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Sodium in PDB 4pnc: E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One

Enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One

All present enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One:
3.4.11.18;

Protein crystallography data

The structure of E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One, PDB code: 4pnc was solved by A.J.Scheidig, M.Altmeyer, C.D.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.69 / 1.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.010, 66.820, 48.450, 90.00, 111.15, 90.00
R / Rfree (%) 13.2 / 16.5

Other elements in 4pnc:

The structure of E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One also contains other interesting chemical elements:

Cobalt (Co) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One (pdb code 4pnc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One, PDB code: 4pnc:

Sodium binding site 1 out of 1 in 4pnc

Go back to Sodium Binding Sites List in 4pnc
Sodium binding site 1 out of 1 in the E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:9.6
occ:1.00
 O A:HOH838 1.7 15.7 1.0
O A:VAL76 2.4 8.6 1.0
O A:SER231 2.4 7.0 1.0
O A:ASN74 2.6 8.6 1.0
O A:HOH660 3.1 7.8 1.0
C A:SER231 3.5 6.1 1.0
C A:ASN74 3.5 8.8 1.0
N A:ASN74 3.5 7.0 1.0
C A:VAL76 3.6 8.8 1.0
O A:SER72 3.7 8.8 1.0
C A:ILE73 3.8 7.0 1.0
CA A:ASN74 3.9 7.5 1.0
N A:VAL76 4.1 8.1 1.0
C A:SER72 4.1 6.9 1.0
O A:ILE73 4.1 7.8 1.0
CA A:SER231 4.2 6.3 1.0
CB A:SER231 4.2 6.9 1.0
N A:SER231 4.2 6.8 1.0
O A:HOH649 4.3 7.1 1.0
CA A:ILE73 4.4 7.7 1.0
N A:ILE73 4.4 6.9 1.0
CA A:VAL76 4.4 7.9 1.0
N A:ALA232 4.4 5.5 1.0
CB A:SER72 4.5 6.2 1.0
N A:GLU75 4.6 8.4 1.0
N A:VAL77 4.6 8.7 1.0
CG1 A:ILE93 4.6 7.2 1.0
CE A:MET112 4.6 5.3 1.0
C A:GLU75 4.6 8.5 1.0
O A:ILE93 4.6 6.8 1.0
CA A:ALA232 4.7 5.4 1.0
CA A:VAL77 4.7 8.6 1.0
CD1 A:ILE93 4.8 8.4 1.0
CA A:GLU75 4.9 9.7 1.0
OG A:SER231 4.9 7.6 1.0
CB A:VAL76 4.9 7.8 1.0
CA A:SER72 5.0 6.3 1.0

Reference:

M.Altmeyer, E.Amtmann, C.Heyl, A.Marschner, A.J.Scheidig, C.D.Klein. Beta-Aminoketones As Prodrugs For Selective Irreversible Inhibitors of Type-1 Methionine Aminopeptidases. Bioorg.Med.Chem.Lett. 2014.
ISSN: ESSN 1464-3405
PubMed: 25293447
DOI: 10.1016/J.BMCL.2014.09.047
Page generated: Tue Dec 15 06:58:31 2020

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