Manganese in PDB 3ig4: Structure of A Putative Aminopeptidase P From Bacillus Anthracis

The structure of Structure of A Putative Aminopeptidase P From Bacillus Anthracis, PDB code: 3ig4 was solved by S.M.Anderson, Z.Wawrzak, T.Skarina, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.40 / 2.89
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.880, 180.880, 254.780, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis (pdb code 3ig4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis, PDB code: 3ig4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn428 b:75.4 occ:1.00 OD1 A:ASP267 2.2 44.8 1.0 OE1 A:GLU384 2.2 45.9 1.0 OD1 A:ASP256 2.3 45.4 1.0 MN A:MN429 2.9 0.6 1.0 CG A:ASP267 3.0 38.8 1.0 CG A:ASP256 3.0 40.0 1.0 CD A:GLU384 3.1 44.1 1.0 OD2 A:ASP256 3.1 44.1 1.0 OD2 A:ASP267 3.2 44.2 1.0 OE2 A:GLU384 3.3 46.2 1.0 OG A:SER269 3.5 39.9 1.0 O4 A:SO4430 4.0 77.9 0.5 CZ A:PHE225 4.1 53.1 1.0 OE1 A:GLU369 4.1 59.4 1.0 O2 A:SO4430 4.1 80.8 0.5 N A:ILE268 4.2 32.1 1.0 C A:ASP267 4.2 32.7 1.0 C A:ILE268 4.3 34.0 1.0 O A:ILE268 4.3 35.1 1.0 CB A:ASP267 4.3 33.1 1.0 CB A:ASP256 4.4 34.8 1.0 N A:SER269 4.5 34.8 1.0 CG A:GLU384 4.5 39.1 1.0 S A:SO4430 4.5 81.8 0.5 O A:ASP267 4.5 32.6 1.0 O3 A:SO4430 4.6 78.8 0.5 CA A:ASP267 4.6 33.4 1.0 CE2 A:PHE225 4.6 51.4 1.0 CB A:SER269 4.7 35.3 1.0 CA A:ILE268 4.7 32.8 1.0 CE1 A:PHE225 4.7 50.3 1.0 CA A:ASP256 4.8 35.4 1.0 CB A:GLU384 4.9 34.5 1.0 N A:LEU257 4.9 33.4 1.0 O4 A:SO4431 4.9 66.9 0.5 CA A:SER269 5.0 35.7 1.0 O A:LEU257 5.0 33.9 1.0

Manganese binding site 2 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn429 b:0.6 occ:1.00 OD2 A:ASP267 2.3 44.2 1.0 NE2 A:HIS343 2.5 42.2 1.0 OE2 A:GLU384 2.8 46.2 1.0 MN A:MN428 2.9 75.4 1.0 OE1 A:GLU369 3.2 59.4 1.0 CG A:ASP267 3.3 38.8 1.0 OE2 A:GLU369 3.3 65.5 1.0 CD2 A:HIS343 3.4 44.7 1.0 O4 A:SO4431 3.4 66.9 0.5 CD A:GLU369 3.5 58.5 1.0 CE1 A:HIS343 3.5 40.5 1.0 O3 A:SO4430 3.5 78.8 0.5 CD A:GLU384 3.6 44.1 1.0 OD1 A:ASP267 3.6 44.8 1.0 OE1 A:GLU384 3.6 45.9 1.0 O2 A:SO4430 4.1 80.8 0.5 NE2 A:HIS350 4.1 50.3 1.0 S A:SO4430 4.3 81.8 0.5 CD2 A:HIS350 4.5 47.9 1.0 CG A:HIS343 4.6 41.6 1.0 O4 A:SO4430 4.6 77.9 0.5 OG1 A:THR367 4.6 33.7 1.0 ND1 A:HIS343 4.6 42.7 1.0 CB A:ASP267 4.6 33.1 1.0 S A:SO4431 4.7 70.5 0.5 CG A:GLU369 4.8 45.8 1.0 OD2 A:ASP256 4.9 44.1 1.0 OD1 A:ASP256 5.0 45.4 1.0 CG A:GLU384 5.0 39.1 1.0

Manganese binding site 3 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn428 b:74.1 occ:1.00 OE1 B:GLU384 2.2 45.9 1.0 OD1 B:ASP267 2.3 45.2 1.0 OD1 B:ASP256 2.4 45.4 1.0 MN B:MN429 2.9 0.1 1.0 CG B:ASP256 3.0 40.0 1.0 OD2 B:ASP256 3.0 43.7 1.0 CD B:GLU384 3.0 44.1 1.0 CG B:ASP267 3.0 38.4 1.0 OE2 B:GLU384 3.2 46.3 1.0 OD2 B:ASP267 3.2 44.7 1.0 OG B:SER269 3.4 39.7 1.0 O1 B:SO4430 3.6 67.0 0.5 O4 B:SO4430 3.8 64.8 0.5 OE1 B:GLU369 4.0 59.0 1.0 N B:ILE268 4.2 31.5 1.0 CZ B:PHE225 4.3 52.8 1.0 C B:ILE268 4.3 34.7 1.0 C B:ASP267 4.3 32.5 1.0 O B:ILE268 4.3 35.8 1.0 S B:SO4430 4.3 70.9 0.5 CB B:ASP267 4.4 33.1 1.0 CB B:ASP256 4.4 34.9 1.0 CG B:GLU384 4.4 38.8 1.0 N B:SER269 4.5 34.5 1.0 O B:ASP267 4.6 32.5 1.0 CB B:SER269 4.6 35.7 1.0 CA B:ASP267 4.7 32.8 1.0 CA B:ILE268 4.7 32.8 1.0 CA B:ASP256 4.8 34.5 1.0 CE2 B:PHE225 4.8 51.1 1.0 CB B:GLU384 4.8 35.0 1.0 CE1 B:PHE225 4.8 50.4 1.0 CA B:SER269 4.9 35.5 1.0 CD B:GLU369 4.9 58.3 1.0 N B:LEU257 5.0 32.8 1.0

Manganese binding site 4 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn429 b:0.1 occ:1.00 OD2 B:ASP267 2.5 44.7 1.0 NE2 B:HIS343 2.7 43.5 1.0 OE2 B:GLU384 2.7 46.3 1.0 OE1 B:GLU369 2.8 59.0 1.0 MN B:MN428 2.9 74.1 1.0 OE2 B:GLU369 3.0 65.1 1.0 O1 B:SO4430 3.0 67.0 0.5 CD B:GLU369 3.1 58.3 1.0 CD B:GLU384 3.4 44.1 1.0 CD2 B:HIS343 3.4 45.6 1.0 OE1 B:GLU384 3.5 45.9 1.0 CG B:ASP267 3.5 38.4 1.0 OD1 B:ASP267 3.7 45.2 1.0 CE1 B:HIS343 3.8 41.7 1.0 O4 B:SO4431 3.8 76.5 0.5 S B:SO4430 4.1 70.9 0.5 O2 B:SO4430 4.2 69.8 0.5 O4 B:SO4430 4.4 64.8 0.5 NE2 B:HIS350 4.4 50.5 1.0 CG B:GLU369 4.5 45.6 1.0 O2 B:SO4431 4.6 79.0 0.5 OG1 B:THR367 4.6 35.0 1.0 CG B:HIS343 4.6 41.2 1.0 CG B:GLU384 4.7 38.8 1.0 OD2 B:ASP256 4.7 43.7 1.0 CD2 B:HIS350 4.8 48.1 1.0 S B:SO4431 4.8 80.8 0.5 ND1 B:HIS343 4.8 42.8 1.0 CB B:ASP267 4.8 33.1 1.0 OD1 B:ASP256 5.0 45.4 1.0 CB B:GLU369 5.0 39.5 1.0

Manganese binding site 5 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn428 b:97.6 occ:1.00 OD1 C:ASP256 2.4 45.7 1.0 OD1 C:ASP267 2.4 45.0 1.0 OE1 C:GLU384 2.5 46.3 1.0 O3 C:SO4430 2.8 75.8 0.5 OD2 C:ASP256 2.9 44.5 1.0 CG C:ASP256 3.0 40.6 1.0 MN C:MN429 3.0 0.8 1.0 CG C:ASP267 3.1 38.4 1.0 OD2 C:ASP267 3.1 44.8 1.0 CD C:GLU384 3.3 43.7 1.0 O2 C:SO4430 3.4 68.5 0.5 OG C:SER269 3.5 40.0 1.0 OE2 C:GLU384 3.5 45.3 1.0 S C:SO4430 3.7 76.5 0.5 OE1 C:GLU369 3.8 59.0 1.0 CZ C:PHE225 4.3 52.7 1.0 CB C:ASP256 4.4 35.1 1.0 CB C:ASP267 4.5 33.4 1.0 O1 C:SO4430 4.6 71.0 0.5 O2 C:SO4431 4.6 68.3 0.5 O4 C:SO4430 4.7 76.2 0.5 O C:ILE268 4.7 36.1 1.0 C C:ASP267 4.7 32.7 1.0 CE2 C:PHE225 4.7 51.6 1.0 CG C:GLU384 4.7 39.0 1.0 C C:ILE268 4.8 34.3 1.0 N C:ILE268 4.8 31.6 1.0 CB C:SER269 4.8 36.0 1.0 CD C:GLU369 4.8 58.3 1.0 NE C:ARG382 4.9 34.6 1.0 O C:ASP267 4.9 33.2 1.0 N C:SER269 5.0 34.5 1.0 CE1 C:PHE225 5.0 50.8 1.0

Manganese binding site 6 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn429 b:0.8 occ:1.00 NE2 C:HIS343 2.2 43.8 1.0 OE2 C:GLU384 2.5 45.3 1.0 OD2 C:ASP267 2.5 44.8 1.0 OE1 C:GLU369 2.9 59.0 1.0 CD2 C:HIS343 3.0 45.6 1.0 OE2 C:GLU369 3.0 65.1 1.0 MN C:MN428 3.0 97.6 1.0 CD C:GLU369 3.1 58.3 1.0 CD C:GLU384 3.3 43.7 1.0 CE1 C:HIS343 3.4 41.6 1.0 OE1 C:GLU384 3.4 46.3 1.0 CG C:ASP267 3.5 38.4 1.0 O3 C:SO4430 3.8 75.8 0.5 OG1 C:THR367 3.9 33.8 1.0 OD1 C:ASP267 3.9 45.0 1.0 CG C:HIS343 4.2 41.6 1.0 CG C:GLU369 4.3 46.2 1.0 ND1 C:HIS343 4.4 43.5 1.0 O2 C:SO4430 4.4 68.5 0.5 CB C:THR367 4.4 32.6 1.0 CG2 C:THR367 4.5 31.8 1.0 O3 C:SO4431 4.5 64.3 0.5 S C:SO4430 4.5 76.5 0.5 CG C:GLU384 4.6 39.0 1.0 NE2 C:HIS350 4.6 51.0 1.0 CB C:ASP267 4.7 33.4 1.0 O4 C:SO4430 4.7 76.2 0.5 CD2 C:HIS350 4.8 48.0 1.0 O2 C:SO4431 4.8 68.3 0.5 CB C:GLU369 4.9 40.6 1.0

Manganese binding site 7 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn428 b:78.1 occ:1.00 OD1 D:ASP267 2.2 44.2 1.0 OE1 D:GLU384 2.3 46.7 1.0 OD1 D:ASP256 2.3 45.4 1.0 MN D:MN429 2.8 0.4 1.0 OD2 D:ASP256 2.9 44.3 1.0 CG D:ASP256 2.9 40.3 1.0 CG D:ASP267 3.0 37.9 1.0 CD D:GLU384 3.2 43.7 1.0 OD2 D:ASP267 3.3 44.3 1.0 O1 D:SO4430 3.4 66.2 0.5 OG D:SER269 3.4 39.4 1.0 OE2 D:GLU384 3.5 46.1 1.0 O2 D:SO4430 3.8 74.7 0.5 CZ D:PHE225 4.0 52.4 1.0 OE1 D:GLU369 4.1 58.3 1.0 S D:SO4430 4.1 74.9 0.5 CB D:ASP256 4.4 34.5 1.0 N D:ILE268 4.4 31.9 1.0 CB D:ASP267 4.4 33.0 1.0 C D:ASP267 4.4 33.5 1.0 O D:ILE268 4.4 35.1 1.0 C D:ILE268 4.5 34.0 1.0 O4 D:SO4430 4.6 74.0 0.5 CE2 D:PHE225 4.6 51.0 1.0 CG D:GLU384 4.6 38.7 1.0 CE1 D:PHE225 4.7 50.7 1.0 CB D:SER269 4.7 35.7 1.0 N D:SER269 4.7 34.4 1.0 O D:ASP267 4.7 33.9 1.0 CA D:ASP267 4.8 34.1 1.0 CA D:ASP256 4.9 34.6 1.0 CA D:ILE268 4.9 32.9 1.0 CB D:GLU384 5.0 34.7 1.0 N D:LEU257 5.0 33.2 1.0 CD D:GLU369 5.0 58.4 1.0

Manganese binding site 8 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn429 b:0.4 occ:1.00 OD2 D:ASP267 2.5 44.3 1.0 NE2 D:HIS343 2.7 43.8 1.0 OE2 D:GLU384 2.8 46.1 1.0 MN D:MN428 2.8 78.1 1.0 OE1 D:GLU369 3.0 58.3 1.0 OE2 D:GLU369 3.1 65.5 1.0 OE1 D:GLU384 3.3 46.7 1.0 CD D:GLU369 3.3 58.4 1.0 CD D:GLU384 3.4 43.7 1.0 CG D:ASP267 3.4 37.9 1.0 CD2 D:HIS343 3.4 46.2 1.0 OD1 D:ASP267 3.6 44.2 1.0 O1 D:SO4430 3.6 66.2 0.5 O4 D:SO4430 3.7 74.0 0.5 CE1 D:HIS343 3.8 41.4 1.0 O2 D:SO4431 3.8 74.0 0.5 S D:SO4430 4.1 74.9 0.5 NE2 D:HIS350 4.2 50.4 1.0 O2 D:SO4430 4.5 74.7 0.5 O1 D:SO4431 4.6 73.3 0.5 OG1 D:THR367 4.6 34.4 1.0 CG D:GLU369 4.6 45.1 1.0 CD2 D:HIS350 4.6 48.1 1.0 CG D:HIS343 4.7 41.3 1.0 CB D:ASP267 4.7 33.0 1.0 S D:SO4431 4.8 78.2 0.5 CG D:GLU384 4.8 38.7 1.0 OD2 D:ASP256 4.8 44.3 1.0 ND1 D:HIS343 4.8 42.9 1.0 OD1 D:ASP256 5.0 45.4 1.0

Manganese binding site 9 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn428 b:0.2 occ:1.00 OD1 E:ASP267 2.2 43.9 1.0 OD1 E:ASP256 2.3 46.1 1.0 OE1 E:GLU384 2.3 46.5 1.0 O1 E:SO4430 2.8 76.8 0.5 OD2 E:ASP256 2.8 44.7 1.0 CG E:ASP256 2.9 40.5 1.0 MN E:MN429 3.0 0.7 1.0 CG E:ASP267 3.0 38.2 1.0 OD2 E:ASP267 3.2 44.5 1.0 CD E:GLU384 3.2 44.1 1.0 OG E:SER269 3.5 39.4 1.0 OE2 E:GLU384 3.5 46.1 1.0 OE1 E:GLU369 3.9 59.3 1.0 S E:SO4430 4.1 81.5 0.5 CZ E:PHE225 4.2 52.2 1.0 CB E:ASP256 4.3 35.2 1.0 O3 E:SO4430 4.4 83.7 0.5 CB E:ASP267 4.5 34.1 1.0 O E:ILE268 4.5 35.9 1.0 C E:ILE268 4.5 34.6 1.0 C E:ASP267 4.6 33.1 1.0 N E:ILE268 4.6 32.8 1.0 CG E:GLU384 4.6 39.0 1.0 CB E:SER269 4.7 35.4 1.0 N E:SER269 4.7 34.7 1.0 CE2 E:PHE225 4.7 50.9 1.0 O4 E:SO4430 4.8 76.7 0.5 CE1 E:PHE225 4.8 50.2 1.0 O E:ASP267 4.8 32.5 1.0 CA E:ASP256 4.9 34.9 1.0 CA E:ASP267 4.9 33.4 1.0 CB E:GLU384 4.9 35.2 1.0 NE E:ARG382 5.0 34.8 1.0 CD E:GLU369 5.0 58.2 1.0

Manganese binding site 10 out of 12 in the Structure of A Putative Aminopeptidase P From Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of A Putative Aminopeptidase P From Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn429 b:0.7 occ:1.00 NE2 E:HIS343 2.4 42.7 1.0 OD2 E:ASP267 2.4 44.5 1.0 OE2 E:GLU384 2.5 46.1 1.0 OE1 E:GLU369 2.9 59.3 1.0 MN E:MN428 3.0 0.2 1.0 CD2 E:HIS343 3.2 45.2 1.0 CD E:GLU384 3.3 44.1 1.0 OE2 E:GLU369 3.3 64.3 1.0 CD E:GLU369 3.3 58.2 1.0 CG E:ASP267 3.3 38.2 1.0 OE1 E:GLU384 3.4 46.5 1.0 CE1 E:HIS343 3.5 41.2 1.0 OD1 E:ASP267 3.6 43.9 1.0 O1 E:SO4430 3.9 76.8 0.5 O3 E:SO4430 4.0 83.7 0.5 OG1 E:THR367 4.0 34.7 1.0 CG E:HIS343 4.4 41.8 1.0 ND1 E:HIS343 4.5 42.9 1.0 CG E:GLU369 4.5 45.8 1.0 O2 E:SO4431 4.6 64.8 0.5 CB E:ASP267 4.6 34.1 1.0 NE2 E:HIS350 4.6 51.0 1.0 S E:SO4430 4.6 81.5 0.5 CB E:THR367 4.6 33.0 1.0 CG E:GLU384 4.6 39.0 1.0 CG2 E:THR367 4.7 32.3 1.0 CD2 E:HIS350 4.8 48.5 1.0 O4 E:SO4431 4.8 72.1 0.5

S.M.Anderson, Z.Wawrzak, T.Skarina, O.Onopriyenko, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of A Putative Aminopeptidase P From Bacillus Anthracis To Be Published.