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Manganese in PDB 2gu5: E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated

Enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated

All present enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated:
3.4.11.18;

Protein crystallography data

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated, PDB code: 2gu5 was solved by Q.Z.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.19 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.790, 64.606, 76.354, 90.00, 107.77, 90.00
R / Rfree (%) 21.1 / 23.3

Other elements in 2gu5:

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated (pdb code 2gu5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated, PDB code: 2gu5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2gu5

Go back to Manganese Binding Sites List in 2gu5
Manganese binding site 1 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn265

b:9.8
occ:0.90
 O2 A:NLP3808 2.0 20.9 1.0
OD2 A:ASP108 2.1 12.5 1.0
OE2 A:GLU235 2.2 10.8 1.0
NE2 A:HIS171 2.3 10.9 1.0
OE2 A:GLU204 2.4 10.7 1.0
CD A:GLU235 3.0 10.8 1.0
CG A:ASP108 3.1 11.7 1.0
CD A:GLU204 3.1 12.0 1.0
P A:NLP3808 3.2 17.3 1.0
CD2 A:HIS171 3.2 11.1 1.0
OE1 A:GLU204 3.2 15.1 1.0
OE1 A:GLU235 3.2 13.3 1.0
CE1 A:HIS171 3.3 11.1 1.0
MN A:MN266 3.3 9.7 0.5
O1 A:NLP3808 3.3 25.6 1.0
OD1 A:ASP108 3.7 13.9 1.0
OG1 A:THR202 3.8 8.4 1.0
N A:NLP3808 3.9 19.1 1.0
CB A:ASP108 4.2 8.5 1.0
CG2 A:THR202 4.2 9.2 1.0
CA A:NLP3808 4.3 20.7 1.0
CB A:THR202 4.4 8.7 1.0
ND1 A:HIS171 4.4 9.1 1.0
O3 A:NLP3808 4.4 20.6 1.0
CG A:HIS171 4.4 10.7 1.0
CG A:GLU235 4.4 9.2 1.0
CG A:GLU204 4.5 10.3 1.0
NE2 A:HIS178 5.0 13.6 1.0

Manganese binding site 2 out of 4 in 2gu5

Go back to Manganese Binding Sites List in 2gu5
Manganese binding site 2 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn266

b:9.7
occ:0.46
 OD1 A:ASP97 2.1 15.3 1.0
OE1 A:GLU235 2.2 13.3 1.0
OD1 A:ASP108 2.2 13.9 1.0
OD2 A:ASP97 2.3 18.9 1.0
N A:NLP3808 2.4 19.1 1.0
CG A:ASP97 2.5 13.7 1.0
O2 A:NLP3808 2.6 20.9 1.0
CG A:ASP108 3.0 11.7 1.0
OD2 A:ASP108 3.0 12.5 1.0
CD A:GLU235 3.2 10.8 1.0
CA A:NLP3808 3.3 20.7 1.0
MN A:MN265 3.3 9.8 0.9
P A:NLP3808 3.5 17.3 1.0
O A:HOH3822 3.6 10.2 1.0
OE2 A:GLU235 3.6 10.8 1.0
CB A:ASP97 4.0 9.3 1.0
OG1 A:THR99 4.0 11.2 1.0
OE1 A:GLU204 4.2 15.1 1.0
O A:HOH3894 4.3 16.2 1.0
CB A:ASP108 4.4 8.5 1.0
N A:THR109 4.5 7.4 1.0
O3 A:NLP3808 4.5 20.6 1.0
CG A:GLU235 4.6 9.2 1.0
O1 A:NLP3808 4.6 25.6 1.0
O A:THR109 4.6 9.1 1.0
CB A:NLP3808 4.7 20.4 1.0
O A:VAL98 4.7 9.9 1.0
CA A:ASP97 4.8 7.0 1.0
C A:ASP108 4.8 7.3 1.0
C A:THR109 4.8 9.0 1.0
CD A:GLU204 4.8 12.0 1.0
CA A:ASP108 4.9 6.8 1.0
OE2 A:GLU204 4.9 10.7 1.0
CB A:GLU235 4.9 7.9 1.0
C A:ASP97 5.0 8.8 1.0
N A:VAL98 5.0 8.1 1.0

Manganese binding site 3 out of 4 in 2gu5

Go back to Manganese Binding Sites List in 2gu5
Manganese binding site 3 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn265

b:10.7
occ:0.91
 O2 B:NLP3808 1.9 21.1 1.0
OD2 B:ASP108 2.1 13.6 1.0
OE2 B:GLU235 2.2 10.6 1.0
NE2 B:HIS171 2.3 10.0 1.0
OE2 B:GLU204 2.3 10.1 1.0
CD B:GLU235 3.1 11.9 1.0
CD B:GLU204 3.1 9.6 1.0
CG B:ASP108 3.1 11.5 1.0
CD2 B:HIS171 3.2 9.3 1.0
CE1 B:HIS171 3.2 10.3 1.0
OE1 B:GLU204 3.2 15.4 1.0
OE1 B:GLU235 3.3 15.1 1.0
P B:NLP3808 3.3 16.6 1.0
MN B:MN266 3.3 9.9 0.5
O1 B:NLP3808 3.7 22.3 1.0
OD1 B:ASP108 3.8 14.5 1.0
N B:NLP3808 3.9 16.0 1.0
OG1 B:THR202 3.9 8.4 1.0
CB B:ASP108 4.2 8.8 1.0
CA B:NLP3808 4.3 19.0 1.0
CG2 B:THR202 4.3 8.5 1.0
ND1 B:HIS171 4.3 9.3 1.0
CG B:HIS171 4.4 8.3 1.0
CB B:THR202 4.4 9.5 1.0
O3 B:NLP3808 4.4 19.8 1.0
CG B:GLU235 4.4 7.8 1.0
CG B:GLU204 4.5 11.1 1.0
NE2 B:HIS178 4.9 14.1 1.0
CE1 B:PHE177 4.9 11.1 1.0

Manganese binding site 4 out of 4 in 2gu5

Go back to Manganese Binding Sites List in 2gu5
Manganese binding site 4 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn266

b:9.9
occ:0.45
 OD1 B:ASP97 2.1 17.0 1.0
N B:NLP3808 2.2 16.0 1.0
OE1 B:GLU235 2.2 15.1 1.0
OD1 B:ASP108 2.3 14.5 1.0
OD2 B:ASP97 2.3 20.9 1.0
CG B:ASP97 2.5 15.8 1.0
O2 B:NLP3808 2.8 21.1 1.0
CG B:ASP108 3.0 11.5 1.0
OD2 B:ASP108 3.0 13.6 1.0
CA B:NLP3808 3.2 19.0 1.0
CD B:GLU235 3.2 11.9 1.0
MN B:MN265 3.3 10.7 0.9
O B:HOH3823 3.5 12.2 1.0
P B:NLP3808 3.6 16.6 1.0
OE2 B:GLU235 3.6 10.6 1.0
CB B:ASP97 4.0 11.0 1.0
OG1 B:THR99 4.1 12.0 1.0
O B:HOH3970 4.3 19.1 1.0
OE1 B:GLU204 4.3 15.4 1.0
CB B:ASP108 4.4 8.8 1.0
O3 B:NLP3808 4.5 19.8 1.0
N B:THR109 4.5 8.4 1.0
CB B:NLP3808 4.5 19.5 1.0
CG B:GLU235 4.6 7.8 1.0
O B:THR109 4.6 9.7 1.0
O1 B:NLP3808 4.7 22.3 1.0
C B:THR109 4.8 8.4 1.0
CA B:ASP97 4.8 8.5 1.0
C B:ASP108 4.8 8.4 1.0
O B:VAL98 4.9 10.6 1.0
CD B:GLU204 4.9 9.6 1.0
OE2 B:GLU204 4.9 10.1 1.0
CA B:ASP108 4.9 8.1 1.0
CB B:GLU235 5.0 7.4 1.0
CB B:SER110 5.0 6.9 1.0

Reference:

Q.Z.Ye, S.X.Xie, Z.Q.Ma, M.Huang, R.P.Hanzlik. Structural Basis of Catalysis By Monometalated Methionine Aminopeptidase. Proc.Natl.Acad.Sci.Usa V. 103 9470 2006.
ISSN: ISSN 0027-8424
PubMed: 16769889
DOI: 10.1073/PNAS.0602433103
Page generated: Sat Oct 5 14:14:03 2024

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