Manganese in PDB 5wze: The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp

Protein crystallography data

The structure of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp, PDB code: 5wze was solved by R.Bao, C.T.Peng, L.Liu, L.H.He, C.C.Li, T.Li, Y.L.Shen, Y.B.Zhu, Y.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.01 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.197, 123.432, 149.485, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 22.1

Other elements in 5wze:

The structure of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp also contains other interesting chemical elements:

Calcium (Ca) 5 atoms
Sodium (Na) 4 atoms

Manganese Binding Sites:

Pages:

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

Binding sites:

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

Manganese binding site 1 out of 12 in 5wze

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Manganese binding site 1 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:28.9
occ:0.50
 OD1 A:ASP271 1.9 22.1 1.0
OE1 A:GLU408 2.0 18.0 1.0
OD1 A:ASP260 2.2 16.6 1.0
O A:HOH673 2.4 29.5 1.0
OD2 A:ASP260 2.6 17.4 1.0
CG A:ASP260 2.7 14.8 1.0
CD A:GLU408 2.8 18.7 1.0
CG A:ASP271 2.9 16.5 1.0
OE2 A:GLU408 3.1 24.2 1.0
MN A:MN508 3.1 28.9 1.0
OD2 A:ASP271 3.2 21.0 1.0
MN A:MN509 3.3 31.6 1.0
OH A:TYR229 3.6 14.3 1.0
OG1 A:THR273 3.6 15.2 1.0
OE1 A:GLU384 3.9 23.1 1.0
CZ A:TYR229 4.1 13.2 1.0
CG A:GLU408 4.2 17.8 1.0
CB A:ASP260 4.2 12.7 1.0
CB A:ASP271 4.3 16.5 1.0
C A:ASP271 4.5 13.5 1.0
N A:ILE272 4.5 12.7 1.0
CE2 A:TYR229 4.6 17.1 1.0
O A:ILE272 4.6 20.8 1.0
C A:ILE272 4.7 13.2 1.0
CD A:GLU384 4.7 21.2 1.0
CA A:ASP271 4.7 13.7 1.0
CB A:GLU408 4.7 15.3 1.0
CE1 A:TYR229 4.8 16.4 1.0
CA A:ASP260 4.9 13.2 1.0
O A:ASP271 4.9 16.9 1.0
CB A:THR273 4.9 16.0 1.0
OE2 A:GLU384 4.9 20.1 1.0
N A:THR273 4.9 15.4 1.0
NE A:ARG406 5.0 15.4 1.0

Manganese binding site 2 out of 12 in 5wze

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Manganese binding site 2 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:28.9
occ:1.00
 OE2 A:GLU408 2.1 24.2 1.0
O A:HOH673 2.2 29.5 1.0
OD2 A:ASP271 2.3 21.0 1.0
NE2 A:HIS354 2.3 14.4 1.0
OE2 A:GLU384 2.4 20.1 1.0
OE1 A:GLU384 2.9 23.1 1.0
CD A:GLU384 2.9 21.2 1.0
CD A:GLU408 3.0 18.7 1.0
CG A:ASP271 3.1 16.5 1.0
MN A:MN507 3.1 28.9 0.5
CE1 A:HIS354 3.2 12.8 1.0
CD2 A:HIS354 3.3 14.6 1.0
OE1 A:GLU408 3.3 18.0 1.0
OD1 A:ASP271 3.4 22.1 1.0
MN A:MN509 3.7 31.6 1.0
OG1 A:THR382 3.8 12.7 1.0
CG2 A:THR382 4.0 14.9 1.0
CB A:THR382 4.1 14.5 1.0
CG A:GLU384 4.3 16.4 1.0
ND1 A:HIS354 4.3 13.0 1.0
CB A:ASP271 4.4 16.5 1.0
CG A:HIS354 4.4 13.7 1.0
CG A:GLU408 4.4 17.8 1.0
NE2 A:HIS361 4.8 20.3 1.0
CB A:GLU384 4.9 18.1 1.0
CA A:PRO504 5.0 37.7 1.0
CD2 A:HIS361 5.0 17.5 1.0

Manganese binding site 3 out of 12 in 5wze

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Manganese binding site 3 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:31.6
occ:1.00
 O A:HOH673 2.2 29.5 1.0
MN A:MN507 3.3 28.9 0.5
MN A:MN508 3.7 28.9 1.0
OD2 A:ASP271 3.7 21.0 1.0
NE2 A:HIS361 3.8 20.3 1.0
OD2 A:ASP260 3.9 17.4 1.0
N A:PRO504 4.1 39.0 1.0
OD1 A:ASP271 4.2 22.1 1.0
CA A:PRO504 4.3 37.7 1.0
OD1 A:ASP260 4.3 16.6 1.0
CG A:ASP271 4.4 16.5 1.0
NE2 A:HIS243 4.4 43.0 1.0
CG A:ASP260 4.4 14.8 1.0
CE2 A:TYR229 4.5 17.1 1.0
CE1 A:HIS361 4.5 18.7 1.0
CZ A:TYR229 4.6 13.2 1.0
NE2 A:HIS354 4.6 14.4 1.0
CD2 A:TYR229 4.6 15.1 1.0
CD2 A:HIS361 4.8 17.5 1.0
OE1 A:GLU384 4.8 23.1 1.0
CE1 A:TYR229 4.8 16.4 1.0
CG A:TYR229 4.9 16.2 1.0
C A:PRO504 4.9 43.1 1.0
CD1 A:TYR229 5.0 16.6 1.0
CD2 A:HIS243 5.0 41.2 1.0

Manganese binding site 4 out of 12 in 5wze

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Manganese binding site 4 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn510

b:28.9
occ:0.50
 O B:HOH801 1.8 28.9 1.0
OE1 B:GLU408 2.2 20.4 1.0
OD1 B:ASP271 2.2 16.9 1.0
OD1 B:ASP260 2.3 16.2 1.0
OD2 B:ASP260 2.4 15.6 1.0
CG B:ASP260 2.7 16.4 1.0
MN B:MN511 2.9 28.9 1.0
CD B:GLU408 3.0 18.0 1.0
CG B:ASP271 3.1 17.4 1.0
MN B:MN512 3.1 34.0 1.0
OE2 B:GLU408 3.2 24.2 1.0
OD2 B:ASP271 3.3 19.2 1.0
OG1 B:THR273 3.6 17.6 1.0
OE1 B:GLU384 3.7 25.8 1.0
OH B:TYR229 3.8 18.3 1.0
CB B:ASP260 4.2 15.4 1.0
CZ B:TYR229 4.3 17.7 1.0
CG B:GLU408 4.4 15.0 1.0
CD B:GLU384 4.5 23.1 1.0
CB B:ASP271 4.6 15.6 1.0
CE2 B:TYR229 4.6 16.4 1.0
NE B:ARG406 4.7 17.5 1.0
OE2 B:GLU384 4.7 22.4 1.0
C B:ASP271 4.8 14.2 1.0
CD B:PRO506 4.9 37.9 1.0
CB B:GLU408 4.9 14.3 1.0
CA B:ASP260 5.0 14.5 1.0
O B:ILE272 5.0 15.8 1.0
O B:ASP271 5.0 15.2 1.0
N B:ILE272 5.0 13.6 1.0

Manganese binding site 5 out of 12 in 5wze

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Manganese binding site 5 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn511

b:28.9
occ:1.00
 O B:HOH801 2.1 28.9 1.0
OD2 B:ASP271 2.1 19.2 1.0
OE2 B:GLU408 2.1 24.2 1.0
NE2 B:HIS354 2.4 17.6 1.0
OE2 B:GLU384 2.6 22.4 1.0
CG B:ASP271 2.9 17.4 1.0
MN B:MN510 2.9 28.9 0.5
OE1 B:GLU384 3.0 25.8 1.0
CD B:GLU408 3.0 18.0 1.0
OD1 B:ASP271 3.1 16.9 1.0
CD B:GLU384 3.1 23.1 1.0
CE1 B:HIS354 3.2 16.3 1.0
OE1 B:GLU408 3.3 20.4 1.0
CD2 B:HIS354 3.4 19.3 1.0
MN B:MN512 3.7 34.0 1.0
OG1 B:THR382 3.9 19.1 1.0
CG2 B:THR382 4.0 18.2 1.0
CB B:ASP271 4.2 15.6 1.0
CB B:THR382 4.2 17.4 1.0
ND1 B:HIS354 4.3 17.4 1.0
CG B:GLU408 4.4 15.0 1.0
CG B:HIS354 4.5 16.4 1.0
CG B:GLU384 4.5 21.5 1.0
N B:PRO506 4.5 47.1 1.0
CA B:PRO506 4.6 43.8 1.0
NE2 B:HIS361 4.8 23.2 1.0
CG2 B:VAL360 5.0 21.1 0.5

Manganese binding site 6 out of 12 in 5wze

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Manganese binding site 6 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn512

b:34.0
occ:1.00
 O B:HOH801 2.0 28.9 1.0
MN B:MN510 3.1 28.9 0.5
MN B:MN511 3.7 28.9 1.0
CD B:PRO506 3.8 37.9 1.0
N B:PRO506 3.8 47.1 1.0
OD2 B:ASP260 4.0 15.6 1.0
NE2 B:HIS361 4.0 23.2 1.0
OD2 B:ASP271 4.0 19.2 1.0
OD1 B:ASP271 4.2 16.9 1.0
OD1 B:ASP260 4.3 16.2 1.0
CE2 B:TYR229 4.4 16.4 1.0
CG B:ASP260 4.4 16.4 1.0
CG B:ASP271 4.5 17.4 1.0
NE2 B:HIS243 4.5 42.1 1.0
CD2 B:TYR229 4.5 16.4 1.0
CE1 B:HIS361 4.6 26.4 1.0
CZ B:TYR229 4.6 17.7 1.0
NE2 B:HIS354 4.7 17.6 1.0
CG B:TYR229 4.9 18.9 1.0
CG2 B:VAL360 4.9 21.1 0.5
CA B:PRO506 4.9 43.8 1.0
CE1 B:TYR229 5.0 16.9 1.0
CD2 B:HIS361 5.0 18.1 1.0
CG1 B:VAL360 5.0 21.1 0.5

Manganese binding site 7 out of 12 in 5wze

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Manganese binding site 7 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn507

b:37.8
occ:1.00
 O C:HOH717 2.3 31.6 1.0
MN C:MN508 3.4 28.9 0.5
MN C:MN509 3.8 28.9 1.0
NE2 C:HIS361 3.8 21.6 1.0
OD2 C:ASP271 4.0 25.2 1.0
OD2 C:ASP260 4.0 19.4 1.0
N C:PRO504 4.2 50.9 1.0
OD1 C:ASP271 4.2 20.4 1.0
OD1 C:ASP260 4.4 15.2 1.0
CD C:PRO504 4.4 38.2 1.0
CE2 C:TYR229 4.4 18.9 1.0
CE1 C:HIS361 4.5 24.6 1.0
CG C:ASP260 4.5 18.1 1.0
CG C:ASP271 4.5 19.6 1.0
CD2 C:TYR229 4.6 18.5 1.0
CZ C:TYR229 4.6 19.6 1.0
NE2 C:HIS243 4.8 58.2 1.0
CG C:TYR229 4.8 19.5 1.0
CD2 C:HIS361 4.8 19.2 1.0
CE1 C:TYR229 4.9 21.0 1.0
NE2 C:HIS354 4.9 17.8 1.0
CD1 C:TYR229 5.0 19.1 1.0

Manganese binding site 8 out of 12 in 5wze

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Manganese binding site 8 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn508

b:28.9
occ:0.50
 OD1 C:ASP271 1.9 20.4 1.0
OE1 C:GLU408 2.0 20.7 1.0
OD1 C:ASP260 2.2 15.2 1.0
O C:HOH717 2.4 31.6 1.0
OD2 C:ASP260 2.6 19.4 1.0
CG C:ASP260 2.7 18.1 1.0
CG C:ASP271 2.9 19.6 1.0
CD C:GLU408 2.9 20.8 1.0
MN C:MN509 3.0 28.9 1.0
OE2 C:GLU408 3.2 22.9 1.0
OD2 C:ASP271 3.2 25.2 1.0
MN C:MN507 3.4 37.8 1.0
OG1 C:THR273 3.6 19.7 1.0
OH C:TYR229 3.6 16.1 1.0
OE1 C:GLU384 4.0 26.8 1.0
CZ C:TYR229 4.1 19.6 1.0
CB C:ASP271 4.2 17.3 1.0
CG C:GLU408 4.2 18.9 1.0
CB C:ASP260 4.3 17.1 1.0
C C:ASP271 4.5 16.6 1.0
N C:ILE272 4.6 16.8 1.0
CE2 C:TYR229 4.6 18.9 1.0
CA C:ASP271 4.6 16.9 1.0
CD C:GLU384 4.7 22.8 1.0
O C:ILE272 4.7 16.1 1.0
C C:ILE272 4.7 14.4 1.0
O C:ASP271 4.8 15.5 1.0
CB C:GLU408 4.8 15.8 1.0
CE1 C:TYR229 4.8 21.0 1.0
OE2 C:GLU384 4.9 27.1 1.0
CA C:ASP260 4.9 15.6 1.0
CB C:THR273 4.9 16.3 1.0
N C:THR273 5.0 15.1 1.0

Manganese binding site 9 out of 12 in 5wze

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Manganese binding site 9 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn509

b:28.9
occ:1.00
 OE2 C:GLU408 2.3 22.9 1.0
OD2 C:ASP271 2.3 25.2 1.0
O C:HOH717 2.4 31.6 1.0
NE2 C:HIS354 2.4 17.8 1.0
OE2 C:GLU384 2.4 27.1 1.0
OE1 C:GLU384 2.9 26.8 1.0
CD C:GLU384 3.0 22.8 1.0
MN C:MN508 3.0 28.9 0.5
CG C:ASP271 3.1 19.6 1.0
CD C:GLU408 3.1 20.8 1.0
CE1 C:HIS354 3.3 16.5 1.0
OE1 C:GLU408 3.3 20.7 1.0
OD1 C:ASP271 3.3 20.4 1.0
CD2 C:HIS354 3.4 16.2 1.0
MN C:MN507 3.8 37.8 1.0
OG1 C:THR382 4.0 16.1 1.0
CG2 C:THR382 4.1 17.5 1.0
CB C:THR382 4.3 16.3 1.0
CB C:ASP271 4.3 17.3 1.0
CG C:GLU384 4.4 21.1 1.0
ND1 C:HIS354 4.4 17.8 1.0
CG C:HIS354 4.5 16.2 1.0
CG C:GLU408 4.5 18.9 1.0
CA C:PRO504 4.6 37.9 1.0
N C:PRO504 4.7 50.9 1.0
NE2 C:HIS361 4.8 21.6 1.0
OD2 C:ASP260 4.9 19.4 1.0
CB C:GLU384 4.9 16.8 1.0

Manganese binding site 10 out of 12 in 5wze

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Manganese binding site 10 out of 12 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:37.3
occ:1.00
 O D:HOH823 2.1 28.9 1.0
MN D:MN509 3.2 28.9 0.5
MN D:MN508 3.8 28.9 1.0
OD2 D:ASP260 3.8 16.3 1.0
CE1 D:HIS361 3.9 23.2 1.0
OD2 D:ASP271 4.2 21.2 1.0
NE2 D:HIS361 4.3 20.4 1.0
OD1 D:ASP271 4.3 19.6 1.0
OD1 D:ASP260 4.4 17.0 1.0
CE1 D:HIS243 4.4 38.7 1.0
CG D:ASP260 4.4 15.1 1.0
CE1 D:TYR229 4.5 16.1 1.0
CD1 D:TYR229 4.6 17.3 1.0
CZ D:TYR229 4.6 17.8 1.0
CG D:ASP271 4.6 18.1 1.0
O D:PRO510 4.7 53.9 1.0
NE2 D:HIS243 4.7 45.3 1.0
CG D:TYR229 4.8 16.5 1.0
CE2 D:TYR229 4.8 17.5 1.0
CD2 D:TYR229 4.9 16.1 1.0
ND1 D:HIS361 4.9 20.3 1.0
NE2 D:HIS354 5.0 22.7 1.0

Reference:

C.T.Peng, L.Liu, C.C.Li, L.H.He, T.Li, Y.L.Shen, C.Gao, N.Y.Wang, Y.Xia, Y.B.Zhu, Y.J.Song, Q.Lei, L.T.Yu, R.Bao. Structure-Function Relationship of Aminopeptidase P From Pseudomonas Aeruginosa. Front Microbiol V. 8 2385 2017.
ISSN: ESSN 1664-302X
PubMed: 29259588
DOI: 10.3389/FMICB.2017.02385
Page generated: Tue Dec 15 04:48:40 2020

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