Manganese in PDB 5nsq: Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin

The structure of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin, PDB code: 5nsq was solved by J.Timm, K.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.50 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.909, 165.730, 121.980, 90.00, 112.45, 90.00
R / Rfree (%)	26.5 / 29.6

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin (pdb code 5nsq). 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 Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin, PDB code: 5nsq:
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 Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:22.3 occ:1.00 OD2 A:ASP312 1.9 19.6 1.0 O2 A:BB2603 1.9 24.8 1.0 OE1 A:GLU373 1.9 24.4 1.0 OD2 A:ASP294 1.9 20.0 1.0 NZ A:LYS289 2.0 21.6 1.0 CG A:ASP312 2.8 18.6 1.0 CD A:GLU373 3.0 25.1 1.0 MN A:MN602 3.0 21.6 1.0 N1 A:BB2603 3.0 29.0 1.0 CG A:ASP294 3.0 18.3 1.0 OD1 A:ASP312 3.1 18.4 1.0 CE A:LYS289 3.2 21.2 1.0 OE2 A:GLU373 3.3 25.6 1.0 CB A:ASP294 3.6 18.7 1.0 C3 A:BB2603 4.0 31.8 1.0 OD1 A:ASP294 4.1 18.2 1.0 O4 A:BB2603 4.1 33.2 1.0 CB A:ASP312 4.2 19.6 1.0 O A:THR401 4.4 17.9 1.0 CG A:GLU373 4.4 24.2 1.0 CD A:LYS289 4.5 20.8 1.0 O A:ASP371 4.6 23.4 1.0 OD1 A:ASP371 4.7 22.1 1.0 O A:LEU402 4.9 18.1 1.0 CG2 A:ILE291 4.9 21.3 1.0 CB A:ILE291 5.0 21.8 1.0 CG1 A:ILE291 5.0 21.5 1.0 N A:GLY374 5.0 26.9 1.0

Manganese binding site 2 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:21.6 occ:1.00 OD1 A:ASP371 1.9 22.1 1.0 O A:ASP371 1.9 23.4 1.0 OE2 A:GLU373 1.9 25.6 1.0 O2 A:BB2603 1.9 24.8 1.0 OD2 A:ASP294 2.0 20.0 1.0 O4 A:BB2603 2.5 33.2 1.0 N1 A:BB2603 2.8 29.0 1.0 CG A:ASP294 2.9 18.3 1.0 CD A:GLU373 2.9 25.1 1.0 MN A:MN601 3.0 22.3 1.0 C3 A:BB2603 3.0 31.8 1.0 OD1 A:ASP294 3.1 18.2 1.0 CG A:ASP371 3.1 24.3 1.0 C A:ASP371 3.1 24.1 1.0 OE1 A:GLU373 3.2 24.4 1.0 CA A:ASP371 3.7 25.2 1.0 CB A:ASP371 3.9 25.3 1.0 OD2 A:ASP371 3.9 22.5 1.0 NZ A:LYS301 4.1 19.5 1.0 N A:ALA372 4.2 24.2 1.0 N A:GLU373 4.3 25.1 1.0 CE A:LYS301 4.3 19.6 1.0 CG A:GLU373 4.3 24.2 1.0 CB A:ASP294 4.3 18.7 1.0 C5 A:BB2603 4.5 32.9 1.0 NZ A:LYS289 4.6 21.6 1.0 ND2 A:ASN344 4.6 29.2 1.0 OD2 A:ASP312 4.6 19.6 1.0 CA A:ALA372 4.7 24.3 1.0 CB A:GLU373 4.7 23.8 1.0 C8 A:BB2603 5.0 37.7 1.0

Manganese binding site 3 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:21.4 occ:1.00 OD2 B:ASP312 1.9 20.2 1.0 O2 B:BB2603 1.9 27.5 1.0 OD2 B:ASP294 1.9 23.7 1.0 OE2 B:GLU373 1.9 21.9 1.0 NZ B:LYS289 2.0 21.5 1.0 CG B:ASP312 2.8 20.2 1.0 CD B:GLU373 2.9 22.0 1.0 MN B:MN602 3.0 25.2 1.0 N1 B:BB2603 3.0 29.4 1.0 CG B:ASP294 3.0 22.1 1.0 OD1 B:ASP312 3.1 20.1 1.0 CE B:LYS289 3.2 20.7 1.0 OE1 B:GLU373 3.2 23.3 1.0 CB B:ASP294 3.6 22.0 1.0 C3 B:BB2603 3.8 29.0 1.0 O4 B:BB2603 3.8 27.9 1.0 OD1 B:ASP294 4.0 21.1 1.0 CB B:ASP312 4.2 20.6 1.0 CG B:GLU373 4.3 20.8 1.0 O B:THR401 4.4 15.2 1.0 O B:ASP371 4.5 23.1 1.0 CD B:LYS289 4.6 19.6 1.0 OD1 B:ASP371 4.7 21.5 1.0 CG2 B:ILE291 4.9 21.1 1.0 CB B:ILE291 4.9 20.5 1.0 CG1 B:ILE291 4.9 20.2 1.0 N B:GLY374 5.0 18.5 1.0 O B:LEU402 5.0 22.6 1.0

Manganese binding site 4 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:25.2 occ:1.00 OD1 B:ASP371 1.9 21.5 1.0 O2 B:BB2603 1.9 27.5 1.0 O4 B:BB2603 1.9 27.9 1.0 O B:ASP371 1.9 23.1 1.0 OE1 B:GLU373 2.0 23.3 1.0 OD2 B:ASP294 2.0 23.7 1.0 C3 B:BB2603 2.7 29.0 1.0 N1 B:BB2603 2.7 29.4 1.0 CG B:ASP294 2.9 22.1 1.0 CD B:GLU373 2.9 22.0 1.0 MN B:MN601 3.0 21.4 1.0 CG B:ASP371 3.1 20.9 1.0 OD1 B:ASP294 3.1 21.1 1.0 C B:ASP371 3.1 20.7 1.0 OE2 B:GLU373 3.2 21.9 1.0 CA B:ASP371 3.7 20.7 1.0 OD2 B:ASP371 3.9 20.9 1.0 CB B:ASP371 3.9 20.6 1.0 NZ B:LYS301 4.0 25.0 1.0 CE B:LYS301 4.2 25.1 1.0 C5 B:BB2603 4.2 29.4 1.0 N B:ALA372 4.2 20.3 1.0 N B:GLU373 4.3 19.1 1.0 CB B:ASP294 4.3 22.0 1.0 CG B:GLU373 4.3 20.8 1.0 NZ B:LYS289 4.6 21.5 1.0 OD2 B:ASP312 4.6 20.2 1.0 CA B:ALA372 4.7 20.2 1.0 ND2 B:ASN344 4.7 21.2 1.0 CB B:GLU373 4.8 19.9 1.0 C6 B:BB2603 4.9 30.5 1.0 C8 B:BB2603 4.9 26.6 1.0

Manganese binding site 5 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:20.4 occ:1.00 O2 C:BB2603 1.9 18.9 1.0 OD2 C:ASP312 1.9 20.9 1.0 OD2 C:ASP294 1.9 17.4 1.0 OE1 C:GLU373 1.9 20.6 1.0 NZ C:LYS289 2.0 19.0 1.0 N1 C:BB2603 2.8 20.8 1.0 CG C:ASP312 2.8 21.6 1.0 CD C:GLU373 3.0 19.9 1.0 MN C:MN602 3.0 17.2 1.0 CG C:ASP294 3.0 16.6 1.0 OD1 C:ASP312 3.1 22.0 1.0 CE C:LYS289 3.2 19.4 1.0 OE2 C:GLU373 3.2 20.5 1.0 CB C:ASP294 3.6 16.6 1.0 C3 C:BB2603 3.7 22.4 1.0 O4 C:BB2603 3.9 21.4 1.0 OD1 C:ASP294 4.1 16.2 1.0 CB C:ASP312 4.2 21.9 1.0 CG C:GLU373 4.4 18.8 1.0 O C:THR401 4.4 17.8 1.0 O C:ASP371 4.5 18.0 1.0 CD C:LYS289 4.6 19.4 1.0 OD1 C:ASP371 4.7 15.3 1.0 C5 C:BB2603 4.9 23.6 1.0 O C:LEU402 4.9 19.1 1.0 CG2 C:ILE291 4.9 18.1 1.0 CB C:ILE291 5.0 18.5 1.0 N C:GLY374 5.0 18.5 1.0 CG1 C:ILE291 5.0 18.0 1.0

Manganese binding site 6 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:17.2 occ:1.00 OD1 C:ASP371 1.9 15.3 1.0 OE2 C:GLU373 1.9 20.5 1.0 O2 C:BB2603 1.9 18.9 1.0 O4 C:BB2603 1.9 21.4 1.0 O C:ASP371 1.9 18.0 1.0 OD2 C:ASP294 1.9 17.4 1.0 C3 C:BB2603 2.7 22.4 1.0 N1 C:BB2603 2.7 20.8 1.0 CG C:ASP294 2.8 16.6 1.0 CD C:GLU373 2.9 19.9 1.0 MN C:MN601 3.0 20.4 1.0 OD1 C:ASP294 3.0 16.2 1.0 CG C:ASP371 3.0 16.3 1.0 C C:ASP371 3.1 17.4 1.0 OE1 C:GLU373 3.2 20.6 1.0 CA C:ASP371 3.7 16.8 1.0 CB C:ASP371 3.9 16.9 1.0 OD2 C:ASP371 3.9 15.9 1.0 NZ C:LYS301 4.1 19.2 1.0 C5 C:BB2603 4.2 23.6 1.0 N C:ALA372 4.2 17.6 1.0 N C:GLU373 4.3 17.9 1.0 CG C:GLU373 4.3 18.8 1.0 CE C:LYS301 4.3 18.9 1.0 CB C:ASP294 4.3 16.6 1.0 ND2 C:ASN344 4.6 23.0 1.0 OD2 C:ASP312 4.6 20.9 1.0 CA C:ALA372 4.7 18.0 1.0 NZ C:LYS289 4.7 19.0 1.0 CB C:GLU373 4.7 18.2 1.0 C6 C:BB2603 4.9 25.9 1.0 C8 C:BB2603 4.9 25.6 1.0

Manganese binding site 7 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:42.3 occ:1.00 OD2 D:ASP312 1.9 37.9 1.0 O2 D:BB2603 1.9 46.3 1.0 OE1 D:GLU373 1.9 50.9 1.0 OD2 D:ASP294 1.9 37.3 1.0 NZ D:LYS289 2.0 49.2 1.0 N1 D:BB2603 2.7 44.4 1.0 CG D:ASP312 2.8 40.0 1.0 CD D:GLU373 2.9 48.2 1.0 MN D:MN602 3.0 45.2 1.0 CG D:ASP294 3.0 30.9 1.0 OD1 D:ASP312 3.1 42.0 1.0 CE D:LYS289 3.2 50.9 1.0 OE2 D:GLU373 3.2 47.8 1.0 CB D:ASP294 3.6 32.5 1.0 C3 D:BB2603 3.7 43.5 1.0 O4 D:BB2603 3.8 45.9 1.0 OD1 D:ASP294 4.1 28.7 1.0 CB D:ASP312 4.2 40.8 1.0 CG D:GLU373 4.3 44.4 1.0 O D:THR401 4.4 38.7 1.0 O D:ASP371 4.5 37.6 1.0 CD D:LYS289 4.5 51.2 1.0 OD1 D:ASP371 4.7 45.0 1.0 C5 D:BB2603 4.9 43.9 1.0 CG2 D:ILE291 4.9 40.7 1.0 CB D:ILE291 4.9 42.3 1.0 N D:GLY374 4.9 37.6 1.0 O D:LEU402 4.9 40.9 1.0 CG1 D:ILE291 4.9 43.5 1.0

Manganese binding site 8 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn602 b:45.2 occ:1.00 OE2 D:GLU373 1.9 47.8 1.0 OD1 D:ASP371 1.9 45.0 1.0 O D:ASP371 1.9 37.6 1.0 O4 D:BB2603 1.9 45.9 1.0 OD2 D:ASP294 1.9 37.3 1.0 O2 D:BB2603 1.9 46.3 1.0 C3 D:BB2603 2.7 43.5 1.0 N1 D:BB2603 2.8 44.4 1.0 CG D:ASP294 2.8 30.9 1.0 CD D:GLU373 2.8 48.2 1.0 MN D:MN601 3.0 42.3 1.0 OD1 D:ASP294 3.0 28.7 1.0 C D:ASP371 3.1 36.5 1.0 CG D:ASP371 3.1 40.9 1.0 OE1 D:GLU373 3.1 50.9 1.0 CA D:ASP371 3.7 34.2 1.0 CB D:ASP371 3.9 37.4 1.0 OD2 D:ASP371 4.0 40.1 1.0 NZ D:LYS301 4.1 28.8 1.0 C5 D:BB2603 4.2 43.9 1.0 N D:ALA372 4.2 36.9 1.0 N D:GLU373 4.2 40.1 1.0 CG D:GLU373 4.2 44.4 1.0 CE D:LYS301 4.3 31.1 1.0 CB D:ASP294 4.3 32.5 1.0 NZ D:LYS289 4.5 49.2 1.0 ND2 D:ASN344 4.6 35.8 1.0 OD2 D:ASP312 4.6 37.9 1.0 CA D:ALA372 4.6 36.6 1.0 CB D:GLU373 4.7 42.6 1.0 C6 D:BB2603 4.9 45.2 1.0 C8 D:BB2603 4.9 41.1 1.0

Manganese binding site 9 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn601 b:20.9 occ:1.00 O2 E:BB2603 1.9 24.0 1.0 OD2 E:ASP312 1.9 22.2 1.0 OE2 E:GLU373 1.9 20.9 1.0 NZ E:LYS289 2.0 16.9 1.0 OD2 E:ASP294 2.0 23.0 1.0 N1 E:BB2603 2.6 25.1 1.0 CG E:ASP312 2.8 22.0 1.0 CD E:GLU373 3.0 20.2 1.0 MN E:MN602 3.0 22.6 1.0 CG E:ASP294 3.1 20.7 1.0 OD1 E:ASP312 3.1 22.9 1.0 CE E:LYS289 3.1 15.6 1.0 OE1 E:GLU373 3.3 22.5 1.0 CB E:ASP294 3.6 20.9 1.0 C3 E:BB2603 3.7 24.8 1.0 O4 E:BB2603 3.8 23.7 1.0 OD1 E:ASP294 4.1 18.5 1.0 CB E:ASP312 4.2 21.9 1.0 CG E:GLU373 4.3 18.1 1.0 O E:THR401 4.4 12.7 1.0 CD E:LYS289 4.5 15.4 1.0 O E:ASP371 4.6 19.4 1.0 OD1 E:ASP371 4.7 20.3 1.0 CG2 E:ILE291 4.9 17.1 1.0 O E:LEU402 4.9 15.6 1.0 CB E:ILE291 4.9 16.9 1.0 N E:GLY374 4.9 16.4 1.0 CG1 E:ILE291 4.9 16.5 1.0 C5 E:BB2603 5.0 25.5 1.0

Manganese binding site 10 out of 12 in the Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of Leucyl Aminopeptidase From Trypanosoma Brucei in Complex with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn602 b:22.6 occ:1.00 OD1 E:ASP371 1.9 20.3 1.0 O E:ASP371 1.9 19.4 1.0 O2 E:BB2603 1.9 24.0 1.0 O4 E:BB2603 1.9 23.7 1.0 OE1 E:GLU373 1.9 22.5 1.0 OD2 E:ASP294 2.0 23.0 1.0 C3 E:BB2603 2.7 24.8 1.0 N1 E:BB2603 2.7 25.1 1.0 CG E:ASP294 2.9 20.7 1.0 CD E:GLU373 2.9 20.2 1.0 CG E:ASP371 3.0 20.2 1.0 MN E:MN601 3.0 20.9 1.0 C E:ASP371 3.1 18.3 1.0 OD1 E:ASP294 3.1 18.5 1.0 OE2 E:GLU373 3.2 20.9 1.0 CA E:ASP371 3.7 18.5 1.0 CB E:ASP371 3.9 19.2 1.0 OD2 E:ASP371 3.9 20.9 1.0 NZ E:LYS301 4.0 26.6 1.0 C5 E:BB2603 4.2 25.5 1.0 N E:ALA372 4.2 17.6 1.0 CE E:LYS301 4.2 26.4 1.0 N E:GLU373 4.3 17.4 1.0 CG E:GLU373 4.3 18.1 1.0 CB E:ASP294 4.3 20.9 1.0 CA E:ALA372 4.6 17.3 1.0 ND2 E:ASN344 4.6 22.5 1.0 OD2 E:ASP312 4.7 22.2 1.0 NZ E:LYS289 4.7 16.9 1.0 CB E:GLU373 4.8 17.3 1.0 C6 E:BB2603 4.8 26.1 1.0 C7 E:BB2603 4.8 25.0 1.0

J.Timm, M.Valente, D.Garcia-Caballero, K.S.Wilson, D.Gonzalez-Pacanowska. Structural Characterization of Acidic M17 Leucine Aminopeptidases From the Tritryps and Evaluation of Their Role in Nutrient Starvation Intrypanosoma Brucei. Msphere V. 2 2018.
ISSN: ESSN 2379-5042
PubMed: 28815215
DOI: 10.1128/MSPHERE.00226-17