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Manganese in PDB 1wkm: The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus

Enzymatic activity of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus

All present enzymatic activity of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus:
3.4.11.18;

Protein crystallography data

The structure of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus, PDB code: 1wkm was solved by A.J.Copik, B.P.Nocek, S.B.Jang, S.I.Swierczek, S.Ruebush, L.Meng, V.M.D'souza, J.W.Peters, B.Bennett, R.C.Holz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 2.30
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 112.010, 112.010, 122.960, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 25.2

Manganese Binding Sites:

The binding sites of Manganese atom in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus (pdb code 1wkm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus, PDB code: 1wkm:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1wkm

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Manganese binding site 1 out of 4 in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn296

b:27.6
occ:1.00
 OXT A:MET1298 1.9 25.2 1.0
OD2 A:ASP93 1.9 27.0 1.0
OE2 A:GLU280 2.0 28.4 1.0
OE2 A:GLU187 2.1 25.3 1.0
NE2 A:HIS153 2.1 24.4 1.0
CD A:GLU187 3.0 28.9 1.0
CE1 A:HIS153 3.0 26.0 1.0
C A:MET1298 3.0 27.7 1.0
CD A:GLU280 3.1 29.6 1.0
CG A:ASP93 3.1 27.5 1.0
CD2 A:HIS153 3.1 24.7 1.0
MN A:MN297 3.3 30.2 1.0
OE1 A:GLU280 3.4 28.9 1.0
OE1 A:GLU187 3.4 29.4 1.0
O A:MET1298 3.6 28.1 1.0
OD1 A:ASP93 3.6 28.5 1.0
CB A:ALA185 3.9 22.9 1.0
CG A:GLU187 4.1 28.5 1.0
O A:HOH1314 4.1 40.9 1.0
ND1 A:HIS153 4.2 25.9 1.0
N A:MET1298 4.2 31.3 1.0
CG A:HIS153 4.2 25.5 1.0
CA A:MET1298 4.3 28.4 1.0
CB A:ASP93 4.3 25.0 1.0
CG A:GLU280 4.4 30.4 1.0
CB A:GLU187 4.8 28.9 1.0
OD1 A:ASP82 4.9 31.9 1.0
NE2 A:HIS161 5.0 40.6 1.0

Manganese binding site 2 out of 4 in 1wkm

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Manganese binding site 2 out of 4 in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn297

b:30.2
occ:1.00
 OE1 A:GLU280 2.0 28.9 1.0
OD2 A:ASP82 2.0 30.5 1.0
OD1 A:ASP93 2.0 28.5 1.0
N A:MET1298 2.1 31.3 1.0
OD1 A:ASP82 2.1 31.9 1.0
CG A:ASP82 2.4 31.6 1.0
OXT A:MET1298 2.7 25.2 1.0
CG A:ASP93 2.9 27.5 1.0
CD A:GLU280 3.0 29.6 1.0
OD2 A:ASP93 3.1 27.0 1.0
CA A:MET1298 3.2 28.4 1.0
C A:MET1298 3.3 27.7 1.0
OE2 A:GLU280 3.3 28.4 1.0
MN A:MN296 3.3 27.6 1.0
CB A:ASP82 3.9 30.6 1.0
CZ A:PHE50 4.0 31.2 1.0
OE1 A:GLU187 4.2 29.4 1.0
CG A:GLU280 4.4 30.4 1.0
O A:HOH1306 4.4 39.0 1.0
CB A:ASP93 4.4 25.0 1.0
NE2 A:GLN278 4.4 27.8 1.0
CB A:MET1298 4.4 31.7 1.0
O A:MET1298 4.5 28.1 1.0
CE2 A:PHE50 4.5 29.9 1.0
O A:THR94 4.6 29.2 1.0
OE2 A:GLU187 4.7 25.3 1.0
CD A:GLU187 4.7 28.9 1.0
CA A:ASP82 4.7 31.6 1.0
CE1 A:PHE50 4.7 30.1 1.0
N A:THR94 4.8 28.4 1.0
C A:ASP93 4.8 29.0 1.0
CA A:ASP93 4.9 27.8 1.0
CB A:ALA95 4.9 28.0 1.0
CB A:GLU280 4.9 29.9 1.0
C A:THR94 4.9 28.5 1.0

Manganese binding site 3 out of 4 in 1wkm

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Manganese binding site 3 out of 4 in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn296

b:22.4
occ:1.00
 OD2 B:ASP82 2.0 23.4 1.0
OE1 B:GLU280 2.0 25.2 1.0
OD1 B:ASP93 2.1 21.5 1.0
OD1 B:ASP82 2.1 23.4 1.0
N B:MET2298 2.1 31.5 1.0
CG B:ASP82 2.3 23.0 1.0
OXT B:MET2298 2.7 26.3 1.0
CG B:ASP93 3.0 20.3 1.0
CD B:GLU280 3.0 23.9 1.0
OD2 B:ASP93 3.1 19.5 1.0
CA B:MET2298 3.2 27.4 1.0
OE2 B:GLU280 3.3 22.7 1.0
C B:MET2298 3.3 27.7 1.0
MN B:MN297 3.3 27.6 1.0
CB B:ASP82 3.9 22.5 1.0
CZ B:PHE50 4.0 23.8 1.0
OE1 B:GLU187 4.3 24.7 1.0
NE2 B:GLN278 4.3 16.6 1.0
CG B:GLU280 4.3 23.3 1.0
CB B:ASP93 4.4 18.5 1.0
CB B:MET2298 4.5 25.6 1.0
O B:MET2298 4.5 28.6 1.0
O B:HOH2313 4.6 29.7 1.0
CE1 B:PHE50 4.6 27.1 1.0
O B:HOH2379 4.6 31.7 1.0
O B:THR94 4.6 21.5 1.0
OE2 B:GLU187 4.7 21.1 1.0
N B:THR94 4.7 17.9 1.0
CA B:ASP82 4.7 25.0 1.0
CD B:GLU187 4.7 24.3 1.0
CE2 B:PHE50 4.7 26.0 1.0
C B:ASP93 4.8 20.1 1.0
CA B:ASP93 4.9 19.6 1.0
CB B:GLU280 4.9 22.4 1.0
CB B:ALA95 4.9 18.3 1.0
C B:THR94 4.9 21.1 1.0
C B:ASP82 5.0 25.1 1.0

Manganese binding site 4 out of 4 in 1wkm

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Manganese binding site 4 out of 4 in the The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Product Bound Form of the Mn(II)Loaded Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn297

b:27.6
occ:1.00
 OXT B:MET2298 1.9 26.3 1.0
OE2 B:GLU280 2.0 22.7 1.0
OD2 B:ASP93 2.0 19.5 1.0
OE2 B:GLU187 2.0 21.1 1.0
NE2 B:HIS153 2.1 21.4 1.0
CD B:GLU187 2.9 24.3 1.0
CE1 B:HIS153 3.0 21.1 1.0
C B:MET2298 3.0 27.7 1.0
CG B:ASP93 3.1 20.3 1.0
CD B:GLU280 3.1 23.9 1.0
CD2 B:HIS153 3.2 21.2 1.0
MN B:MN296 3.3 22.4 1.0
OE1 B:GLU187 3.4 24.7 1.0
OE1 B:GLU280 3.4 25.2 1.0
OD1 B:ASP93 3.6 21.5 1.0
O B:MET2298 3.6 28.6 1.0
CB B:ALA185 3.9 20.1 1.0
CG B:GLU187 4.0 21.7 1.0
ND1 B:HIS153 4.2 23.9 1.0
O B:HOH2306 4.2 24.9 1.0
N B:MET2298 4.2 31.5 1.0
CG B:HIS153 4.3 22.6 1.0
CA B:MET2298 4.3 27.4 1.0
CB B:ASP93 4.3 18.5 1.0
CG B:GLU280 4.4 23.3 1.0
O B:HOH2379 4.8 31.7 1.0
CB B:GLU187 4.8 21.1 1.0
CE1 B:HIS161 4.9 29.2 1.0
OD1 B:ASP82 4.9 23.4 1.0

Reference:

A.J.Copik, B.P.Nocek, S.I.Swierczek, S.Ruebush, S.B.Jang, L.Meng, V.M.D'souza, J.W.Peters, B.Bennett, R.C.Holz. Epr and X-Ray Crystallographic Characterization of the Product-Bound Form of the Mnii-Loaded Methionyl Aminopeptidase From Pyrococcus Furiosus Biochemistry V. 44 121 2005.
ISSN: ISSN 0006-2960
PubMed: 15628852
DOI: 10.1021/BI048123+
Page generated: Sat Oct 5 12:54:51 2024

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