Manganese in PDB 5nsm: Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei

The structure of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei, PDB code: 5nsm 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)	32.73 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.368, 143.760, 270.085, 90.00, 95.47, 90.00
R / Rfree (%)	20.6 / 22.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei (pdb code 5nsm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei, PDB code: 5nsm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:31.2 occ:1.00 OE2 A:GLU373 1.9 25.9 1.0 O A:ASP371 1.9 30.8 1.0 OD1 A:ASP371 2.0 30.5 1.0 OD2 A:ASP294 2.0 32.9 1.0 O A:HOH752 2.7 27.3 1.0 CG A:ASP294 2.8 27.6 1.0 CD A:GLU373 2.9 27.4 1.0 C A:ASP371 3.0 26.8 1.0 OD1 A:ASP294 3.0 31.3 1.0 CG A:ASP371 3.0 25.8 1.0 MN A:MN603 3.1 29.6 1.0 OE1 A:GLU373 3.2 26.3 1.0 CA A:ASP371 3.6 26.5 1.0 O A:HOH708 3.8 25.1 1.0 CB A:ASP371 3.9 25.7 1.0 OD2 A:ASP371 3.9 25.6 1.0 NZ A:LYS301 4.0 31.6 1.0 N A:ALA372 4.2 26.0 1.0 O1 A:BCT601 4.2 34.1 1.0 CE A:LYS301 4.3 32.6 1.0 CB A:ASP294 4.3 29.8 1.0 CG A:GLU373 4.3 26.7 1.0 N A:GLU373 4.4 25.8 1.0 ND2 A:ASN344 4.6 28.4 1.0 OD2 A:ASP312 4.6 33.0 1.0 CA A:ALA372 4.7 26.2 1.0 NZ A:LYS289 4.7 28.5 1.0 CB A:GLU373 4.9 26.1 1.0 N A:ASP371 5.0 26.1 1.0

Manganese binding site 2 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:29.6 occ:1.00 OE1 A:GLU373 1.8 26.3 1.0 OD2 A:ASP312 1.9 33.0 1.0 OD2 A:ASP294 2.0 32.9 1.0 NZ A:LYS289 2.0 28.5 1.0 O A:HOH708 2.0 25.1 1.0 CD A:GLU373 2.9 27.4 1.0 CG A:ASP312 2.9 30.9 1.0 CG A:ASP294 3.0 27.6 1.0 CE A:LYS289 3.0 27.9 1.0 MN A:MN602 3.1 31.2 1.0 OD1 A:ASP312 3.2 30.8 1.0 OE2 A:GLU373 3.2 25.9 1.0 CB A:ASP294 3.7 29.8 1.0 O1 A:BCT601 4.0 34.1 1.0 OD1 A:ASP294 4.0 31.3 1.0 O A:HOH752 4.1 27.3 1.0 CG A:GLU373 4.2 26.7 1.0 CB A:ASP312 4.3 32.4 1.0 O A:THR401 4.4 28.4 1.0 CD A:LYS289 4.5 27.9 1.0 O A:ASP371 4.6 30.8 1.0 CG2 A:ILE291 4.7 27.6 1.0 CB A:ILE291 4.7 27.8 1.0 CG1 A:ILE291 4.8 27.2 1.0 OD1 A:ASP371 4.9 30.5 1.0 N A:GLY374 4.9 25.9 1.0

Manganese binding site 3 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:37.0 occ:1.00 OD1 B:ASP371 1.9 37.1 1.0 O B:ASP371 1.9 32.4 1.0 OD2 B:ASP294 2.0 36.3 1.0 OE1 B:GLU373 2.0 34.0 1.0 CG B:ASP294 2.8 30.1 1.0 O B:HOH740 2.8 28.1 1.0 OD1 B:ASP294 3.0 28.5 1.0 CD B:GLU373 3.0 33.8 1.0 C B:ASP371 3.0 29.5 1.0 CG B:ASP371 3.0 32.2 1.0 MN B:MN603 3.1 32.2 1.0 OE2 B:GLU373 3.3 32.5 1.0 CA B:ASP371 3.5 32.1 1.0 CB B:ASP371 3.8 31.7 1.0 OD2 B:ASP371 3.8 30.5 1.0 NZ B:LYS301 3.9 29.6 1.0 N B:ALA372 4.1 29.6 1.0 O2 B:BCT601 4.2 42.8 1.0 CE B:LYS301 4.2 30.8 1.0 CB B:ASP294 4.3 30.1 1.0 CG B:GLU373 4.3 33.6 1.0 N B:GLU373 4.4 30.9 1.0 ND2 B:ASN344 4.6 29.3 1.0 CA B:ALA372 4.7 28.7 1.0 OD2 B:ASP312 4.7 30.1 1.0 NZ B:LYS289 4.8 30.5 1.0 CB B:GLU373 4.9 32.2 1.0 CA B:GLY296 4.9 31.1 1.0 N B:ASP371 4.9 33.3 1.0

Manganese binding site 4 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:32.2 occ:1.00 OE2 B:GLU373 1.9 32.5 1.0 OD2 B:ASP312 1.9 30.1 1.0 OD2 B:ASP294 2.0 36.3 1.0 NZ B:LYS289 2.1 30.5 1.0 CG B:ASP312 2.9 27.5 1.0 CD B:GLU373 2.9 33.8 1.0 CG B:ASP294 3.0 30.1 1.0 CE B:LYS289 3.1 29.6 1.0 MN B:MN602 3.1 37.0 1.0 OD1 B:ASP312 3.2 28.1 1.0 OE1 B:GLU373 3.3 34.0 1.0 CB B:ASP294 3.7 30.1 1.0 O2 B:BCT601 3.9 42.8 1.0 O B:HOH740 4.0 28.1 1.0 OD1 B:ASP294 4.0 28.5 1.0 CB B:ASP312 4.3 28.4 1.0 CG B:GLU373 4.3 33.6 1.0 O B:THR401 4.4 31.7 1.0 CD B:LYS289 4.6 31.1 1.0 O B:ASP371 4.6 32.4 1.0 CG2 B:ILE291 4.8 26.3 1.0 CB B:ILE291 4.8 27.7 1.0 OD1 B:ASP371 4.8 37.1 1.0 CG1 B:ILE291 4.9 26.9 1.0 N B:GLY374 5.0 30.9 1.0

Manganese binding site 5 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:31.2 occ:1.00 OD1 C:ASP371 1.9 29.8 1.0 OE2 C:GLU373 1.9 28.9 1.0 O C:ASP371 1.9 29.1 1.0 OD2 C:ASP294 2.0 30.8 1.0 O C:HOH751 2.8 38.3 1.0 CG C:ASP294 2.8 27.5 1.0 CD C:GLU373 2.9 28.4 1.0 OD1 C:ASP294 3.0 29.1 1.0 CG C:ASP371 3.0 27.5 1.0 C C:ASP371 3.0 25.4 1.0 MN C:MN603 3.1 29.2 1.0 OE1 C:GLU373 3.3 27.0 1.0 CA C:ASP371 3.5 26.3 1.0 CB C:ASP371 3.8 26.7 1.0 OD2 C:ASP371 3.8 28.1 1.0 NZ C:LYS301 3.9 28.2 1.0 O1 C:BCT601 4.0 42.9 1.0 N C:ALA372 4.1 24.4 1.0 CE C:LYS301 4.3 27.9 1.0 CB C:ASP294 4.3 28.2 1.0 CG C:GLU373 4.3 27.4 1.0 N C:GLU373 4.4 25.1 1.0 ND2 C:ASN344 4.5 28.7 1.0 CA C:ALA372 4.7 23.9 1.0 OD2 C:ASP312 4.7 26.6 1.0 NZ C:LYS289 4.8 28.4 1.0 C C:BCT601 4.9 37.3 1.0 CB C:GLU373 4.9 26.6 1.0 N C:ASP371 4.9 26.6 1.0 CA C:GLY296 4.9 27.5 1.0 O3 C:BCT601 5.0 44.6 1.0

Manganese binding site 6 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn603 b:29.2 occ:1.00 OE1 C:GLU373 1.9 27.0 1.0 OD2 C:ASP312 1.9 26.6 1.0 OD2 C:ASP294 2.0 30.8 1.0 NZ C:LYS289 2.0 28.4 1.0 CG C:ASP312 2.9 23.4 1.0 CD C:GLU373 3.0 28.4 1.0 CG C:ASP294 3.0 27.5 1.0 MN C:MN602 3.1 31.2 1.0 CE C:LYS289 3.1 26.3 1.0 OD1 C:ASP312 3.2 24.5 1.0 OE2 C:GLU373 3.3 28.9 1.0 CB C:ASP294 3.7 28.2 1.0 O1 C:BCT601 3.7 42.9 1.0 O C:HOH751 3.9 38.3 1.0 OD1 C:ASP294 4.0 29.1 1.0 CB C:ASP312 4.3 24.2 1.0 O C:THR401 4.3 27.0 1.0 CG C:GLU373 4.3 27.4 1.0 CD C:LYS289 4.6 26.1 1.0 O C:ASP371 4.6 29.1 1.0 OD1 C:ASP371 4.8 29.8 1.0 CG2 C:ILE291 4.8 28.4 1.0 CB C:ILE291 4.9 27.9 1.0 CG1 C:ILE291 4.9 28.1 1.0 C C:BCT601 4.9 37.3 1.0 N C:GLY374 5.0 27.6 1.0

Manganese binding site 7 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn602 b:32.4 occ:1.00 OD1 D:ASP371 2.0 30.9 1.0 OD2 D:ASP294 2.0 34.0 1.0 O D:ASP371 2.0 32.1 1.0 OE2 D:GLU373 2.0 29.1 1.0 O D:HOH758 2.5 35.8 1.0 CG D:ASP294 2.8 29.0 1.0 CD D:GLU373 2.9 30.4 1.0 OD1 D:ASP294 3.0 30.0 1.0 C D:ASP371 3.0 27.9 1.0 CG D:ASP371 3.0 28.0 1.0 MN D:MN603 3.1 31.2 1.0 OE1 D:GLU373 3.2 31.2 1.0 CA D:ASP371 3.6 29.7 1.0 CB D:ASP371 3.9 28.9 1.0 OD2 D:ASP371 3.9 26.8 1.0 NZ D:LYS301 3.9 33.3 1.0 N D:ALA372 4.2 28.7 1.0 CE D:LYS301 4.3 33.2 1.0 O2 D:BCT601 4.3 40.3 1.0 CB D:ASP294 4.3 29.6 1.0 CG D:GLU373 4.3 30.5 1.0 N D:GLU373 4.4 29.0 1.0 ND2 D:ASN344 4.6 29.4 1.0 OD2 D:ASP312 4.6 28.7 1.0 CA D:ALA372 4.7 28.3 1.0 NZ D:LYS289 4.7 30.8 1.0 CB D:GLU373 4.9 29.7 1.0

Manganese binding site 8 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn603 b:31.2 occ:1.00 OD2 D:ASP312 1.9 28.7 1.0 OE1 D:GLU373 1.9 31.2 1.0 NZ D:LYS289 2.0 30.8 1.0 OD2 D:ASP294 2.0 34.0 1.0 CG D:ASP312 2.9 25.4 1.0 CD D:GLU373 3.0 30.4 1.0 CG D:ASP294 3.0 29.0 1.0 CE D:LYS289 3.1 28.3 1.0 MN D:MN602 3.1 32.4 1.0 OD1 D:ASP312 3.1 24.5 1.0 OE2 D:GLU373 3.3 29.1 1.0 O D:HOH758 3.6 35.8 1.0 CB D:ASP294 3.6 29.6 1.0 O2 D:BCT601 4.0 40.3 1.0 OD1 D:ASP294 4.0 30.0 1.0 CB D:ASP312 4.3 25.8 1.0 CG D:GLU373 4.3 30.5 1.0 O D:THR401 4.3 28.9 1.0 CD D:LYS289 4.5 29.3 1.0 O D:ASP371 4.7 32.1 1.0 CG2 D:ILE291 4.7 28.1 1.0 CB D:ILE291 4.8 27.9 1.0 CG1 D:ILE291 4.8 27.9 1.0 OD1 D:ASP371 4.9 30.9 1.0 N D:GLY374 5.0 28.2 1.0

Manganese binding site 9 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn602 b:33.6 occ:1.00 OD1 E:ASP371 1.9 30.0 1.0 O E:ASP371 2.0 31.5 1.0 OD2 E:ASP294 2.0 32.5 1.0 OE1 E:GLU373 2.0 32.0 1.0 O E:HOH754 2.7 29.2 1.0 CG E:ASP294 2.8 29.0 1.0 CD E:GLU373 3.0 31.2 1.0 C E:ASP371 3.0 27.9 1.0 CG E:ASP371 3.0 29.0 1.0 OD1 E:ASP294 3.0 26.5 1.0 MN E:MN603 3.1 31.5 1.0 OE2 E:GLU373 3.3 34.5 1.0 CA E:ASP371 3.6 27.4 1.0 CB E:ASP371 3.9 28.1 1.0 OD2 E:ASP371 3.9 28.5 1.0 NZ E:LYS301 3.9 26.7 1.0 O2 E:BCT601 4.1 43.2 1.0 N E:ALA372 4.2 28.0 1.0 CE E:LYS301 4.2 26.3 1.0 CB E:ASP294 4.3 30.6 1.0 CG E:GLU373 4.4 34.0 1.0 N E:GLU373 4.4 30.8 1.0 ND2 E:ASN344 4.6 29.7 1.0 OD2 E:ASP312 4.7 32.1 1.0 CA E:ALA372 4.7 29.0 1.0 NZ E:LYS289 4.7 26.7 1.0 O3 E:BCT601 4.9 48.5 1.0 C E:BCT601 4.9 42.5 1.0 CB E:GLU373 4.9 31.8 1.0 N E:ASP371 5.0 26.9 1.0

Manganese binding site 10 out of 24 in the Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Unliganded Structure of Leucyl Aminopeptidase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn603 b:31.5 occ:1.00 OE2 E:GLU373 1.9 34.5 1.0 OD2 E:ASP312 1.9 32.1 1.0 OD2 E:ASP294 1.9 32.5 1.0 NZ E:LYS289 2.0 26.7 1.0 CG E:ASP312 2.9 28.2 1.0 CD E:GLU373 2.9 31.2 1.0 CG E:ASP294 3.0 29.0 1.0 CE E:LYS289 3.1 27.1 1.0 MN E:MN602 3.1 33.6 1.0 OD1 E:ASP312 3.2 27.1 1.0 OE1 E:GLU373 3.2 32.0 1.0 CB E:ASP294 3.6 30.6 1.0 O E:HOH754 3.9 29.2 1.0 O2 E:BCT601 3.9 43.2 1.0 OD1 E:ASP294 4.0 26.5 1.0 CB E:ASP312 4.3 28.6 1.0 CG E:GLU373 4.3 34.0 1.0 O E:THR401 4.4 25.9 1.0 CD E:LYS289 4.6 26.8 1.0 O E:ASP371 4.6 31.5 1.0 CG2 E:ILE291 4.7 26.2 1.0 CB E:ILE291 4.8 26.4 1.0 OD1 E:ASP371 4.8 30.0 1.0 CG1 E:ILE291 4.8 27.9 1.0 N E:GLY374 5.0 29.8 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