Atomistry » Cobalt » PDB 4ngo-4rum » 4pnc
Atomistry »
  Cobalt »
    PDB 4ngo-4rum »
      4pnc »

Cobalt 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:

Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 3 binding sites of Cobalt where determined in the E. Coli Methionine Aminopeptidase in Complex with Inhibitor 7-Methoxy- 2-Methylen-3,4-Dihydronaphthalen-1(2H)-One, PDB code: 4pnc:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4pnc

Go back to Cobalt Binding Sites List in 4pnc
Cobalt binding site 1 out of 3 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 Cobalt with other atoms in the Co 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:Co302

b:4.2
occ:1.00
 OD1 A:ASP108 2.0 5.3 1.0
O A:HOH684 2.0 7.1 1.0
OD1 A:ASP97 2.1 7.9 1.0
OE1 A:GLU235 2.2 6.1 1.0
O A:HOH634 2.2 7.3 1.0
OD2 A:ASP97 2.4 8.4 1.0
CG A:ASP97 2.6 6.2 1.0
CG A:ASP108 3.0 5.6 1.0
CD A:GLU235 3.1 5.7 1.0
CO A:CO303 3.2 4.6 1.0
OD2 A:ASP108 3.2 5.1 1.0
OE2 A:GLU235 3.3 5.0 1.0
O A:HOH629 3.8 6.0 1.0
O A:HOH628 4.0 11.6 1.0
OG1 A:THR99 4.0 7.2 1.0
CB A:ASP97 4.1 5.3 1.0
OE1 A:GLU204 4.2 10.7 1.0
CB A:ASP108 4.4 5.0 1.0
O A:HOH688 4.4 16.2 1.0
CG A:GLU235 4.4 4.8 1.0
N A:THR109 4.4 4.8 1.0
O A:HOH873 4.5 32.8 1.0
O A:VAL98 4.5 6.2 1.0
OE2 A:GLU204 4.6 6.5 1.0
O A:HOH734 4.6 26.1 1.0
O A:THR109 4.7 4.6 1.0
O A:HOH658 4.7 9.8 1.0
C A:ASP108 4.7 4.7 1.0
CD A:GLU204 4.7 8.3 1.0
C A:THR109 4.8 4.2 1.0
CA A:ASP108 4.8 5.0 1.0
CA A:ASP97 4.9 5.1 1.0
N A:VAL98 4.9 5.5 1.0
CB A:GLU235 4.9 4.5 1.0
C A:ASP97 5.0 6.0 1.0

Cobalt binding site 2 out of 3 in 4pnc

Go back to Cobalt Binding Sites List in 4pnc
Cobalt binding site 2 out of 3 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 Cobalt with other atoms in the Co binding site number 2 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:Co303

b:4.6
occ:1.00
 OE2 A:GLU235 2.0 5.0 1.0
O A:HOH684 2.0 7.1 1.0
NE2 A:HIS171 2.0 4.8 1.0
OD2 A:ASP108 2.1 5.1 1.0
OE2 A:GLU204 2.2 6.5 1.0
CG A:ASP108 3.0 5.6 1.0
CD A:GLU235 3.0 5.7 1.0
CE1 A:HIS171 3.0 5.5 1.0
CD2 A:HIS171 3.1 5.3 1.0
CD A:GLU204 3.1 8.3 1.0
CO A:CO302 3.2 4.2 1.0
OE1 A:GLU235 3.3 6.1 1.0
OE1 A:GLU204 3.3 10.7 1.0
OD1 A:ASP108 3.3 5.3 1.0
OG1 A:THR202 3.6 5.3 1.0
O A:HOH628 3.8 11.6 1.0
CG2 A:THR202 3.8 5.3 1.0
CB A:THR202 4.0 5.2 1.0
O A:HOH869 4.1 28.4 1.0
ND1 A:HIS171 4.1 5.5 1.0
CB A:ASP108 4.2 5.0 1.0
CG A:HIS171 4.2 5.2 1.0
O A:HOH634 4.3 7.3 1.0
CG A:GLU235 4.4 4.8 1.0
CG A:GLU204 4.4 6.7 1.0
NE2 A:HIS178 4.8 8.5 1.0
CB A:GLU204 4.9 7.2 1.0
CE1 A:PHE177 5.0 7.9 1.0

Cobalt binding site 3 out of 3 in 4pnc

Go back to Cobalt Binding Sites List in 4pnc
Cobalt binding site 3 out of 3 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 Cobalt with other atoms in the Co binding site number 3 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:Co304

b:18.6
occ:1.00
 O A:HOH538 2.0 29.7 1.0
O A:HOH517 2.0 23.6 1.0
O A:HOH425 2.1 15.9 1.0
O A:HOH489 2.2 20.8 1.0
NE2 A:HIS54 2.2 18.2 1.0
CE1 A:HIS54 3.1 17.4 1.0
CD2 A:HIS54 3.2 17.6 1.0
O A:GLU52 4.0 10.9 1.0
O A:HOH450 4.1 11.9 1.0
ND1 A:HIS54 4.3 16.6 1.0
CG A:HIS54 4.4 15.0 1.0
O A:ASN51 4.4 13.7 1.0
C A:GLU52 4.8 10.0 1.0
OE1 A:GLU52 5.0 17.7 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 Jul 30 17:24:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy