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Manganese in PDB 1k23: Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis

Enzymatic activity of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis

All present enzymatic activity of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis:
3.6.1.1;

Protein crystallography data

The structure of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis, PDB code: 1k23 was solved by S.Ahn, A.J.Milner, K.Futterer, M.Konopka, M.Ilias, T.W.Young, S.A.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.290, 130.560, 150.470, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 29.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis (pdb code 1k23). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis, PDB code: 1k23:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1k23

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Manganese binding site 1 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:42.8
occ:1.00
 OD1 A:ASP13 1.9 35.9 1.0
OD2 A:ASP75 2.0 31.2 1.0
O A:HOH403 2.1 12.8 1.0
NE2 A:HIS9 2.4 37.7 1.0
CG A:ASP13 2.8 37.3 1.0
CG A:ASP75 3.0 30.1 1.0
OD2 A:ASP13 3.2 40.2 1.0
CD2 A:HIS9 3.2 37.4 1.0
OD1 A:ASP75 3.3 29.7 1.0
CE1 A:HIS9 3.5 37.8 1.0
MN A:MN402 3.8 35.4 1.0
O A:HOH405 4.1 34.0 1.0
OG1 A:THR16 4.2 33.8 1.0
O A:ASP75 4.2 29.8 1.0
CB A:ASP13 4.2 36.9 1.0
CB A:ASP75 4.3 28.2 1.0
NE2 A:HIS98 4.4 37.0 1.0
CG A:HIS9 4.4 37.2 1.0
CE1 A:HIS98 4.4 38.1 1.0
ND1 A:HIS9 4.5 36.8 1.0
CB A:ASP15 4.6 33.2 1.0
OD1 A:ASP149 4.7 43.7 1.0
N A:THR16 5.0 33.6 1.0
OD2 A:ASP149 5.0 44.1 1.0

Manganese binding site 2 out of 8 in 1k23

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Manganese binding site 2 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:35.4
occ:1.00
 O A:HOH403 1.9 12.8 1.0
NE2 A:HIS97 2.0 31.4 1.0
OD1 A:ASP75 2.0 29.7 1.0
OD1 A:ASP15 2.1 33.8 1.0
OD2 A:ASP149 2.2 44.1 1.0
CE1 A:HIS97 2.9 31.2 1.0
CD2 A:HIS97 3.0 31.3 1.0
CG A:ASP75 3.1 30.1 1.0
CG A:ASP15 3.2 32.9 1.0
CG A:ASP149 3.3 44.6 1.0
OG1 A:THR119 3.4 24.9 1.0
CB A:ASP15 3.6 33.2 1.0
OD2 A:ASP75 3.6 31.2 1.0
OD1 A:ASP149 3.7 43.7 1.0
CE1 A:HIS98 3.8 38.1 1.0
MN A:MN401 3.8 42.8 1.0
N A:THR119 4.0 30.6 1.0
ND1 A:HIS97 4.0 31.8 1.0
CG A:HIS97 4.1 30.9 1.0
NE2 A:HIS98 4.2 37.0 1.0
O A:HOH405 4.2 34.0 1.0
OD2 A:ASP15 4.3 32.5 1.0
CA A:CYS118 4.3 34.9 1.0
CB A:ASP75 4.4 28.2 1.0
CB A:ASP149 4.5 44.5 1.0
CB A:THR119 4.6 27.4 1.0
O A:GLY117 4.6 38.4 1.0
C A:CYS118 4.7 32.9 1.0
OD1 A:ASP13 4.7 35.9 1.0
CA A:THR119 4.9 29.0 1.0
ND1 A:HIS98 4.9 36.9 1.0
CA A:ASP75 4.9 27.3 1.0

Manganese binding site 3 out of 8 in 1k23

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Manganese binding site 3 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:53.5
occ:1.00
 OD1 B:ASP13 1.9 44.2 1.0
OD2 B:ASP75 2.1 32.1 1.0
O B:HOH405 2.2 18.2 1.0
NE2 B:HIS9 2.5 40.9 1.0
CG B:ASP13 3.0 44.3 1.0
CG B:ASP75 3.1 32.2 1.0
CD2 B:HIS9 3.3 41.8 1.0
OD1 B:ASP75 3.3 33.9 1.0
OD2 B:ASP13 3.4 46.7 1.0
CE1 B:HIS9 3.5 41.3 1.0
MN B:MN404 3.8 48.4 1.0
O B:ASP75 4.2 27.6 1.0
NE2 B:HIS98 4.2 39.7 1.0
CB B:ASP13 4.3 41.9 1.0
CE1 B:HIS98 4.4 39.3 1.0
CB B:ASP75 4.4 29.7 1.0
CG B:HIS9 4.4 41.7 1.0
OG1 B:THR16 4.5 36.8 1.0
ND1 B:HIS9 4.5 41.5 1.0
OD1 B:ASP149 4.7 46.5 1.0
CB B:ASP15 4.8 37.3 1.0

Manganese binding site 4 out of 8 in 1k23

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Manganese binding site 4 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:48.4
occ:1.00
 O B:HOH405 1.8 18.2 1.0
OD2 B:ASP149 1.9 47.5 1.0
OD1 B:ASP15 2.0 34.3 1.0
NE2 B:HIS97 2.2 34.6 1.0
OD1 B:ASP75 2.3 33.9 1.0
CG B:ASP149 3.0 47.3 1.0
CG B:ASP15 3.0 35.5 1.0
CE1 B:HIS97 3.0 34.8 1.0
CD2 B:HIS97 3.3 34.5 1.0
CG B:ASP75 3.3 32.2 1.0
CB B:ASP15 3.4 37.3 1.0
OD1 B:ASP149 3.4 46.5 1.0
OG1 B:THR119 3.6 30.3 1.0
OD2 B:ASP75 3.7 32.1 1.0
MN B:MN403 3.8 53.5 1.0
CE1 B:HIS98 4.0 39.3 1.0
N B:THR119 4.1 34.7 1.0
OD2 B:ASP15 4.2 33.4 1.0
ND1 B:HIS97 4.2 35.8 1.0
CA B:CYS118 4.2 37.2 1.0
CB B:ASP149 4.3 46.3 1.0
CG B:HIS97 4.3 34.4 1.0
NE2 B:HIS98 4.4 39.7 1.0
O B:GLY117 4.5 40.2 1.0
CB B:ASP75 4.5 29.7 1.0
OD1 B:ASP13 4.5 44.2 1.0
C B:CYS118 4.7 36.4 1.0
CB B:THR119 4.8 30.2 1.0
SG B:CYS118 4.8 43.6 1.0
CA B:ASP15 4.9 38.5 1.0
CB B:CYS118 4.9 38.5 1.0

Manganese binding site 5 out of 8 in 1k23

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Manganese binding site 5 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn405

b:39.8
occ:1.00
 OD1 C:ASP13 1.9 33.6 1.0
OD2 C:ASP75 2.0 29.3 1.0
NE2 C:HIS9 2.3 35.0 1.0
O C:HOH407 2.3 11.0 1.0
CG C:ASP13 2.9 36.2 1.0
CG C:ASP75 3.0 28.3 1.0
CD2 C:HIS9 3.1 36.1 1.0
OD2 C:ASP13 3.2 39.9 1.0
CE1 C:HIS9 3.4 35.4 1.0
OD1 C:ASP75 3.4 29.3 1.0
MN C:MN406 3.9 40.0 1.0
OG1 C:THR16 4.2 31.2 1.0
O C:ASP75 4.2 28.7 1.0
CB C:ASP13 4.2 36.0 1.0
CG C:HIS9 4.3 35.6 1.0
CB C:ASP75 4.3 26.6 1.0
NE2 C:HIS98 4.4 37.9 1.0
ND1 C:HIS9 4.4 35.1 1.0
CE1 C:HIS98 4.5 39.2 1.0
CB C:ASP15 4.7 33.7 1.0
OD1 C:ASP149 4.8 41.0 1.0
CB C:THR16 5.0 32.1 1.0

Manganese binding site 6 out of 8 in 1k23

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Manganese binding site 6 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn406

b:40.0
occ:1.00
 O C:HOH407 1.8 11.0 1.0
OD1 C:ASP15 1.9 32.3 1.0
OD2 C:ASP149 2.0 42.6 1.0
OD1 C:ASP75 2.2 29.3 1.0
NE2 C:HIS97 2.2 31.4 1.0
CG C:ASP15 2.9 31.7 1.0
CG C:ASP149 3.0 42.6 1.0
CE1 C:HIS97 3.1 31.6 1.0
CG C:ASP75 3.2 28.3 1.0
CD2 C:HIS97 3.3 31.7 1.0
CB C:ASP15 3.3 33.7 1.0
OD1 C:ASP149 3.5 41.0 1.0
OG1 C:THR119 3.5 29.1 1.0
OD2 C:ASP75 3.6 29.3 1.0
MN C:MN405 3.9 39.8 1.0
N C:THR119 4.0 31.8 1.0
OD2 C:ASP15 4.1 29.7 1.0
CE1 C:HIS98 4.1 39.2 1.0
ND1 C:HIS97 4.3 31.4 1.0
CA C:CYS118 4.3 34.5 1.0
CB C:ASP149 4.3 43.4 1.0
CG C:HIS97 4.4 29.9 1.0
CB C:ASP75 4.4 26.6 1.0
NE2 C:HIS98 4.4 37.9 1.0
OD1 C:ASP13 4.6 33.6 1.0
CB C:THR119 4.7 28.9 1.0
O C:GLY117 4.7 37.2 1.0
C C:CYS118 4.7 32.8 1.0
CA C:ASP15 4.8 34.3 1.0
SG C:CYS118 4.9 36.5 1.0
CA C:THR119 4.9 30.4 1.0

Manganese binding site 7 out of 8 in 1k23

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Manganese binding site 7 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn407

b:46.2
occ:1.00
 OD1 D:ASP13 1.8 43.5 1.0
OD2 D:ASP75 2.0 31.3 1.0
NE2 D:HIS9 2.5 39.7 1.0
CG D:ASP13 2.8 43.4 1.0
O D:HOH410 2.9 23.9 1.0
CG D:ASP75 2.9 31.3 1.0
OD2 D:ASP13 3.2 45.2 1.0
OD1 D:ASP75 3.2 32.5 1.0
CD2 D:HIS9 3.3 41.4 1.0
MN D:MN408 3.4 42.6 1.0
CE1 D:HIS9 3.6 40.8 1.0
O D:HOH411 4.0 26.5 1.0
CB D:ASP13 4.2 41.6 1.0
O D:HOH414 4.2 50.2 1.0
O D:ASP75 4.3 28.4 1.0
NE2 D:HIS98 4.3 39.1 1.0
CB D:ASP75 4.3 28.9 1.0
OG1 D:THR16 4.3 36.3 1.0
CE1 D:HIS98 4.4 39.3 1.0
CG D:HIS9 4.5 41.8 1.0
CB D:ASP15 4.6 36.6 1.0
OD1 D:ASP149 4.6 47.4 1.0
ND1 D:HIS9 4.6 41.3 1.0
OD2 D:ASP149 4.9 47.7 1.0
OD1 D:ASP15 4.9 36.7 1.0

Manganese binding site 8 out of 8 in 1k23

Go back to Manganese Binding Sites List in 1k23
Manganese binding site 8 out of 8 in the Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Inorganic Pyrophosphatase (Family II) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn408

b:42.6
occ:1.00
 O D:HOH410 1.7 23.9 1.0
OD1 D:ASP15 1.9 36.7 1.0
OD1 D:ASP75 1.9 32.5 1.0
OD2 D:ASP149 2.2 47.7 1.0
NE2 D:HIS97 2.4 35.3 1.0
CG D:ASP15 2.8 36.0 1.0
CG D:ASP75 2.9 31.3 1.0
CB D:ASP15 3.1 36.6 1.0
CG D:ASP149 3.3 47.3 1.0
OD2 D:ASP75 3.3 31.3 1.0
CD2 D:HIS97 3.4 35.1 1.0
CE1 D:HIS97 3.4 34.7 1.0
OG1 D:THR119 3.4 28.4 1.0
MN D:MN407 3.4 46.2 1.0
OD1 D:ASP149 3.6 47.4 1.0
OD2 D:ASP15 4.0 34.3 1.0
CE1 D:HIS98 4.0 39.3 1.0
CB D:ASP75 4.1 28.9 1.0
N D:THR119 4.1 32.9 1.0
OD1 D:ASP13 4.3 43.5 1.0
NE2 D:HIS98 4.5 39.1 1.0
ND1 D:HIS97 4.5 34.9 1.0
CA D:CYS118 4.5 36.9 1.0
CG D:HIS97 4.6 33.5 1.0
CB D:ASP149 4.6 46.5 1.0
CB D:THR119 4.6 30.0 1.0
CA D:ASP15 4.6 36.7 1.0
O D:HOH411 4.8 26.5 1.0
CA D:ASP75 4.8 27.6 1.0
C D:CYS118 4.9 35.3 1.0
OD2 D:ASP13 4.9 45.2 1.0
CG D:ASP13 4.9 43.4 1.0
O D:GLY117 4.9 38.4 1.0
SG D:CYS118 5.0 43.0 1.0

Reference:

S.Ahn, A.J.Milner, K.Futterer, M.Konopka, M.Ilias, T.W.Young, S.A.White. The "Open" and "Closed" Structures of the Type-C Inorganic Pyrophosphatases From Bacillus Subtilis and Streptococcus Gordonii. J.Mol.Biol. V. 313 797 2001.
ISSN: ISSN 0022-2836
PubMed: 11697905
DOI: 10.1006/JMBI.2001.5070
Page generated: Sat Oct 5 11:18:41 2024

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