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Manganese in PDB 3mx6: Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine

Enzymatic activity of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine

All present enzymatic activity of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine, PDB code: 3mx6 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.370, 67.550, 80.890, 90.00, 97.43, 90.00
R / Rfree (%) 16.8 / 20.7

Other elements in 3mx6:

The structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine (pdb code 3mx6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine, PDB code: 3mx6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3mx6

Go back to Manganese Binding Sites List in 3mx6
Manganese binding site 1 out of 4 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn259

b:7.2
occ:1.00
 NE2 A:HIS168 2.1 3.1 1.0
OE2 A:GLU233 2.2 7.2 1.0
OE1 A:GLU201 2.2 6.9 1.0
O A:MET262 2.2 17.3 1.0
OD2 A:ASP105 2.3 8.6 1.0
OXT A:MET262 2.5 19.0 1.0
C A:MET262 2.7 20.8 1.0
CD2 A:HIS168 3.1 7.2 1.0
CD A:GLU201 3.1 11.3 1.0
CD A:GLU233 3.1 8.8 1.0
CE1 A:HIS168 3.2 4.7 1.0
CG A:ASP105 3.2 7.9 1.0
OE1 A:GLU233 3.4 8.8 1.0
OE2 A:GLU201 3.4 14.1 1.0
MN A:MN260 3.5 6.6 1.0
OD1 A:ASP105 3.6 6.6 1.0
OG1 A:THR199 3.8 5.2 1.0
CG2 A:THR199 4.0 5.8 1.0
CA A:MET262 4.1 22.8 1.0
O A:HOH623 4.2 38.4 1.0
CB A:THR199 4.2 5.6 1.0
CG A:HIS168 4.2 4.7 1.0
ND1 A:HIS168 4.2 5.6 1.0
CG A:GLU201 4.4 10.3 1.0
CB A:ASP105 4.4 7.3 1.0
O A:HOH532 4.5 9.4 1.0
CG A:GLU233 4.5 6.5 1.0
NE2 A:HIS175 4.6 11.1 1.0
N A:MET262 4.8 24.7 1.0
CE1 A:PHE174 4.9 7.7 1.0
CD2 A:HIS175 4.9 10.0 1.0
CB A:MET262 4.9 24.3 1.0
CB A:GLU201 5.0 7.7 1.0

Manganese binding site 2 out of 4 in 3mx6

Go back to Manganese Binding Sites List in 3mx6
Manganese binding site 2 out of 4 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn260

b:6.6
occ:1.00
 OD1 A:ASP105 2.1 6.6 1.0
OD1 A:ASP94 2.1 9.0 1.0
O A:MET262 2.1 17.3 1.0
OE1 A:GLU233 2.3 8.8 1.0
O A:HOH532 2.3 9.4 1.0
OD2 A:ASP94 2.6 14.2 1.0
CG A:ASP94 2.7 8.3 1.0
CG A:ASP105 3.1 7.9 1.0
CD A:GLU233 3.2 8.8 1.0
C A:MET262 3.2 20.8 1.0
OD2 A:ASP105 3.3 8.6 1.0
OE2 A:GLU233 3.5 7.2 1.0
MN A:MN259 3.5 7.2 1.0
N A:MET262 3.7 24.7 1.0
O A:HOH263 3.8 10.5 1.0
OG1 A:THR96 3.9 7.0 1.0
CA A:MET262 4.0 22.8 1.0
OXT A:MET262 4.1 19.0 1.0
CB A:ASP94 4.2 7.9 1.0
O A:HOH463 4.3 28.8 1.0
O A:HOH535 4.3 13.3 1.0
O A:VAL95 4.4 8.0 1.0
CB A:ASP105 4.4 7.3 1.0
CG A:GLU233 4.5 6.5 1.0
N A:THR106 4.5 5.8 1.0
CB A:MET262 4.6 24.3 1.0
C A:ASP105 4.8 6.5 1.0
O A:THR106 4.8 5.3 1.0
CA A:ASP105 4.8 6.5 1.0
OE2 A:GLU201 4.9 14.1 1.0
CB A:GLU233 4.9 4.9 1.0
C A:THR106 4.9 5.8 1.0
CA A:ASP94 4.9 6.6 1.0
N A:VAL95 4.9 6.3 1.0
C A:ASP94 4.9 6.7 1.0
OE1 A:GLU201 5.0 6.9 1.0

Manganese binding site 3 out of 4 in 3mx6

Go back to Manganese Binding Sites List in 3mx6
Manganese binding site 3 out of 4 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn259

b:6.8
occ:1.00
 NE2 B:HIS168 2.1 3.2 1.0
OE2 B:GLU233 2.1 6.8 1.0
O B:MET262 2.2 17.9 1.0
OE1 B:GLU201 2.2 7.8 1.0
OD2 B:ASP105 2.3 6.0 1.0
OXT B:MET262 2.4 19.2 1.0
C B:MET262 2.6 20.4 1.0
CD2 B:HIS168 3.1 7.7 1.0
CD B:GLU201 3.1 12.7 1.0
CE1 B:HIS168 3.1 5.8 1.0
CD B:GLU233 3.2 8.1 1.0
CG B:ASP105 3.2 5.0 1.0
OE2 B:GLU201 3.5 14.1 1.0
OE1 B:GLU233 3.5 6.3 1.0
MN B:MN260 3.5 6.0 1.0
OD1 B:ASP105 3.6 5.9 1.0
OG1 B:THR199 3.8 4.1 1.0
CG2 B:THR199 4.0 6.4 1.0
CA B:MET262 4.1 22.4 1.0
O B:HOH625 4.2 37.7 1.0
ND1 B:HIS168 4.2 4.9 1.0
CB B:THR199 4.2 3.6 1.0
CG B:HIS168 4.2 4.8 1.0
CB B:ASP105 4.4 5.2 1.0
CG B:GLU201 4.4 9.0 1.0
CG B:GLU233 4.5 4.9 1.0
O B:HOH496 4.5 10.1 1.0
NE2 B:HIS175 4.6 8.8 1.0
N B:MET262 4.8 24.3 1.0
CE1 B:PHE174 4.9 8.0 1.0
CD2 B:HIS175 4.9 9.9 1.0
CB B:MET262 5.0 23.9 1.0

Manganese binding site 4 out of 4 in 3mx6

Go back to Manganese Binding Sites List in 3mx6
Manganese binding site 4 out of 4 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn260

b:6.0
occ:1.00
 OD1 B:ASP94 2.0 7.2 1.0
OD1 B:ASP105 2.1 5.9 1.0
O B:MET262 2.2 17.9 1.0
OE1 B:GLU233 2.2 6.3 1.0
O B:HOH496 2.3 10.1 1.0
OD2 B:ASP94 2.4 12.5 1.0
CG B:ASP94 2.6 6.2 1.0
CG B:ASP105 3.1 5.0 1.0
CD B:GLU233 3.1 8.1 1.0
C B:MET262 3.2 20.4 1.0
OD2 B:ASP105 3.4 6.0 1.0
OE2 B:GLU233 3.4 6.8 1.0
MN B:MN259 3.5 6.8 1.0
N B:MET262 3.7 24.3 1.0
OG1 B:THR96 3.9 8.2 1.0
O B:HOH282 3.9 11.5 1.0
CA B:MET262 4.0 22.4 1.0
OXT B:MET262 4.1 19.2 1.0
CB B:ASP94 4.1 6.3 1.0
O B:HOH392 4.3 11.2 1.0
O B:HOH346 4.3 23.2 1.0
O B:VAL95 4.4 8.4 1.0
CB B:ASP105 4.4 5.2 1.0
CG B:GLU233 4.5 4.9 1.0
N B:THR106 4.5 5.5 1.0
CB B:MET262 4.6 23.9 1.0
C B:ASP105 4.7 4.7 1.0
O B:THR106 4.8 5.8 1.0
CA B:ASP105 4.8 5.1 1.0
CA B:ASP94 4.9 5.5 1.0
CB B:GLU233 4.9 3.0 1.0
C B:THR106 4.9 5.4 1.0
C B:ASP94 4.9 6.1 1.0
N B:VAL95 4.9 5.5 1.0
OE2 B:GLU201 4.9 14.1 1.0
C B:VAL95 5.0 7.2 1.0
OE1 B:GLU201 5.0 7.8 1.0

Reference:

T.R.Helgren, C.Chen, P.Wangtrakuldee, T.E.Edwards, B.L.Staker, J.Abendroth, B.Sankaran, N.A.Housley, P.J.Myler, J.P.Audia, J.R.Horn, T.J.Hagen. Rickettsia Prowazekii Methionine Aminopeptidase As A Promising Target For the Development of Antibacterial Agents. Bioorg.Med.Chem. V. 25 813 2017.
ISSN: ISSN 0968-0896
PubMed: 28089350
DOI: 10.1016/J.BMC.2016.11.013
Page generated: Sat Oct 5 17:12:24 2024

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