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Manganese in PDB 2gu4: E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated

Enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated

All present enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated:
3.4.11.18;

Protein crystallography data

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated, PDB code: 2gu4 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) 14.85 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.704, 64.034, 76.347, 90.00, 108.10, 90.00
R / Rfree (%) 19.5 / 22.7

Other elements in 2gu4:

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, 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: 0.5, Di-Metalated (pdb code 2gu4). 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: 0.5, Di-Metalated, PDB code: 2gu4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2gu4

Go back to Manganese Binding Sites List in 2gu4
Manganese binding site 1 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, 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: 0.5, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn265

b:10.4
occ:0.81
 O2 A:NLP3808 1.9 20.1 1.0
OD2 A:ASP108 2.0 14.0 1.0
OE2 A:GLU235 2.1 13.1 1.0
NE2 A:HIS171 2.4 13.7 1.0
OE2 A:GLU204 2.4 13.1 1.0
CD A:GLU235 3.0 15.2 1.0
CG A:ASP108 3.1 12.9 1.0
OE1 A:GLU235 3.1 18.2 1.0
MN A:MN266 3.1 12.5 0.3
CD A:GLU204 3.1 13.3 1.0
CE1 A:HIS171 3.3 13.9 1.0
CD2 A:HIS171 3.3 13.4 1.0
OE1 A:GLU204 3.3 14.2 1.0
P A:NLP3808 3.4 20.0 1.0
OD1 A:ASP108 3.7 16.5 1.0
O1 A:NLP3808 3.7 22.9 1.0
OG1 A:THR202 3.8 8.8 1.0
N A:NLP3808 4.0 18.9 1.0
CB A:ASP108 4.1 11.5 1.0
CG2 A:THR202 4.2 9.4 1.0
CB A:THR202 4.3 8.2 1.0
CA A:NLP3808 4.4 21.2 1.0
ND1 A:HIS171 4.4 11.8 1.0
CG A:GLU235 4.4 12.0 1.0
O3 A:NLP3808 4.4 21.1 1.0
CG A:HIS171 4.4 12.2 1.0
CG A:GLU204 4.5 11.4 1.0

Manganese binding site 2 out of 4 in 2gu4

Go back to Manganese Binding Sites List in 2gu4
Manganese binding site 2 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, 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: 0.5, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn266

b:12.5
occ:0.29
 OE1 A:GLU235 2.2 18.2 1.0
OD1 A:ASP97 2.2 18.3 1.0
OD1 A:ASP108 2.3 16.5 1.0
OD2 A:ASP97 2.4 23.1 1.0
N A:NLP3808 2.5 18.9 1.0
O2 A:NLP3808 2.6 20.1 1.0
CG A:ASP97 2.6 17.6 1.0
OD2 A:ASP108 2.9 14.0 1.0
CG A:ASP108 2.9 12.9 1.0
MN A:MN265 3.1 10.4 0.8
CD A:GLU235 3.2 15.2 1.0
CA A:NLP3808 3.3 21.2 1.0
O A:HOH3814 3.5 9.8 1.0
P A:NLP3808 3.5 20.0 1.0
OE2 A:GLU235 3.6 13.1 1.0
OG1 A:THR99 4.1 11.2 1.0
CB A:ASP97 4.1 11.5 1.0
O A:HOH3901 4.2 18.1 1.0
OE1 A:GLU204 4.2 14.2 1.0
O3 A:NLP3808 4.3 21.1 1.0
CB A:ASP108 4.4 11.5 1.0
CG A:GLU235 4.5 12.0 1.0
N A:THR109 4.6 10.0 1.0
O1 A:NLP3808 4.7 22.9 1.0
OE2 A:GLU204 4.7 13.1 1.0
CB A:NLP3808 4.7 21.9 1.0
CD A:GLU204 4.8 13.3 1.0
O A:THR109 4.8 7.9 1.0
O A:VAL98 4.8 9.4 1.0
C A:ASP108 4.9 10.8 1.0
CB A:GLU235 4.9 11.1 1.0
CA A:ASP97 4.9 9.9 1.0
C A:THR109 5.0 8.1 1.0
CA A:ASP108 5.0 10.8 1.0

Manganese binding site 3 out of 4 in 2gu4

Go back to Manganese Binding Sites List in 2gu4
Manganese binding site 3 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, 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: 0.5, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn265

b:12.3
occ:0.83
 O2 B:NLP3808 1.9 24.3 1.0
OD2 B:ASP108 2.1 16.7 1.0
OE2 B:GLU235 2.1 13.4 1.0
NE2 B:HIS171 2.2 11.5 1.0
OE2 B:GLU204 2.3 10.5 1.0
CD B:GLU235 3.0 14.5 1.0
CD B:GLU204 3.1 11.7 1.0
CD2 B:HIS171 3.2 12.0 1.0
CG B:ASP108 3.2 15.3 1.0
CE1 B:HIS171 3.2 12.1 1.0
OE1 B:GLU235 3.2 16.6 1.0
MN B:MN266 3.2 13.2 0.3
OE1 B:GLU204 3.3 14.8 1.0
P B:NLP3808 3.4 20.5 1.0
O1 B:NLP3808 3.8 24.0 1.0
N B:NLP3808 3.8 22.2 1.0
OG1 B:THR202 3.9 10.6 1.0
OD1 B:ASP108 3.9 18.8 1.0
CB B:ASP108 4.2 11.8 1.0
CG2 B:THR202 4.3 7.7 1.0
CA B:NLP3808 4.3 22.8 1.0
ND1 B:HIS171 4.3 10.7 1.0
CG B:HIS171 4.3 11.3 1.0
CB B:THR202 4.4 9.8 1.0
CG B:GLU235 4.4 12.2 1.0
CG B:GLU204 4.5 11.7 1.0
O3 B:NLP3808 4.5 21.9 1.0
NE2 B:HIS178 4.9 17.0 1.0
CE1 B:PHE177 5.0 15.9 1.0

Manganese binding site 4 out of 4 in 2gu4

Go back to Manganese Binding Sites List in 2gu4
Manganese binding site 4 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, 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: 0.5, Di-Metalated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn266

b:13.2
occ:0.33
 N B:NLP3808 2.2 22.2 1.0
OE1 B:GLU235 2.2 16.6 1.0
OD2 B:ASP97 2.3 23.5 1.0
OD1 B:ASP97 2.3 19.6 1.0
OD1 B:ASP108 2.3 18.8 1.0
CG B:ASP97 2.6 15.8 1.0
O2 B:NLP3808 2.7 24.3 1.0
OD2 B:ASP108 2.8 16.7 1.0
CG B:ASP108 2.9 15.3 1.0
CA B:NLP3808 3.1 22.8 1.0
CD B:GLU235 3.2 14.5 1.0
MN B:MN265 3.2 12.3 0.8
O B:HOH3815 3.5 15.2 1.0
P B:NLP3808 3.5 20.5 1.0
OE2 B:GLU235 3.5 13.4 1.0
CB B:ASP97 4.1 14.1 1.0
OG1 B:THR99 4.2 12.0 1.0
O B:HOH3939 4.2 32.1 1.0
OE1 B:GLU204 4.2 14.8 1.0
CB B:ASP108 4.4 11.8 1.0
O3 B:NLP3808 4.4 21.9 1.0
CB B:NLP3808 4.5 21.4 1.0
CG B:GLU235 4.5 12.2 1.0
N B:THR109 4.6 10.0 1.0
O B:THR109 4.6 10.3 1.0
O1 B:NLP3808 4.7 24.0 1.0
OE2 B:GLU204 4.8 10.5 1.0
CD B:GLU204 4.8 11.7 1.0
C B:ASP108 4.9 11.1 1.0
C B:THR109 4.9 8.9 1.0
O B:VAL98 4.9 12.5 1.0
CA B:ASP97 4.9 11.3 1.0
CB B:GLU235 5.0 10.5 1.0
CA B:ASP108 5.0 10.1 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 14:13:56 2024

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