Atomistry » Manganese » PDB 2dvd-2fer » 2eb0
Atomistry »
  Manganese »
    PDB 2dvd-2fer »
      2eb0 »

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

Go back to Manganese Binding Sites List in 2eb0
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

Go back to Manganese Binding Sites List in 2eb0
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

Go back to Manganese Binding Sites List in 2eb0
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: Tue Dec 15 04:01:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy