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Manganese in PDB 2eb0: Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase

Enzymatic activity of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase

All present enzymatic activity of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase, PDB code: 2eb0 was solved by A.Shimada, S.Kuramitsu, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.44 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.843, 146.761, 54.286, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 27.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase (pdb code 2eb0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase, PDB code: 2eb0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2eb0

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Manganese binding site 1 out of 4 in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:40.1
occ:1.00
 OD1 A:ASP66 2.3 23.8 1.0
O A:HOH662 2.3 68.3 1.0
NE2 A:HIS7 2.4 17.0 1.0
OD2 A:ASP11 2.7 39.6 1.0
OD1 A:ASP11 2.8 33.2 1.0
CG A:ASP11 3.0 32.4 1.0
CG A:ASP66 3.1 22.4 1.0
CD2 A:HIS7 3.1 19.1 1.0
OD2 A:ASP66 3.4 25.9 1.0
CE1 A:HIS7 3.5 16.6 1.0
NZ A:LYS204 3.5 35.8 1.0
MN A:MN502 3.6 40.9 1.0
OG A:SER14 3.8 27.4 1.0
O A:HOH541 3.9 53.2 1.0
O A:HOH511 4.0 30.3 1.0
CB A:ASP11 4.3 27.7 1.0
CE A:LYS204 4.3 34.0 1.0
O A:ASP66 4.3 13.7 1.0
CG A:HIS7 4.4 17.7 1.0
CB A:ASP66 4.4 21.5 1.0
ND1 A:HIS7 4.5 17.8 1.0
OD1 A:ASP147 4.5 40.5 1.0
CB A:ASP13 4.6 23.5 1.0
O A:HOH629 4.6 54.1 1.0
O A:HOH633 4.6 49.4 1.0
CE1 A:HIS89 4.8 26.8 1.0
N A:SER14 4.8 23.6 1.0
CB A:SER14 4.9 25.6 1.0
O A:HOH685 4.9 65.0 1.0

Manganese binding site 2 out of 4 in 2eb0

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Manganese binding site 2 out of 4 in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:40.9
occ:1.00
 OD1 A:ASP13 2.2 25.3 1.0
O A:HOH662 2.3 68.3 1.0
OD2 A:ASP147 2.3 43.2 1.0
OD2 A:ASP66 2.4 25.9 1.0
NE2 A:HIS88 2.5 25.0 1.0
CG A:ASP66 3.1 22.4 1.0
CG A:ASP13 3.1 24.9 1.0
CG A:ASP147 3.2 41.1 1.0
OD1 A:ASP66 3.2 23.8 1.0
CB A:ASP13 3.3 23.5 1.0
OD1 A:ASP147 3.3 40.5 1.0
CE1 A:HIS88 3.4 21.5 1.0
CD2 A:HIS88 3.4 24.9 1.0
O A:HOH629 3.5 54.1 1.0
MN A:MN501 3.6 40.1 1.0
N A:THR109 4.0 21.3 1.0
OG1 A:THR109 4.0 24.0 1.0
CA A:SER108 4.2 21.2 1.0
CE1 A:HIS89 4.3 26.8 1.0
OD2 A:ASP13 4.3 22.0 1.0
CB A:ASP66 4.4 21.5 1.0
OD2 A:ASP11 4.4 39.6 1.0
ND1 A:HIS88 4.5 25.4 1.0
CB A:SER108 4.5 21.9 1.0
CG A:HIS88 4.5 24.8 1.0
CB A:ASP147 4.5 37.9 1.0
C A:SER108 4.6 21.2 1.0
CB A:THR109 4.6 26.9 1.0
CA A:ASP13 4.8 25.6 1.0
O A:GLY107 4.9 26.6 1.0
O A:HOH511 4.9 30.3 1.0
CA A:THR109 4.9 21.2 1.0
CA A:ASP66 5.0 18.4 1.0

Manganese binding site 3 out of 4 in 2eb0

Go back to Manganese Binding Sites List in 2eb0
Manganese binding site 3 out of 4 in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:34.6
occ:1.00
 OD1 B:ASP13 2.1 25.7 1.0
OD2 B:ASP66 2.3 15.6 1.0
NE2 B:HIS88 2.3 16.9 1.0
OD2 B:ASP147 2.4 37.7 1.0
O B:HOH669 2.8 53.3 1.0
CG B:ASP66 3.0 16.7 1.0
CG B:ASP13 3.1 24.0 1.0
OD1 B:ASP66 3.1 18.1 1.0
CG B:ASP147 3.1 35.7 1.0
CE1 B:HIS88 3.2 11.7 1.0
OD1 B:ASP147 3.3 39.6 1.0
CB B:ASP13 3.3 21.9 1.0
MN B:MN504 3.4 34.4 1.0
CD2 B:HIS88 3.4 8.0 1.0
CE1 B:HIS89 3.9 19.4 1.0
OG1 B:THR109 4.1 22.3 1.0
OD2 B:ASP13 4.2 22.1 1.0
N B:THR109 4.2 20.4 1.0
ND1 B:HIS88 4.4 15.1 1.0
NE2 B:HIS89 4.4 21.6 1.0
CB B:ASP66 4.4 16.9 1.0
CA B:SER108 4.5 21.0 1.0
CG B:HIS88 4.5 12.6 1.0
CB B:ASP147 4.5 29.2 1.0
OD2 B:ASP11 4.6 31.6 1.0
CB B:SER108 4.7 23.4 1.0
CA B:ASP13 4.8 22.4 1.0
O B:HOH670 4.8 78.6 1.0
CB B:THR109 4.9 23.2 1.0
OD1 B:ASP11 4.9 27.8 1.0
C B:SER108 4.9 21.0 1.0
O B:GLY107 4.9 18.0 1.0
NZ B:LYS294 4.9 28.0 1.0
ND1 B:HIS89 5.0 22.1 1.0

Manganese binding site 4 out of 4 in 2eb0

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Manganese binding site 4 out of 4 in the Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Methanococcus Jannaschii Putative Family II Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:34.4
occ:1.00
 OD1 B:ASP66 2.2 18.1 1.0
OD2 B:ASP11 2.3 31.6 1.0
NE2 B:HIS7 2.4 27.9 1.0
OD1 B:ASP11 2.9 27.8 1.0
CG B:ASP11 2.9 27.3 1.0
CG B:ASP66 3.1 16.7 1.0
CD2 B:HIS7 3.3 27.1 1.0
CE1 B:HIS7 3.4 27.2 1.0
MN B:MN503 3.4 34.6 1.0
O B:HOH669 3.5 53.3 1.0
O B:HOH717 3.5 70.2 1.0
OD2 B:ASP66 3.5 15.6 1.0
OG B:SER14 3.8 18.4 1.0
O B:HOH670 4.0 78.6 1.0
NZ B:LYS204 4.1 34.9 1.0
O B:ASP66 4.3 10.5 1.0
CB B:ASP66 4.3 16.9 1.0
CB B:ASP11 4.3 22.6 1.0
CB B:ASP13 4.5 21.9 1.0
CE1 B:HIS89 4.5 19.4 1.0
ND1 B:HIS7 4.5 28.7 1.0
N B:SER14 4.5 19.2 1.0
CG B:HIS7 4.5 27.2 1.0
CB B:SER14 4.5 15.7 1.0
OD1 B:ASP147 4.6 39.6 1.0
NE2 B:HIS89 4.6 21.6 1.0
OD1 B:ASP13 4.8 25.7 1.0
CE B:LYS204 4.8 32.0 1.0
O B:HOH575 4.9 32.7 1.0
N B:ASP11 5.0 27.5 1.0
CA B:SER14 5.0 17.7 1.0

Reference:

A.Shimada, S.Kuramitsu, S.Yokoyama. Crystal Structure of Methanococcus Jannaschii Inorganic Pyrophosphatase To Be Published.
Page generated: Sat Aug 16 10:06:10 2025

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