Cobalt in PDB 2gz5: Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang

All present enzymatic activity of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang:
3.4.11.18;

The structure of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang, PDB code: 2gz5 was solved by A.Addlagatta, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.568, 77.689, 48.644, 90.00, 90.63, 90.00
R / Rfree (%)	13.5 / 14.5

The structure of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Cobalt atom in the Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang (pdb code 2gz5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang, PDB code: 2gz5:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:10.7 occ:1.00 O A:HOH711 2.0 11.9 1.0 NE2 A:HIS303 2.0 10.7 1.0 OE2 A:GLU367 2.0 10.3 1.0 OD2 A:ASP240 2.1 10.5 1.0 OE1 A:GLU336 2.2 11.2 1.0 CD A:GLU367 3.0 8.7 1.0 CE1 A:HIS303 3.0 11.3 1.0 CG A:ASP240 3.0 9.1 1.0 CO A:CO402 3.1 9.6 1.0 CD2 A:HIS303 3.1 11.2 1.0 CD A:GLU336 3.1 11.2 1.0 OE1 A:GLU367 3.3 9.6 1.0 OE2 A:GLU336 3.4 13.6 1.0 OD1 A:ASP240 3.4 9.2 1.0 O11 A:OVA480 3.5 16.8 1.0 OG1 A:THR334 3.7 11.2 1.0 CG2 A:THR334 3.9 11.0 1.0 O A:HOH710 4.1 12.3 1.0 CB A:THR334 4.1 10.7 1.0 ND1 A:HIS303 4.2 12.2 1.0 CG A:HIS303 4.2 11.5 1.0 CB A:ASP240 4.2 9.2 1.0 CG A:GLU367 4.3 8.9 1.0 CG A:GLU336 4.4 11.7 1.0 C5 A:OVA480 4.9 17.1 1.0 C1 A:OVA480 4.9 14.6 1.0 OD2 A:ASP229 4.9 15.7 0.7 CB A:GLU336 4.9 10.3 1.0 OD1 A:ASP229 4.9 5.2 0.3

Cobalt binding site 2 out of 3 in the Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:9.6 occ:1.00 OD1 A:ASP229 2.0 5.2 0.3 O A:HOH711 2.0 11.9 1.0 OD1 A:ASP240 2.0 9.2 1.0 OE1 A:GLU367 2.1 9.6 1.0 OD1 A:ASP229 2.1 14.4 0.7 O A:HOH710 2.2 12.3 1.0 OD2 A:ASP229 2.3 15.7 0.7 CG A:ASP229 2.6 11.5 0.7 CG A:ASP240 2.9 9.1 1.0 CG A:ASP229 2.9 5.8 0.3 CD A:GLU367 3.0 8.7 1.0 CO A:CO401 3.1 10.7 1.0 OD2 A:ASP240 3.1 10.5 1.0 OD2 A:ASP229 3.2 6.9 0.3 OE2 A:GLU367 3.3 10.3 1.0 OG1 A:THR231 4.0 12.0 1.0 ND2 A:ASN242 4.1 9.6 1.0 OE2 A:GLU336 4.1 13.6 1.0 CB A:ASP229 4.1 9.3 0.7 CB A:ASP240 4.3 9.2 1.0 CB A:ASP229 4.3 6.8 0.3 O A:HOH542 4.3 17.4 1.0 O11 A:OVA480 4.4 16.8 1.0 CG A:GLU367 4.4 8.9 1.0 O A:LEU241 4.4 8.2 1.0 N A:LEU241 4.5 7.9 1.0 O A:ILE230 4.5 9.3 1.0 OE1 A:GLU336 4.6 11.2 1.0 C A:LEU241 4.7 7.2 1.0 CD A:GLU336 4.7 11.2 1.0 C A:ASP240 4.8 8.7 1.0 CA A:ASP240 4.9 9.0 1.0 CB A:GLU367 4.9 8.7 1.0 CB A:ASN242 4.9 8.2 1.0 O A:HOH712 4.9 39.3 1.0 NE2 A:HIS303 4.9 10.7 1.0 CA A:ASP229 5.0 7.6 1.0 CA A:LEU241 5.0 7.8 1.0

Cobalt binding site 3 out of 3 in the Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Human Type 1 Methionine Aminopeptidase in Complex with Ovalicin at 1.1 Ang within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:31.4 occ:1.00 O A:HOH829 1.7 48.3 1.0 OH A:TYR195 2.0 27.2 1.0 O1 A:GOL471 2.0 58.7 1.0 NE2 A:HIS310 2.2 36.4 1.0 OE1 A:GLU128 2.5 29.4 1.0 O A:HOH830 2.7 59.6 1.0 CZ A:TYR195 3.1 19.7 1.0 CE1 A:HIS310 3.2 36.3 1.0 CD2 A:HIS310 3.2 31.1 1.0 CE1 A:TYR196 3.2 30.9 1.0 C1 A:GOL471 3.3 53.6 1.0 CD A:GLU128 3.7 28.1 1.0 CE2 A:TYR195 3.8 22.8 1.0 O2 A:GOL471 3.8 64.4 1.0 CZ A:TYR196 3.8 30.9 1.0 OH A:TYR196 3.9 43.6 1.0 C2 A:GOL471 4.0 52.5 1.0 CD1 A:TYR196 4.1 27.2 1.0 CE1 A:TYR195 4.1 18.4 1.0 ND1 A:HIS310 4.3 32.4 1.0 CG A:HIS310 4.3 25.4 1.0 OE2 A:GLU128 4.4 34.7 1.0 CB A:GLU128 4.6 31.7 1.0 CG A:GLU128 4.7 30.4 1.0 CE2 A:TYR196 4.9 29.2 1.0

A.Addlagatta, B.W.Matthews. Structure of the Angiogenesis Inhibitor Ovalicin Bound to Its Noncognate Target, Human Type 1 Methionine Aminopeptidase. Protein Sci. V. 15 1842 2006.
ISSN: ISSN 0961-8368
PubMed: 16823043
DOI: 10.1110/PS.062278006