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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: Sun Dec 13 10:45:31 2020

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