B:ASP89 3.4 32.2 1.0
O B:HOH714 3.6 42.9 1.0
OD1 B:ASP52 3.7 32.8 1.0
O B:HOH617 3.8 43.6 1.0
OD2 B:ASP89 4.0 32.4 1.0
O B:HOH778 4.1 44.9 1.0
O B:HOH628 4.1 36.4 1.0
O B:ASP90 4.3 23.4 1.0
CB B:ASP57 4.3 21.8 1.0
N B:ASP57 4.4 20.5 1.0
O B:HOH665 4.5 26.2 1.0
O B:PRO55 4.5 22.7 1.0
CB B:ASP52 4.5 33.2 1.0
CB B:ASP89 4.6 31.6 1.0
N B:ASP90 4.8 26.9 1.0
CB B:ASP54 4.9 30.3 1.0
OD2 B:ASP54 4.9 31.5 1.0
CA B:ASP89 4.9 30.6 1.0
CA B:ASP57 5.0 20.6 1.0

Magnesium binding site 5 out of 6 in 4z71

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Magnesium binding site 5 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:44.8
occ:1.00
 O B:HOH734 2.2 45.4 1.0
O B:HOH617 2.2 43.6 1.0
O B:HOH790 2.2 44.9 1.0
O B:HOH677 2.2 44.2 1.0
O B:HOH646 2.2 45.3 1.0
O B:HOH778 2.2 44.9 1.0
CB B:HIS86 4.0 37.9 1.0
O B:HOH678 4.0 48.1 1.0
CB B:ASP89 4.1 31.6 1.0
OD1 B:ASP89 4.1 32.0 1.0
CG B:ASP89 4.1 32.2 1.0
OD2 B:ASP52 4.2 32.1 1.0
OD2 B:ASP84 4.3 33.4 1.0
O B:GLY88 4.3 31.1 1.0
OD1 B:ASP84 4.4 33.3 1.0
O B:HOH714 4.5 42.9 1.0
O B:HOH762 4.7 51.4 1.0
OD2 B:ASP89 4.7 32.4 1.0
CG B:ASP84 4.8 33.0 1.0
O B:HIS86 4.8 34.3 1.0
CB B:ASP52 4.8 33.2 1.0
O B:HOH759 4.8 51.7 1.0
ND1 B:HIS86 4.8 40.8 1.0
CG B:HIS86 4.8 39.7 1.0
C B:HIS86 5.0 34.6 1.0
CG B:ASP52 5.0 33.0 1.0

Magnesium binding site 6 out of 6 in 4z71

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Magnesium binding site 6 out of 6 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions


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 Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg500

b:36.9
occ:1.00
 OD1 C:ASP89 2.2 36.6 1.0
OD2 C:ASP57 2.2 28.6 1.0
O C:HOH655 2.2 36.0 1.0
OD2 C:ASP52 2.2 44.9 1.0
O C:HOH616 2.2 37.7 1.0
CG C:ASP57 3.2 25.1 1.0
CG C:ASP89 3.4 35.9 1.0
CG C:ASP52 3.4 49.1 1.0
OD1 C:ASP57 3.8 26.0 1.0
OD1 C:ASP52 4.0 48.9 1.0
O C:HOH751 4.0 34.6 1.0
OD2 C:ASP89 4.1 36.5 1.0
O C:ASP90 4.2 25.9 1.0
NZ C:LYS91 4.2 26.5 1.0
CB C:ASP57 4.3 23.5 1.0
CA C:ASP89 4.3 34.0 1.0
CB C:ASP89 4.4 35.1 1.0
C C:ASP89 4.4 32.5 1.0
O C:HOH752 4.5 38.6 1.0
CB C:ASP52 4.6 50.1 1.0
O C:HOH682 4.7 40.8 1.0
N C:ASP57 4.7 22.1 1.0
N C:ASP90 4.7 30.1 1.0
O C:PRO55 4.8 26.4 1.0
O C:ASP89 4.8 33.0 1.0

Reference:

A.C.Pratt, S.W.Dewage, A.H.Pang, T.Biswas, S.Barnard-Britson, G.A.Cisneros, O.V.Tsodikov. Structural and Computational Dissection of the Catalytic Mechanism of the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis. J.Struct.Biol. V. 192 76 2015.
ISSN: ESSN 1095-8657
PubMed: 26296329
DOI: 10.1016/J.JSB.2015.08.010
Page generated: Mon Dec 14 19:56:40 2020

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