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Manganese in PDB 8pzy: Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound

Enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound

All present enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound, PDB code: 8pzy was solved by M.C.Simpson, C.M.Czekster, C.J.Harding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.75 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.53, 183.03, 316.53, 90, 90, 90
R / Rfree (%) 17.6 / 20.4

Other elements in 8pzy:

The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound (pdb code 8pzy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound, PDB code: 8pzy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 8pzy

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Manganese binding site 1 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn609

b:33.4
occ:1.00
 OE2 A:GLU371 2.1 36.5 1.0
OD2 A:ASP310 2.1 35.0 1.0
O A:HOH770 2.2 38.1 1.0
NZ A:LYS287 2.2 34.5 1.0
OD2 A:ASP292 2.4 33.0 1.0
NA A:NA611 2.9 59.9 1.0
CG A:ASP310 3.0 36.4 1.0
CD A:GLU371 3.1 34.5 1.0
CE A:LYS287 3.1 35.3 1.0
OD1 A:ASP310 3.2 38.0 1.0
MN A:MN610 3.2 34.6 1.0
CG A:ASP292 3.3 33.7 1.0
OE1 A:GLU371 3.4 34.1 1.0
O1 A:BCT601 3.8 39.4 1.0
CB A:ASP292 3.8 35.9 1.0
O A:HOH915 4.2 37.8 1.0
OD1 A:ASP292 4.2 33.7 1.0
O A:THR396 4.4 38.2 1.0
CB A:ASP310 4.4 32.6 1.0
CG A:GLU371 4.4 33.7 1.0
CD A:LYS287 4.6 29.7 1.0
CG1 A:ILE289 4.7 33.7 1.0
N A:GLY372 4.7 34.5 1.0
CB A:ILE289 4.7 32.3 1.0
CG2 A:ILE289 4.7 33.3 1.0
O A:ASP369 4.9 34.4 1.0

Manganese binding site 2 out of 12 in 8pzy

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Manganese binding site 2 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn610

b:34.6
occ:1.00
 O A:ASP369 2.1 34.4 1.0
O A:HOH770 2.2 38.1 1.0
OD2 A:ASP292 2.2 33.0 1.0
OE1 A:GLU371 2.2 34.1 1.0
OD1 A:ASP369 2.2 37.1 1.0
O A:HOH915 2.3 37.8 1.0
CG A:ASP292 3.1 33.7 1.0
C A:ASP369 3.1 30.9 1.0
CD A:GLU371 3.1 34.5 1.0
CG A:ASP369 3.2 31.1 1.0
MN A:MN609 3.2 33.4 1.0
OD1 A:ASP292 3.3 33.7 1.0
OE2 A:GLU371 3.4 36.5 1.0
CA A:ASP369 3.6 32.4 1.0
NZ A:LYS299 3.9 33.5 1.0
CB A:ASP369 3.9 30.5 1.0
OD2 A:ASP369 4.0 38.2 1.0
NA A:NA611 4.1 59.9 1.0
O1 A:BCT601 4.2 39.4 1.0
N A:ALA370 4.2 32.6 1.0
CE A:LYS299 4.3 34.8 1.0
N A:GLU371 4.3 32.2 1.0
CB A:ASP292 4.5 35.9 1.0
CG A:GLU371 4.5 33.7 1.0
CA A:ALA370 4.6 33.5 1.0
HO3 A:BCT601 4.7 52.2 1.0
ND2 A:ASN342 4.8 31.4 1.0
CA A:GLY294 4.9 33.8 1.0
OD2 A:ASP310 4.9 35.0 1.0
C A:BCT601 4.9 43.9 1.0
NZ A:LYS287 5.0 34.5 1.0
CB A:GLU371 5.0 32.3 1.0
N A:ASP369 5.0 30.7 1.0

Manganese binding site 3 out of 12 in 8pzy

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Manganese binding site 3 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn607

b:35.3
occ:1.00
 OE2 B:GLU371 2.1 33.9 1.0
OD2 B:ASP310 2.1 37.5 1.0
O B:HOH789 2.2 36.1 1.0
NZ B:LYS287 2.3 33.6 1.0
OD2 B:ASP292 2.5 36.6 1.0
O B:HOH839 2.5 47.7 1.0
CG B:ASP310 2.9 35.0 1.0
OD1 B:ASP310 3.1 38.4 1.0
CD B:GLU371 3.1 36.9 1.0
CE B:LYS287 3.1 35.6 1.0
MN B:MN608 3.2 36.2 1.0
CG B:ASP292 3.3 34.8 1.0
OE1 B:GLU371 3.4 33.5 1.0
CB B:ASP292 3.8 33.7 1.0
O1 B:BCT602 3.9 41.9 1.0
O B:HOH877 4.0 41.4 1.0
OD1 B:ASP292 4.3 33.6 1.0
O B:THR396 4.3 38.7 1.0
CB B:ASP310 4.4 36.2 1.0
CG B:GLU371 4.5 33.2 1.0
CD B:LYS287 4.6 32.7 1.0
N B:GLY372 4.7 33.5 1.0
O B:HOH999 4.7 51.4 1.0
CG1 B:ILE289 4.7 32.1 1.0
CB B:ILE289 4.8 32.2 1.0
CG2 B:ILE289 4.8 31.6 1.0
O B:ASP369 5.0 34.2 1.0

Manganese binding site 4 out of 12 in 8pzy

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Manganese binding site 4 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn608

b:36.2
occ:1.00
 OD1 B:ASP369 2.1 38.1 1.0
OD2 B:ASP292 2.2 36.6 1.0
OE1 B:GLU371 2.2 33.5 1.0
O B:HOH877 2.2 41.4 1.0
O B:ASP369 2.2 34.2 1.0
O B:HOH789 2.3 36.1 1.0
CG B:ASP292 3.0 34.8 1.0
CG B:ASP369 3.1 34.4 1.0
CD B:GLU371 3.1 36.9 1.0
C B:ASP369 3.1 33.9 1.0
MN B:MN607 3.2 35.3 1.0
OD1 B:ASP292 3.2 33.6 1.0
OE2 B:GLU371 3.4 33.9 1.0
HO1 B:EDO603 3.5 73.9 1.0
CA B:ASP369 3.5 34.1 1.0
CB B:ASP369 3.8 32.3 1.0
OD2 B:ASP369 3.9 36.9 1.0
NZ B:LYS299 3.9 33.9 1.0
O B:HOH839 4.0 47.7 1.0
CE B:LYS299 4.2 35.0 1.0
O1 B:BCT602 4.2 41.9 1.0
N B:ALA370 4.3 34.3 1.0
O1 B:EDO603 4.4 61.6 1.0
H21 B:EDO603 4.4 65.8 1.0
N B:GLU371 4.4 33.9 1.0
CB B:ASP292 4.5 33.7 1.0
CG B:GLU371 4.5 33.2 1.0
H11 B:EDO603 4.6 69.6 1.0
CA B:ALA370 4.7 34.1 1.0
ND2 B:ASN342 4.8 33.3 1.0
CA B:GLY294 4.8 34.3 1.0
OD2 B:ASP310 4.9 37.5 1.0
C1 B:EDO603 4.9 58.0 1.0
CB B:GLU371 4.9 34.5 1.0
N B:ASP369 4.9 31.5 1.0

Manganese binding site 5 out of 12 in 8pzy

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Manganese binding site 5 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn606

b:35.6
occ:1.00
 OD2 C:ASP310 2.0 35.9 1.0
O C:HOH851 2.1 39.8 1.0
OE2 C:GLU371 2.1 34.0 1.0
NZ C:LYS287 2.3 35.2 1.0
OD2 C:ASP292 2.4 33.7 1.0
O C:HOH796 2.4 44.3 1.0
CG C:ASP310 2.9 34.4 1.0
OD1 C:ASP310 3.0 35.9 1.0
CD C:GLU371 3.1 35.3 1.0
CE C:LYS287 3.2 35.1 1.0
MN C:MN607 3.2 34.6 1.0
CG C:ASP292 3.3 34.1 1.0
OE1 C:GLU371 3.4 32.5 1.0
HO3 C:BCT601 3.6 51.3 1.0
CB C:ASP292 3.8 30.1 1.0
O3 C:BCT601 3.8 42.8 1.0
O C:HOH947 4.2 39.6 1.0
OD1 C:ASP292 4.2 31.5 1.0
O C:THR396 4.3 36.2 1.0
CB C:ASP310 4.3 31.9 1.0
CG C:GLU371 4.5 34.4 1.0
CD C:LYS287 4.6 28.0 1.0
N C:GLY372 4.7 35.8 1.0
CG2 C:ILE289 4.7 33.6 1.0
CB C:ILE289 4.8 32.8 1.0
O C:HOH1021 4.8 55.4 1.0
CG1 C:ILE289 4.8 31.6 1.0
O C:ASP369 4.9 35.9 1.0

Manganese binding site 6 out of 12 in 8pzy

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Manganese binding site 6 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn607

b:34.6
occ:1.00
 OD1 C:ASP369 2.1 37.8 1.0
O C:HOH851 2.2 39.8 1.0
O C:ASP369 2.2 35.9 1.0
OD2 C:ASP292 2.2 33.7 1.0
OE1 C:GLU371 2.3 32.5 1.0
O C:HOH947 2.3 39.6 1.0
CG C:ASP292 3.1 34.1 1.0
CG C:ASP369 3.1 34.5 1.0
C C:ASP369 3.1 34.1 1.0
CD C:GLU371 3.2 35.3 1.0
MN C:MN606 3.2 35.6 1.0
OD1 C:ASP292 3.2 31.5 1.0
OE2 C:GLU371 3.4 34.0 1.0
CA C:ASP369 3.6 34.4 1.0
CB C:ASP369 3.9 34.7 1.0
O C:HOH796 3.9 44.3 1.0
OD2 C:ASP369 3.9 34.8 1.0
NZ C:LYS299 3.9 39.6 1.0
O3 C:BCT601 4.1 42.8 1.0
CE C:LYS299 4.2 37.4 1.0
N C:ALA370 4.3 32.8 1.0
N C:GLU371 4.4 32.6 1.0
CB C:ASP292 4.5 30.1 1.0
HO3 C:BCT601 4.5 51.3 1.0
CG C:GLU371 4.6 34.4 1.0
O C:HOH1028 4.6 59.4 1.0
CA C:ALA370 4.7 35.5 1.0
ND2 C:ASN342 4.8 31.5 1.0
OD2 C:ASP310 4.8 35.9 1.0
N C:ASP369 5.0 30.9 1.0
CA C:GLY294 5.0 34.5 1.0
CB C:GLU371 5.0 32.0 1.0

Manganese binding site 7 out of 12 in 8pzy

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Manganese binding site 7 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn604

b:35.4
occ:1.00
 OD2 D:ASP310 2.1 35.8 1.0
OE2 D:GLU371 2.1 35.2 1.0
O D:HOH798 2.2 35.6 1.0
NZ D:LYS287 2.3 35.8 1.0
O D:HOH854 2.5 48.5 1.0
OD2 D:ASP292 2.6 36.4 1.0
CG D:ASP310 2.9 37.2 1.0
OD1 D:ASP310 3.1 37.5 1.0
CD D:GLU371 3.1 37.0 1.0
CE D:LYS287 3.2 35.6 1.0
MN D:MN605 3.2 36.0 1.0
CG D:ASP292 3.3 34.0 1.0
OE1 D:GLU371 3.4 34.4 1.0
HO3 D:BCT601 3.6 49.3 1.0
CB D:ASP292 3.8 34.5 1.0
O3 D:BCT601 3.9 41.1 1.0
O D:HOH851 3.9 41.0 1.0
OD1 D:ASP292 4.2 33.8 1.0
O D:THR396 4.3 37.8 1.0
CB D:ASP310 4.4 35.8 1.0
CG D:GLU371 4.5 33.0 1.0
CD D:LYS287 4.6 34.6 1.0
CG1 D:ILE289 4.7 31.9 1.0
N D:GLY372 4.7 34.9 1.0
CG2 D:ILE289 4.7 31.9 1.0
CB D:ILE289 4.7 35.4 1.0
O D:ASP369 4.9 34.9 1.0

Manganese binding site 8 out of 12 in 8pzy

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Manganese binding site 8 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn605

b:36.0
occ:1.00
 O D:HOH851 2.1 41.0 1.0
OD2 D:ASP292 2.1 36.4 1.0
OE1 D:GLU371 2.2 34.4 1.0
O D:ASP369 2.2 34.9 1.0
OD1 D:ASP369 2.2 38.6 1.0
O D:HOH798 2.2 35.6 1.0
CG D:ASP292 3.0 34.0 1.0
C D:ASP369 3.1 37.5 1.0
CD D:GLU371 3.1 37.0 1.0
CG D:ASP369 3.1 35.2 1.0
MN D:MN604 3.2 35.4 1.0
OD1 D:ASP292 3.3 33.8 1.0
OE2 D:GLU371 3.4 35.2 1.0
CA D:ASP369 3.5 34.5 1.0
NZ D:LYS299 3.8 36.0 1.0
CB D:ASP369 3.9 35.2 1.0
O D:HOH854 4.0 48.5 1.0
OD2 D:ASP369 4.0 35.9 1.0
O3 D:BCT601 4.1 41.1 1.0
CE D:LYS299 4.2 35.5 1.0
N D:ALA370 4.3 35.4 1.0
N D:GLU371 4.3 34.9 1.0
HO3 D:BCT601 4.4 49.3 1.0
CB D:ASP292 4.4 34.5 1.0
CG D:GLU371 4.5 33.0 1.0
CA D:ALA370 4.7 34.6 1.0
ND2 D:ASN342 4.7 33.0 1.0
OD2 D:ASP310 4.9 35.8 1.0
N D:ASP369 4.9 32.6 1.0
CB D:GLU371 4.9 31.4 1.0
CA D:GLY294 4.9 34.4 1.0

Manganese binding site 9 out of 12 in 8pzy

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Manganese binding site 9 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn605

b:34.7
occ:1.00
 OE2 E:GLU371 2.0 34.8 1.0
O E:HOH767 2.1 33.3 1.0
OD2 E:ASP310 2.1 35.9 1.0
NZ E:LYS287 2.3 33.0 1.0
OD2 E:ASP292 2.4 33.4 1.0
CG E:ASP310 3.0 37.4 1.0
CD E:GLU371 3.0 33.2 1.0
MN E:MN606 3.1 34.6 1.0
OD1 E:ASP310 3.2 34.2 1.0
CE E:LYS287 3.2 34.1 1.0
CG E:ASP292 3.2 33.6 1.0
OE1 E:GLU371 3.4 32.7 1.0
CB E:ASP292 3.8 34.5 1.0
O2 E:BCT602 3.8 37.7 1.0
O E:HOH902 4.0 43.9 1.0
OD1 E:ASP292 4.2 32.0 1.0
O E:THR396 4.4 42.8 1.0
CG E:GLU371 4.4 33.5 1.0
CB E:ASP310 4.4 35.2 1.0
CD E:LYS287 4.6 33.5 1.0
N E:GLY372 4.7 34.7 1.0
CG1 E:ILE289 4.7 32.5 1.0
CB E:ILE289 4.7 32.4 1.0
CG2 E:ILE289 4.7 34.4 1.0
C E:BCT602 4.9 41.0 1.0
O E:ASP369 5.0 34.2 1.0
CA E:GLY372 5.0 34.8 1.0

Manganese binding site 10 out of 12 in 8pzy

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Manganese binding site 10 out of 12 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14 - Hexameric Assembly with Manganese Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn606

b:34.6
occ:1.00
 O E:HOH902 2.1 43.9 1.0
OD2 E:ASP292 2.1 33.4 1.0
O E:HOH767 2.1 33.3 1.0
OE1 E:GLU371 2.2 32.7 1.0
OD1 E:ASP369 2.2 35.3 1.0
O E:ASP369 2.3 34.2 1.0
CG E:ASP292 3.0 33.6 1.0
CD E:GLU371 3.1 33.2 1.0
CG E:ASP369 3.1 34.0 1.0
MN E:MN605 3.1 34.7 1.0
C E:ASP369 3.2 37.2 1.0
OD1 E:ASP292 3.2 32.0 1.0
OE2 E:GLU371 3.3 34.8 1.0
CA E:ASP369 3.6 33.0 1.0
CB E:ASP369 3.9 31.1 1.0
OD2 E:ASP369 3.9 33.4 1.0
NZ E:LYS299 4.0 32.3 1.0
O2 E:BCT602 4.2 37.7 1.0
CE E:LYS299 4.3 33.1 1.0
N E:ALA370 4.3 33.3 1.0
N E:GLU371 4.4 34.5 1.0
CB E:ASP292 4.4 34.5 1.0
CG E:GLU371 4.5 33.5 1.0
CA E:ALA370 4.7 34.3 1.0
ND2 E:ASN342 4.7 33.0 1.0
O E:HOH996 4.9 56.2 1.0
OD2 E:ASP310 4.9 35.9 1.0
CA E:GLY294 4.9 32.0 1.0
CB E:GLU371 4.9 35.0 1.0
C E:BCT602 4.9 41.0 1.0
N E:ASP369 4.9 33.4 1.0
NZ E:LYS287 5.0 33.0 1.0

Reference:

M.C.Simpson, C.J.Harding, R.M.Czekster, L.Remmel, B.E.Bode, C.M.Czekster. Unveiling the Catalytic Mechanism of A Processive Metalloaminopeptidase. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37924287
DOI: 10.1021/ACS.BIOCHEM.3C00420
Page generated: Thu Dec 28 11:06:52 2023

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