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Manganese in PDB 3h8g: Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida

Enzymatic activity of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida

All present enzymatic activity of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida:
3.4.11.1;

Protein crystallography data

The structure of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8g was solved by A.Kale, B.W.Dijkstra, T.Sonke, A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.976, 95.989, 95.998, 100.82, 107.78, 93.23
R / Rfree (%) 14.9 / 17.3

Other elements in 3h8g:

The structure of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida also contains other interesting chemical elements:

Potassium (K) 6 atoms
Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida (pdb code 3h8g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3h8g

Go back to Manganese Binding Sites List in 3h8g
Manganese binding site 1 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:5.3
occ:1.00
 OD1 A:ASP349 2.1 5.2 1.0
OE1 A:GLU351 2.1 5.4 1.0
O2 A:BES505 2.2 4.8 1.0
OD2 A:ASP272 2.2 5.1 1.0
O A:ASP349 2.2 5.3 1.0
O3 A:BES505 2.4 7.9 1.0
C3 A:BES505 3.0 8.4 1.0
CG A:ASP349 3.0 4.9 1.0
CG A:ASP272 3.0 4.5 1.0
C2 A:BES505 3.1 6.0 1.0
C A:ASP349 3.1 3.2 1.0
CD A:GLU351 3.1 3.2 1.0
OD1 A:ASP272 3.2 4.8 1.0
ZN A:ZN501 3.3 5.7 0.8
OE2 A:GLU351 3.4 5.2 1.0
CA A:ASP349 3.5 4.7 1.0
C1 A:BES505 3.8 7.0 1.0
CB A:ASP349 3.8 4.9 1.0
NZ A:LYS279 3.8 8.0 1.0
OD2 A:ASP349 3.9 6.8 1.0
O1 A:BCT504 4.0 6.6 1.0
CE A:LYS279 4.1 7.0 1.0
N1 A:BES505 4.1 10.2 1.0
N2 A:BES505 4.2 7.0 1.0
N A:ALA350 4.3 4.2 1.0
N A:GLU351 4.3 4.4 1.0
CB A:ASP272 4.4 5.2 1.0
CG A:GLU351 4.5 4.4 1.0
ND2 A:ASN322 4.7 5.4 1.0
CA A:ALA350 4.7 4.3 1.0
C A:BCT504 4.7 7.1 1.0
O2 A:BCT504 4.8 8.2 1.0
C4 A:BES505 4.8 13.1 1.0
CA A:GLY274 4.8 5.0 1.0
OD2 A:ASP290 4.9 5.6 1.0
N A:ASP349 4.9 3.6 1.0
CB A:GLU351 4.9 5.5 1.0

Manganese binding site 2 out of 6 in 3h8g

Go back to Manganese Binding Sites List in 3h8g
Manganese binding site 2 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:6.1
occ:1.00
 OD1 B:ASP349 2.1 6.1 1.0
OD2 B:ASP272 2.1 5.4 1.0
O2 B:BES505 2.2 5.2 1.0
OE1 B:GLU351 2.2 5.4 1.0
O B:ASP349 2.2 5.8 1.0
O3 B:BES505 2.4 8.1 1.0
C3 B:BES505 3.0 8.6 1.0
CG B:ASP272 3.0 4.8 1.0
CG B:ASP349 3.0 6.2 1.0
C2 B:BES505 3.1 7.3 1.0
CD B:GLU351 3.1 5.8 1.0
C B:ASP349 3.1 5.3 1.0
OD1 B:ASP272 3.2 5.0 1.0
ZN B:ZN501 3.3 6.3 0.8
OE2 B:GLU351 3.4 5.8 1.0
CA B:ASP349 3.5 4.4 1.0
C1 B:BES505 3.8 7.8 1.0
CB B:ASP349 3.8 5.2 1.0
NZ B:LYS279 3.9 8.4 1.0
OD2 B:ASP349 3.9 7.0 1.0
O2 B:BCT504 4.0 7.7 1.0
CE B:LYS279 4.1 8.5 1.0
N1 B:BES505 4.1 10.1 1.0
N2 B:BES505 4.2 7.4 1.0
N B:ALA350 4.3 4.8 1.0
N B:GLU351 4.3 4.8 1.0
CB B:ASP272 4.4 6.8 1.0
CG B:GLU351 4.5 5.5 1.0
O1 B:BCT504 4.7 8.3 1.0
CA B:ALA350 4.7 4.6 1.0
C B:BCT504 4.7 7.6 1.0
ND2 B:ASN322 4.7 6.5 1.0
C4 B:BES505 4.8 12.9 1.0
CA B:GLY274 4.9 5.8 1.0
OD2 B:ASP290 4.9 6.0 1.0
CB B:GLU351 5.0 5.2 1.0
N B:ASP349 5.0 4.3 1.0

Manganese binding site 3 out of 6 in 3h8g

Go back to Manganese Binding Sites List in 3h8g
Manganese binding site 3 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:5.1
occ:1.00
 OD1 C:ASP349 2.1 4.7 1.0
OE1 C:GLU351 2.1 4.2 1.0
OD2 C:ASP272 2.1 4.7 1.0
O C:ASP349 2.2 4.5 1.0
O2 C:BES505 2.2 6.1 1.0
O3 C:BES505 2.5 7.6 1.0
C3 C:BES505 3.0 7.8 1.0
CG C:ASP272 3.0 4.0 1.0
CG C:ASP349 3.0 4.7 1.0
C C:ASP349 3.1 4.3 1.0
CD C:GLU351 3.1 5.1 1.0
C2 C:BES505 3.1 6.2 1.0
OD1 C:ASP272 3.2 5.1 1.0
ZN C:ZN501 3.3 6.6 0.8
OE2 C:GLU351 3.4 6.1 1.0
CA C:ASP349 3.5 4.2 1.0
CB C:ASP349 3.8 4.7 1.0
NZ C:LYS279 3.8 7.3 1.0
C1 C:BES505 3.8 6.0 1.0
OD2 C:ASP349 3.9 6.2 1.0
O1 C:BCT504 4.0 7.3 1.0
CE C:LYS279 4.1 7.3 1.0
N1 C:BES505 4.1 9.7 1.0
N2 C:BES505 4.2 8.1 1.0
N C:ALA350 4.3 4.7 1.0
N C:GLU351 4.3 4.0 1.0
CB C:ASP272 4.5 5.1 1.0
CG C:GLU351 4.5 5.1 1.0
ND2 C:ASN322 4.7 5.7 1.0
CA C:ALA350 4.7 4.2 1.0
O3 C:BCT504 4.8 7.2 1.0
C C:BCT504 4.8 6.8 1.0
C4 C:BES505 4.8 12.3 1.0
CA C:GLY274 4.9 6.1 1.0
OD2 C:ASP290 4.9 6.0 1.0
N C:ASP349 4.9 4.5 1.0
CB C:GLU351 5.0 4.0 1.0

Manganese binding site 4 out of 6 in 3h8g

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Manganese binding site 4 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:5.6
occ:1.00
 OD1 D:ASP349 2.1 5.3 1.0
OE1 D:GLU351 2.1 5.3 1.0
OD2 D:ASP272 2.2 5.0 1.0
O2 D:BES505 2.2 6.0 1.0
O D:ASP349 2.2 5.8 1.0
O3 D:BES505 2.5 8.0 1.0
C3 D:BES505 3.0 9.1 1.0
C2 D:BES505 3.1 6.9 1.0
CG D:ASP272 3.1 5.9 1.0
CG D:ASP349 3.1 5.5 1.0
CD D:GLU351 3.1 5.2 1.0
C D:ASP349 3.1 4.5 1.0
OD1 D:ASP272 3.3 5.9 1.0
ZN D:ZN501 3.3 6.9 0.8
OE2 D:GLU351 3.4 6.1 1.0
CA D:ASP349 3.5 5.2 1.0
C1 D:BES505 3.8 7.2 1.0
NZ D:LYS279 3.8 7.5 1.0
CB D:ASP349 3.8 5.3 1.0
OD2 D:ASP349 3.9 7.0 1.0
O3 D:BCT504 4.0 6.8 1.0
CE D:LYS279 4.1 5.7 1.0
N1 D:BES505 4.1 9.3 1.0
N2 D:BES505 4.2 7.4 1.0
N D:ALA350 4.3 5.0 1.0
N D:GLU351 4.3 5.5 1.0
CB D:ASP272 4.5 6.5 1.0
CG D:GLU351 4.5 5.5 1.0
CA D:ALA350 4.7 5.2 1.0
ND2 D:ASN322 4.7 6.5 1.0
O1 D:BCT504 4.8 8.4 1.0
C D:BCT504 4.8 7.1 1.0
C4 D:BES505 4.8 13.4 1.0
CA D:GLY274 4.9 7.0 1.0
OD2 D:ASP290 4.9 6.3 1.0
N D:ASP349 4.9 5.0 1.0
CB D:GLU351 5.0 5.9 1.0

Manganese binding site 5 out of 6 in 3h8g

Go back to Manganese Binding Sites List in 3h8g
Manganese binding site 5 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:5.6
occ:1.00
 OD1 E:ASP349 2.1 6.8 1.0
OE1 E:GLU351 2.1 5.1 1.0
O2 E:BES505 2.1 5.7 1.0
O E:ASP349 2.2 5.1 1.0
OD2 E:ASP272 2.2 5.4 1.0
O3 E:BES505 2.4 7.8 1.0
C3 E:BES505 3.0 7.9 1.0
CG E:ASP272 3.0 6.7 1.0
CG E:ASP349 3.1 5.5 1.0
C2 E:BES505 3.1 6.4 1.0
C E:ASP349 3.1 3.9 1.0
CD E:GLU351 3.1 3.1 1.0
OD1 E:ASP272 3.2 5.6 1.0
ZN E:ZN501 3.3 6.8 0.8
OE2 E:GLU351 3.4 5.1 1.0
CA E:ASP349 3.5 4.4 1.0
C1 E:BES505 3.8 7.6 1.0
NZ E:LYS279 3.8 7.9 1.0
CB E:ASP349 3.8 5.3 1.0
OD2 E:ASP349 3.9 6.1 1.0
O3 E:BCT504 4.0 7.0 1.0
CE E:LYS279 4.1 6.4 1.0
N1 E:BES505 4.1 10.4 1.0
N2 E:BES505 4.2 7.7 1.0
N E:ALA350 4.3 4.0 1.0
N E:GLU351 4.3 4.1 1.0
CB E:ASP272 4.5 5.4 1.0
CG E:GLU351 4.5 5.1 1.0
CA E:ALA350 4.7 5.0 1.0
ND2 E:ASN322 4.7 6.2 1.0
C E:BCT504 4.7 6.8 1.0
O2 E:BCT504 4.7 7.4 1.0
C4 E:BES505 4.8 13.9 1.0
CA E:GLY274 4.9 6.5 1.0
N E:ASP349 4.9 4.2 1.0
OD2 E:ASP290 4.9 5.5 1.0
CB E:GLU351 5.0 5.0 1.0

Manganese binding site 6 out of 6 in 3h8g

Go back to Manganese Binding Sites List in 3h8g
Manganese binding site 6 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Bestatin Complex Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn502

b:5.3
occ:1.00
 O2 F:BES505 2.1 4.7 1.0
OD1 F:ASP349 2.1 5.1 1.0
OE1 F:GLU351 2.1 4.9 1.0
OD2 F:ASP272 2.1 5.2 1.0
O F:ASP349 2.2 4.8 1.0
O3 F:BES505 2.4 6.5 1.0
C3 F:BES505 3.0 7.4 1.0
CG F:ASP272 3.0 6.2 1.0
C2 F:BES505 3.1 5.4 1.0
CG F:ASP349 3.1 4.0 1.0
CD F:GLU351 3.1 3.2 1.0
C F:ASP349 3.1 3.9 1.0
OD1 F:ASP272 3.2 4.3 1.0
ZN F:ZN501 3.3 6.3 0.8
OE2 F:GLU351 3.4 5.1 1.0
CA F:ASP349 3.5 4.1 1.0
C1 F:BES505 3.8 6.9 1.0
NZ F:LYS279 3.8 7.5 1.0
CB F:ASP349 3.8 4.8 1.0
OD2 F:ASP349 3.9 6.9 1.0
O2 F:BCT504 4.0 7.1 1.0
CE F:LYS279 4.1 7.9 1.0
N1 F:BES505 4.1 10.2 1.0
N2 F:BES505 4.2 7.7 1.0
N F:ALA350 4.3 3.8 1.0
N F:GLU351 4.3 4.0 1.0
CG F:GLU351 4.5 4.2 1.0
CB F:ASP272 4.5 5.0 1.0
ND2 F:ASN322 4.7 6.0 1.0
C F:BCT504 4.7 7.8 1.0
CA F:ALA350 4.7 5.7 1.0
O3 F:BCT504 4.7 8.7 1.0
C4 F:BES505 4.8 12.0 1.0
CA F:GLY274 4.9 5.7 1.0
OD2 F:ASP290 4.9 5.4 1.0
N F:ASP349 4.9 4.2 1.0
CB F:GLU351 4.9 5.5 1.0

Reference:

A.Kale, T.Pijning, T.Sonke, B.W.Dijkstra, A.M.Thunnissen. Crystal Structure of the Leucine Aminopeptidase From Pseudomonas Putida Reveals the Molecular Basis For Its Enantioselectivity and Broad Substrate Specificity. J.Mol.Biol. V. 398 703 2010.
ISSN: ISSN 0022-2836
PubMed: 20359484
DOI: 10.1016/J.JMB.2010.03.042
Page generated: Sat Oct 5 16:29:17 2024

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