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Manganese in PDB 3mr1: Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii

Enzymatic activity of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii

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

Protein crystallography data

The structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii, PDB code: 3mr1 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) 42.40 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.480, 114.850, 115.800, 90.00, 92.66, 90.00
R / Rfree (%) 17.1 / 21.2

Other elements in 3mr1:

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

Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii (pdb code 3mr1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii, PDB code: 3mr1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3mr1

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Manganese binding site 1 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn249

b:8.2
occ:1.00
O1 A:PO4252 2.1 10.1 1.0
OD2 A:ASP105 2.1 11.1 1.0
OE2 A:GLU233 2.2 4.8 1.0
NE2 A:HIS168 2.2 6.7 1.0
OE1 A:GLU201 2.2 14.1 1.0
O4 A:PO4252 2.7 19.7 1.0
P A:PO4252 2.9 16.0 1.0
CG A:ASP105 3.1 12.1 1.0
CD A:GLU233 3.2 4.8 1.0
CE1 A:HIS168 3.2 7.8 1.0
CD A:GLU201 3.2 12.0 1.0
CD2 A:HIS168 3.2 7.9 1.0
OD1 A:ASP105 3.4 9.8 1.0
MN A:MN250 3.5 7.8 1.0
OE1 A:GLU233 3.5 4.1 1.0
OE2 A:GLU201 3.5 13.5 1.0
O2 A:PO4252 3.7 23.3 1.0
OG1 A:THR199 3.8 5.9 1.0
O A:HOH744 4.1 40.6 1.0
CG2 A:THR199 4.1 7.1 1.0
O3 A:PO4252 4.2 19.2 1.0
CB A:THR199 4.3 8.5 1.0
ND1 A:HIS168 4.3 6.6 1.0
CG A:HIS168 4.3 7.2 1.0
CB A:ASP105 4.3 9.4 1.0
CG A:GLU201 4.5 8.3 1.0
O A:HOH728 4.5 6.5 1.0
CG A:GLU233 4.5 5.7 1.0
NE2 A:HIS175 4.5 12.7 1.0
CE1 A:PHE174 4.8 7.0 1.0
CD2 A:HIS175 4.9 11.8 1.0

Manganese binding site 2 out of 8 in 3mr1

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Manganese binding site 2 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn250

b:7.8
occ:1.00
O1 A:PO4252 2.1 10.1 1.0
OD1 A:ASP105 2.1 9.8 1.0
O A:HOH728 2.1 6.5 1.0
OD1 A:ASP94 2.2 11.4 1.0
OE1 A:GLU233 2.2 4.1 1.0
OD2 A:ASP94 2.5 12.8 1.0
CG A:ASP94 2.7 8.7 1.0
CG A:ASP105 3.1 12.1 1.0
CD A:GLU233 3.2 4.8 1.0
OD2 A:ASP105 3.4 11.1 1.0
P A:PO4252 3.4 16.0 1.0
OE2 A:GLU233 3.4 4.8 1.0
MN A:MN249 3.5 8.2 1.0
O3 A:PO4252 3.7 19.2 1.0
O A:HOH253 3.9 8.5 1.0
OG1 A:THR96 3.9 9.2 1.0
CB A:ASP94 4.2 6.4 1.0
O A:HOH525 4.2 18.8 1.0
O2 A:PO4252 4.2 23.3 1.0
O A:HOH760 4.3 34.1 1.0
O A:HOH1037 4.4 35.6 1.0
O A:VAL95 4.4 7.7 1.0
O4 A:PO4252 4.4 19.7 1.0
N A:THR106 4.5 7.1 1.0
CB A:ASP105 4.5 9.4 1.0
CG A:GLU233 4.5 5.7 1.0
O A:THR106 4.7 6.7 1.0
C A:ASP105 4.8 7.8 1.0
OE2 A:GLU201 4.8 13.5 1.0
C A:THR106 4.8 5.9 1.0
CA A:ASP105 4.9 8.9 1.0
CA A:ASP94 4.9 7.8 1.0
CB A:GLU233 4.9 5.9 1.0
OE1 A:GLU201 4.9 14.1 1.0
C A:ASP94 5.0 8.5 1.0
N A:VAL95 5.0 8.7 1.0

Manganese binding site 3 out of 8 in 3mr1

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Manganese binding site 3 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn249

b:8.6
occ:1.00
O2 B:PO4252 2.1 14.0 1.0
OE2 B:GLU233 2.2 8.1 1.0
OE1 B:GLU201 2.2 12.7 1.0
NE2 B:HIS168 2.2 8.2 1.0
OD2 B:ASP105 2.3 9.2 1.0
O3 B:PO4252 2.6 19.6 1.0
P B:PO4252 2.9 19.6 1.0
CD B:GLU233 3.1 7.7 1.0
CD2 B:HIS168 3.2 8.8 1.0
CD B:GLU201 3.2 14.0 1.0
CG B:ASP105 3.2 8.9 1.0
CE1 B:HIS168 3.2 7.9 1.0
OE1 B:GLU233 3.4 6.2 1.0
MN B:MN250 3.4 9.4 1.0
OD1 B:ASP105 3.5 9.0 1.0
OE2 B:GLU201 3.6 17.3 1.0
O1 B:PO4252 3.7 22.2 1.0
OG1 B:THR199 3.9 9.9 1.0
CG2 B:THR199 4.1 7.6 1.0
O4 B:PO4252 4.2 22.7 1.0
CB B:THR199 4.3 8.6 1.0
ND1 B:HIS168 4.3 7.3 1.0
CG B:HIS168 4.3 8.9 1.0
CG B:GLU201 4.4 11.5 1.0
CG B:GLU233 4.4 7.8 1.0
CB B:ASP105 4.5 8.3 1.0
NE2 B:HIS175 4.5 16.9 1.0
O B:HOH786 4.5 5.0 1.0
CD2 B:HIS175 4.8 15.8 1.0
CE1 B:PHE174 4.8 13.8 1.0

Manganese binding site 4 out of 8 in 3mr1

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Manganese binding site 4 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn250

b:9.4
occ:1.00
O2 B:PO4252 2.0 14.0 1.0
OD1 B:ASP105 2.2 9.0 1.0
OE1 B:GLU233 2.2 6.2 1.0
OD1 B:ASP94 2.2 11.6 1.0
O B:HOH786 2.3 5.0 1.0
OD2 B:ASP94 2.5 11.0 1.0
CG B:ASP94 2.7 10.9 1.0
CD B:GLU233 3.1 7.7 1.0
CG B:ASP105 3.1 8.9 1.0
P B:PO4252 3.3 19.6 1.0
OD2 B:ASP105 3.4 9.2 1.0
OE2 B:GLU233 3.4 8.1 1.0
MN B:MN249 3.4 8.6 1.0
O4 B:PO4252 3.7 22.7 1.0
O B:HOH259 3.9 12.4 1.0
OG1 B:THR96 3.9 8.9 1.0
O1 B:PO4252 4.2 22.2 1.0
CB B:ASP94 4.2 8.4 1.0
O B:HOH552 4.3 20.4 1.0
O B:HOH799 4.3 30.4 1.0
O3 B:PO4252 4.3 19.6 1.0
O B:VAL95 4.4 9.3 1.0
CG B:GLU233 4.4 7.8 1.0
N B:THR106 4.5 7.6 1.0
CB B:ASP105 4.5 8.3 1.0
O B:HOH787 4.6 25.1 1.0
O B:THR106 4.7 7.5 1.0
C B:ASP105 4.8 8.2 1.0
OE1 B:GLU201 4.8 12.7 1.0
OE2 B:GLU201 4.8 17.3 1.0
CB B:GLU233 4.9 7.2 1.0
N B:VAL95 4.9 8.7 1.0
C B:THR106 4.9 7.3 1.0
CA B:ASP105 4.9 8.3 1.0
CA B:ASP94 5.0 8.9 1.0

Manganese binding site 5 out of 8 in 3mr1

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Manganese binding site 5 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn249

b:10.0
occ:1.00
OE2 C:GLU233 2.1 7.7 1.0
OD2 C:ASP105 2.1 8.5 1.0
O1 C:PO4252 2.2 16.4 1.0
NE2 C:HIS168 2.2 8.3 1.0
OE1 C:GLU201 2.4 12.5 1.0
O4 C:PO4252 2.6 22.7 1.0
P C:PO4252 2.9 25.0 1.0
CG C:ASP105 3.1 7.9 1.0
CD C:GLU233 3.1 7.6 1.0
CE1 C:HIS168 3.1 7.3 1.0
CD2 C:HIS168 3.2 7.6 1.0
CD C:GLU201 3.3 12.1 1.0
OD1 C:ASP105 3.4 7.1 1.0
MN C:MN250 3.4 9.7 1.0
OE1 C:GLU233 3.4 7.2 1.0
OE2 C:GLU201 3.6 13.9 1.0
O2 C:PO4252 3.7 27.9 1.0
OG1 C:THR199 3.8 9.4 1.0
CG2 C:THR199 4.0 7.0 1.0
O3 C:PO4252 4.1 26.4 1.0
CB C:THR199 4.2 9.0 1.0
ND1 C:HIS168 4.3 7.9 1.0
CG C:HIS168 4.3 8.7 1.0
CB C:ASP105 4.3 9.7 1.0
CG C:GLU233 4.5 6.4 1.0
O C:HOH712 4.5 8.2 1.0
CG C:GLU201 4.5 8.6 1.0
NE2 C:HIS175 4.7 17.9 1.0
CE1 C:PHE174 4.8 9.9 1.0
CD2 C:HIS175 4.8 17.5 1.0
O C:HOH626 4.9 20.3 1.0

Manganese binding site 6 out of 8 in 3mr1

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Manganese binding site 6 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn250

b:9.7
occ:1.00
O1 C:PO4252 2.0 16.4 1.0
OD1 C:ASP105 2.1 7.1 1.0
OD1 C:ASP94 2.1 11.2 1.0
OE1 C:GLU233 2.2 7.2 1.0
O C:HOH712 2.2 8.2 1.0
OD2 C:ASP94 2.7 12.5 1.0
CG C:ASP94 2.8 11.1 1.0
CD C:GLU233 3.1 7.6 1.0
CG C:ASP105 3.1 7.9 1.0
P C:PO4252 3.3 25.0 1.0
OE2 C:GLU233 3.4 7.7 1.0
OD2 C:ASP105 3.4 8.5 1.0
MN C:MN249 3.4 10.0 1.0
O3 C:PO4252 3.6 26.4 1.0
O C:HOH261 3.9 11.8 1.0
OG1 C:THR96 3.9 9.4 1.0
O C:HOH626 4.0 20.3 1.0
O4 C:PO4252 4.2 22.7 1.0
O2 C:PO4252 4.2 27.9 1.0
CB C:ASP94 4.3 8.1 1.0
O C:HOH540 4.3 21.6 1.0
CG C:GLU233 4.4 6.4 1.0
O C:VAL95 4.4 8.3 1.0
CB C:ASP105 4.5 9.7 1.0
N C:THR106 4.5 8.8 1.0
C C:ASP105 4.7 9.5 1.0
O C:THR106 4.7 8.6 1.0
OE2 C:GLU201 4.7 13.9 1.0
CA C:ASP105 4.8 9.4 1.0
N C:VAL95 4.9 8.6 1.0
CB C:GLU233 4.9 7.7 1.0
C C:THR106 4.9 9.0 1.0
CA C:ASP94 5.0 8.1 1.0
C C:ASP94 5.0 8.6 1.0
C C:VAL95 5.0 8.5 1.0

Manganese binding site 7 out of 8 in 3mr1

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Manganese binding site 7 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn249

b:9.9
occ:1.00
O3 D:PO4252 2.1 18.4 1.0
OE2 D:GLU233 2.1 8.4 1.0
OE1 D:GLU201 2.1 16.3 1.0
NE2 D:HIS168 2.2 10.0 1.0
OD2 D:ASP105 2.2 8.3 1.0
O2 D:PO4252 2.7 25.4 1.0
P D:PO4252 3.0 22.0 1.0
CD D:GLU233 3.1 8.6 1.0
CG D:ASP105 3.1 10.6 1.0
CD D:GLU201 3.1 15.5 1.0
CD2 D:HIS168 3.1 10.8 1.0
CE1 D:HIS168 3.1 10.4 1.0
OE1 D:GLU233 3.4 8.1 1.0
MN D:MN250 3.5 9.7 1.0
OE2 D:GLU201 3.5 17.6 1.0
OD1 D:ASP105 3.5 9.7 1.0
OG1 D:THR199 3.8 7.9 1.0
O1 D:PO4252 3.9 26.2 1.0
CG2 D:THR199 4.1 9.5 1.0
O4 D:PO4252 4.1 26.9 1.0
ND1 D:HIS168 4.2 12.4 1.0
CG D:HIS168 4.3 10.9 1.0
CB D:THR199 4.3 9.9 1.0
CB D:ASP105 4.3 7.6 1.0
CG D:GLU201 4.4 12.8 1.0
CG D:GLU233 4.4 6.4 1.0
O D:HOH929 4.6 7.4 1.0
NE2 D:HIS175 4.6 15.6 1.0
CE1 D:PHE174 4.8 11.7 1.0
CD2 D:HIS175 4.9 16.1 1.0

Manganese binding site 8 out of 8 in 3mr1

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Manganese binding site 8 out of 8 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn250

b:9.7
occ:1.00
OD1 D:ASP105 2.1 9.7 1.0
O3 D:PO4252 2.1 18.4 1.0
OE1 D:GLU233 2.2 8.1 1.0
OD1 D:ASP94 2.2 7.6 1.0
O D:HOH929 2.2 7.4 1.0
OD2 D:ASP94 2.4 12.0 1.0
CG D:ASP94 2.7 8.8 1.0
CG D:ASP105 3.1 10.6 1.0
CD D:GLU233 3.1 8.6 1.0
P D:PO4252 3.3 22.0 1.0
OD2 D:ASP105 3.4 8.3 1.0
OE2 D:GLU233 3.4 8.4 1.0
O1 D:PO4252 3.5 26.2 1.0
MN D:MN249 3.5 9.9 1.0
O D:HOH255 3.8 10.9 1.0
OG1 D:THR96 3.9 8.7 1.0
O4 D:PO4252 4.0 26.9 1.0
CB D:ASP94 4.2 8.3 1.0
O D:HOH549 4.2 18.5 1.0
O D:HOH976 4.4 27.5 1.0
O D:VAL95 4.4 8.7 1.0
O2 D:PO4252 4.5 25.4 1.0
CG D:GLU233 4.5 6.4 1.0
N D:THR106 4.5 7.4 1.0
CB D:ASP105 4.5 7.6 1.0
O D:THR106 4.7 7.0 1.0
OE2 D:GLU201 4.7 17.6 1.0
C D:ASP105 4.8 7.4 1.0
CA D:ASP105 4.9 7.5 1.0
OE1 D:GLU201 4.9 16.3 1.0
C D:THR106 4.9 7.1 1.0
N D:VAL95 4.9 9.8 1.0
CB D:GLU233 4.9 7.6 1.0
CA D:ASP94 4.9 9.0 1.0
C D:VAL95 5.0 9.9 1.0
C D:ASP94 5.0 9.9 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: Tue Dec 15 04:12:37 2020

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