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Manganese in PDB 6ll7: Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form

Protein crystallography data

The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form, PDB code: 6ll7 was solved by M.Horitani, K.Kusubayashi, K.Oshima, A.Yato, H.Sugimoto, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.51 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.530, 75.570, 85.670, 107.40, 90.06, 92.17
R / Rfree (%) 25.6 / 29.7

Other elements in 6ll7:

The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form (pdb code 6ll7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form, PDB code: 6ll7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6ll7

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Manganese binding site 1 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:31.7
occ:1.00
 O A:HOH520 1.9 21.4 1.0
OD2 A:ASP12 2.0 30.4 1.0
OD2 A:ASP72 2.2 30.6 1.0
NE2 A:HIS8 2.2 34.8 1.0
CG A:ASP12 2.8 27.9 1.0
O A:HOH540 3.0 24.2 1.0
OD1 A:ASP12 3.0 26.8 1.0
CG A:ASP72 3.2 29.2 1.0
CD2 A:HIS8 3.2 34.8 1.0
CE1 A:HIS8 3.3 34.5 1.0
OD1 A:ASP72 3.6 28.6 1.0
MN A:MN402 3.8 27.3 1.0
OG A:SER15 4.1 25.3 1.0
O A:HOH539 4.2 27.9 1.0
CB A:ASP12 4.2 27.7 1.0
CB A:ASP72 4.4 29.2 1.0
CG A:HIS8 4.4 33.8 1.0
ND1 A:HIS8 4.4 34.2 1.0
O A:ASP72 4.5 27.8 1.0
CB A:ASP14 4.6 27.8 1.0
OD1 A:ASP146 4.7 34.0 1.0
OD2 A:ASP14 4.9 26.6 1.0
CE1 A:HIS95 5.0 33.8 1.0

Manganese binding site 2 out of 8 in 6ll7

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Manganese binding site 2 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:27.3
occ:1.00
 OD1 A:ASP72 2.1 28.6 1.0
OD2 A:ASP14 2.2 26.6 1.0
NE2 A:HIS94 2.3 28.9 1.0
OD2 A:ASP146 2.4 31.4 1.0
O A:HOH540 2.4 24.2 1.0
CG A:ASP72 2.9 29.2 1.0
CE1 A:HIS94 3.1 30.0 1.0
OD2 A:ASP72 3.1 30.6 1.0
CG A:ASP14 3.2 27.5 1.0
CG A:ASP146 3.2 32.3 1.0
OD1 A:ASP146 3.3 34.0 1.0
CD2 A:HIS94 3.4 29.6 1.0
O A:HOH520 3.4 21.4 1.0
CB A:ASP14 3.6 27.8 1.0
MN A:MN401 3.8 31.7 1.0
OG A:SER116 4.0 28.6 1.0
CE1 A:HIS95 4.1 33.8 1.0
CB A:ASP72 4.3 29.2 1.0
ND1 A:HIS94 4.3 30.0 1.0
N A:SER116 4.3 30.5 1.0
OD1 A:ASP14 4.3 27.9 1.0
CG A:HIS94 4.4 29.7 1.0
CA A:CYS115 4.5 32.5 1.0
O A:GLY114 4.6 35.4 1.0
CB A:ASP146 4.6 32.4 1.0
OD2 A:ASP12 4.7 30.4 1.0
NE2 A:HIS95 4.7 33.4 1.0
CA A:ASP72 4.9 28.6 1.0
C A:CYS115 4.9 32.7 1.0
CB A:SER116 4.9 28.9 1.0

Manganese binding site 3 out of 8 in 6ll7

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Manganese binding site 3 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:27.6
occ:1.00
 OD2 B:ASP12 2.0 25.3 1.0
O B:HOH515 2.1 13.1 1.0
OD2 B:ASP72 2.2 25.7 1.0
NE2 B:HIS8 2.4 25.1 1.0
CG B:ASP12 2.9 24.2 1.0
O B:HOH548 2.9 22.5 1.0
OD1 B:ASP12 3.2 24.8 1.0
CG B:ASP72 3.2 25.1 1.0
CD2 B:HIS8 3.4 25.1 1.0
CE1 B:HIS8 3.4 25.1 1.0
OD1 B:ASP72 3.6 24.2 1.0
MN B:MN402 3.7 24.1 1.0
CB B:ASP12 4.3 24.2 1.0
OG B:SER15 4.3 26.7 1.0
O B:HOH565 4.3 36.0 1.0
CB B:ASP72 4.4 25.8 1.0
O B:ASP72 4.4 26.3 1.0
ND1 B:HIS8 4.5 25.4 1.0
CG B:HIS8 4.5 25.1 1.0
OD1 B:ASP146 4.6 28.6 1.0
CB B:ASP14 4.6 26.1 1.0
CE1 B:HIS95 4.8 30.2 1.0
OD2 B:ASP14 4.9 26.1 1.0

Manganese binding site 4 out of 8 in 6ll7

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Manganese binding site 4 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:24.1
occ:1.00
 OD1 B:ASP72 2.2 24.2 1.0
OD2 B:ASP14 2.2 26.1 1.0
NE2 B:HIS94 2.3 23.1 1.0
O B:HOH548 2.4 22.5 1.0
OD2 B:ASP146 2.4 25.9 1.0
CG B:ASP72 2.9 25.1 1.0
O B:HOH515 3.0 13.1 1.0
OD2 B:ASP72 3.1 25.7 1.0
CE1 B:HIS94 3.1 23.1 1.0
CG B:ASP146 3.2 26.9 1.0
CG B:ASP14 3.2 26.3 1.0
OD1 B:ASP146 3.3 28.6 1.0
CD2 B:HIS94 3.4 23.5 1.0
CB B:ASP14 3.6 26.1 1.0
MN B:MN401 3.7 27.6 1.0
OG B:SER116 4.0 27.9 1.0
CE1 B:HIS95 4.1 30.2 1.0
CB B:ASP72 4.3 25.8 1.0
N B:SER116 4.3 27.9 1.0
ND1 B:HIS94 4.3 23.0 1.0
OD1 B:ASP14 4.3 26.9 1.0
CG B:HIS94 4.5 23.5 1.0
CA B:CYS115 4.5 26.5 1.0
OD2 B:ASP12 4.6 25.3 1.0
CB B:ASP146 4.6 26.6 1.0
NE2 B:HIS95 4.6 30.7 1.0
O B:GLY114 4.6 25.9 1.0
CB B:SER116 4.9 27.8 1.0
CA B:ASP72 5.0 26.2 1.0
C B:CYS115 5.0 27.8 1.0

Manganese binding site 5 out of 8 in 6ll7

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Manganese binding site 5 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:29.5
occ:1.00
 OD2 C:ASP12 2.1 27.1 1.0
OD2 C:ASP72 2.2 27.3 1.0
O C:HOH544 2.2 23.8 1.0
O C:HOH503 2.3 26.3 1.0
NE2 C:HIS8 2.4 31.4 1.0
O C:HOH541 2.7 23.9 1.0
CG C:ASP12 2.9 26.3 1.0
CG C:ASP72 3.1 25.9 1.0
OD1 C:ASP12 3.2 26.6 1.0
CD2 C:HIS8 3.3 30.6 1.0
CE1 C:HIS8 3.4 30.4 1.0
OD1 C:ASP72 3.5 26.1 1.0
MN C:MN402 3.7 27.7 1.0
O C:HOH570 4.1 23.9 1.0
OG C:SER15 4.2 29.3 1.0
CB C:ASP12 4.3 26.3 1.0
CB C:ASP72 4.4 25.7 1.0
NZ C:LYS203 4.4 53.6 1.0
O C:ASP72 4.4 24.4 1.0
CG C:HIS8 4.5 29.9 1.0
ND1 C:HIS8 4.5 30.0 1.0
CB C:ASP14 4.6 29.3 1.0
OD1 C:ASP146 4.7 30.9 1.0
CE1 C:HIS95 4.8 31.2 1.0
O C:HOH552 4.8 29.2 1.0
OD2 C:ASP14 4.8 28.4 1.0

Manganese binding site 6 out of 8 in 6ll7

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Manganese binding site 6 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:27.7
occ:1.00
 OD2 C:ASP14 2.2 28.4 1.0
NE2 C:HIS94 2.2 25.9 1.0
OD1 C:ASP72 2.3 26.1 1.0
OD2 C:ASP146 2.3 28.0 1.0
O C:HOH541 2.4 23.9 1.0
CG C:ASP72 3.0 25.9 1.0
CE1 C:HIS94 3.1 25.5 1.0
CG C:ASP146 3.1 29.6 1.0
OD1 C:ASP146 3.2 30.9 1.0
CG C:ASP14 3.2 29.6 1.0
OD2 C:ASP72 3.2 27.3 1.0
CD2 C:HIS94 3.4 26.1 1.0
CB C:ASP14 3.6 29.3 1.0
MN C:MN401 3.7 29.5 1.0
OG C:SER116 4.0 27.3 1.0
O C:HOH544 4.1 23.8 1.0
CE1 C:HIS95 4.1 31.2 1.0
ND1 C:HIS94 4.3 25.9 1.0
N C:SER116 4.3 29.1 1.0
OD1 C:ASP14 4.3 29.6 1.0
CB C:ASP72 4.4 25.7 1.0
CA C:CYS115 4.4 29.0 1.0
CG C:HIS94 4.4 26.8 1.0
CB C:ASP146 4.5 29.2 1.0
O C:GLY114 4.6 29.2 1.0
OD2 C:ASP12 4.6 27.1 1.0
NE2 C:HIS95 4.7 30.7 1.0
C C:CYS115 4.9 29.6 1.0
CB C:SER116 5.0 27.3 1.0
SG C:CYS115 5.0 26.9 1.0

Manganese binding site 7 out of 8 in 6ll7

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Manganese binding site 7 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:32.8
occ:1.00
 O D:HOH542 2.0 31.0 1.0
OD2 D:ASP12 2.1 30.7 1.0
NE2 D:HIS8 2.2 31.0 1.0
OD2 D:ASP72 2.2 30.1 1.0
CG D:ASP12 2.9 29.0 1.0
O D:HOH522 2.9 41.5 1.0
OD1 D:ASP12 3.1 29.6 1.0
CD2 D:HIS8 3.1 30.8 1.0
CG D:ASP72 3.1 29.2 1.0
CE1 D:HIS8 3.2 30.8 1.0
O D:HOH514 3.5 26.1 1.0
OD1 D:ASP72 3.6 29.1 1.0
MN D:MN402 3.8 31.2 1.0
OG D:SER15 4.1 35.8 1.0
O D:HOH556 4.1 35.4 1.0
CB D:ASP12 4.2 28.0 1.0
CG D:HIS8 4.3 30.4 1.0
ND1 D:HIS8 4.3 30.3 1.0
CB D:ASP72 4.3 29.8 1.0
O D:ASP72 4.4 28.3 1.0
O D:HOH521 4.6 24.8 1.0
CB D:ASP14 4.7 33.4 1.0
O D:HOH531 4.8 33.7 1.0
OD1 D:ASP146 4.8 35.7 1.0
CE1 D:HIS95 4.9 35.1 1.0
OD2 D:ASP14 4.9 33.7 1.0

Manganese binding site 8 out of 8 in 6ll7

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Manganese binding site 8 out of 8 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mn-Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:31.2
occ:1.00
 OD1 D:ASP72 2.2 29.1 1.0
OD2 D:ASP14 2.3 33.7 1.0
NE2 D:HIS94 2.3 27.9 1.0
OD2 D:ASP146 2.4 33.9 1.0
O D:HOH514 2.4 26.1 1.0
O D:HOH542 2.9 31.0 1.0
CG D:ASP72 2.9 29.2 1.0
CE1 D:HIS94 3.1 27.6 1.0
OD2 D:ASP72 3.1 30.1 1.0
CG D:ASP146 3.2 34.6 1.0
OD1 D:ASP146 3.2 35.7 1.0
CG D:ASP14 3.3 33.7 1.0
CD2 D:HIS94 3.4 27.5 1.0
CB D:ASP14 3.6 33.4 1.0
MN D:MN401 3.8 32.8 1.0
CE1 D:HIS95 4.1 35.1 1.0
OG D:SER116 4.1 27.0 1.0
ND1 D:HIS94 4.3 27.6 1.0
CB D:ASP72 4.3 29.8 1.0
N D:SER116 4.4 27.8 1.0
OD1 D:ASP14 4.4 34.8 1.0
CG D:HIS94 4.5 28.0 1.0
CA D:CYS115 4.5 27.6 1.0
OD2 D:ASP12 4.5 30.7 1.0
O D:GLY114 4.6 26.7 1.0
CB D:ASP146 4.6 33.9 1.0
NE2 D:HIS95 4.6 35.5 1.0
O D:HOH556 4.7 35.4 1.0

Reference:

M.Horitani, K.Kusubayashi, K.Oshima, A.Yato, H.Sugimoto, K.Watanabe. X-Ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase. Sci Rep V. 10 4368 2020.
ISSN: ESSN 2045-2322
PubMed: 32152422
DOI: 10.1038/S41598-020-61217-6
Page generated: Sun Oct 6 05:24:09 2024

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