Cobalt in PDB 1xgm: Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus

All present enzymatic activity of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus:
3.4.11.18;

The structure of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus, PDB code: 1xgm was solved by T.H.Tahirov, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.385, 85.059, 72.705, 90.00, 107.71, 90.00
R / Rfree (%)	18.1 / 26.3

The binding sites of Cobalt atom in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus (pdb code 1xgm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus, PDB code: 1xgm:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co296 b:14.3 occ:1.00 OE2 A:GLU187 1.9 2.8 1.0 NE2 A:HIS153 1.9 17.9 1.0 OE2 A:GLU280 2.0 12.9 1.0 OD2 A:ASP93 2.0 9.2 1.0 CD2 A:HIS153 2.8 22.1 1.0 CO A:CO297 2.9 14.0 1.0 CD A:GLU187 3.0 3.3 1.0 CD A:GLU280 3.0 15.5 1.0 CE1 A:HIS153 3.1 23.0 1.0 CG A:ASP93 3.1 7.5 1.0 OE1 A:GLU187 3.4 4.5 1.0 OE1 A:GLU280 3.5 13.4 1.0 OD1 A:ASP93 3.7 2.0 1.0 CG A:HIS153 4.0 23.0 1.0 ND1 A:HIS153 4.1 25.9 1.0 CG A:GLU187 4.3 2.8 1.0 CB A:ALA185 4.3 4.3 1.0 CB A:ASP93 4.3 3.6 1.0 OD1 A:ASP82 4.3 16.8 1.0 CG A:GLU280 4.4 15.2 1.0 NE2 A:HIS161 4.7 18.0 1.0 OD2 A:ASP82 4.8 2.5 1.0 CB A:GLU187 4.8 8.7 1.0

Cobalt binding site 2 out of 4 in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Co297 b:14.0 occ:1.00 OD1 A:ASP82 2.0 16.8 1.0 OE1 A:GLU280 2.0 13.4 1.0 OD1 A:ASP93 2.0 2.0 1.0 OD2 A:ASP82 2.0 2.5 1.0 CG A:ASP82 2.2 12.1 1.0 OD2 A:ASP93 2.5 9.2 1.0 CG A:ASP93 2.6 7.5 1.0 CD A:GLU280 2.8 15.5 1.0 CO A:CO296 2.9 14.3 1.0 OE2 A:GLU280 2.9 12.9 1.0 CB A:ASP82 3.8 14.6 1.0 OE2 A:GLU187 3.9 2.8 1.0 OE1 A:GLU187 3.9 4.5 1.0 CZ A:PHE50 4.1 30.0 1.0 CB A:ASP93 4.2 3.6 1.0 CD A:GLU187 4.2 3.3 1.0 CG A:GLU280 4.3 15.2 1.0 O A:THR94 4.5 15.0 1.0 NE2 A:HIS153 4.6 17.9 1.0 CB A:ALA95 4.6 7.0 1.0 CA A:ASP82 4.7 17.4 1.0 CE2 A:PHE50 4.7 32.5 1.0 CE1 A:PHE50 4.8 29.6 1.0 CA A:ASP93 4.9 12.8 1.0 C A:ASP93 4.9 13.7 1.0 CB A:GLU280 4.9 6.9 1.0 O A:VAL83 5.0 9.6 1.0

Cobalt binding site 3 out of 4 in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Co296 b:14.8 occ:1.00 OE2 B:GLU187 1.9 19.7 1.0 OE2 B:GLU280 2.0 13.3 1.0 OD2 B:ASP93 2.0 16.0 1.0 NE2 B:HIS153 2.0 27.2 1.0 CO B:CO297 2.8 20.6 1.0 CD2 B:HIS153 2.8 27.7 1.0 CD B:GLU187 2.9 20.4 1.0 CD B:GLU280 3.0 12.7 1.0 CG B:ASP93 3.1 12.5 1.0 CE1 B:HIS153 3.1 27.2 1.0 OE1 B:GLU187 3.3 19.9 1.0 OE1 B:GLU280 3.5 2.4 1.0 OD1 B:ASP93 3.7 2.0 1.0 CG B:HIS153 4.1 24.0 1.0 ND1 B:HIS153 4.2 27.5 1.0 OD1 B:ASP82 4.2 22.5 1.0 CB B:ALA185 4.3 4.0 1.0 CG B:GLU187 4.3 11.0 1.0 CB B:ASP93 4.3 9.4 1.0 CG B:GLU280 4.3 14.9 1.0 NE2 B:HIS161 4.8 23.9 1.0 OD2 B:ASP82 4.8 27.2 1.0 CB B:GLU187 4.8 4.9 1.0 CG B:ASP82 5.0 22.7 1.0

Cobalt binding site 4 out of 4 in the Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Co297 b:20.6 occ:1.00 OD1 B:ASP93 1.9 2.0 1.0 OE1 B:GLU280 2.0 2.4 1.0 OD2 B:ASP82 2.0 27.2 1.0 OD1 B:ASP82 2.0 22.5 1.0 CG B:ASP82 2.3 22.7 1.0 OD2 B:ASP93 2.5 16.0 1.0 CG B:ASP93 2.5 12.5 1.0 CD B:GLU280 2.7 12.7 1.0 OE2 B:GLU280 2.8 13.3 1.0 CO B:CO296 2.8 14.8 1.0 CB B:ASP82 3.8 18.2 1.0 OE1 B:GLU187 3.9 19.9 1.0 OE2 B:GLU187 4.0 19.7 1.0 CZ B:PHE50 4.0 26.6 1.0 CB B:ASP93 4.1 9.4 1.0 CG B:GLU280 4.2 14.9 1.0 CD B:GLU187 4.3 20.4 1.0 O B:THR94 4.4 14.9 1.0 NE2 B:HIS153 4.6 27.2 1.0 CE2 B:PHE50 4.7 35.9 1.0 C B:ASP93 4.7 21.3 1.0 CA B:ASP82 4.7 10.5 1.0 CB B:ALA95 4.7 21.7 1.0 CE1 B:PHE50 4.7 26.4 1.0 CA B:ASP93 4.7 19.6 1.0 CB B:GLU280 4.9 12.2 1.0 C B:THR94 5.0 12.8 1.0 N B:THR94 5.0 17.6 1.0 O B:ASP93 5.0 24.3 1.0

T.H.Tahirov, H.Oki, T.Tsukihara, K.Ogasahara, K.Yutani, K.Ogata, Y.Izu, S.Tsunasawa, I.Kato. Crystal Structure of Methionine Aminopeptidase From Hyperthermophile, Pyrococcus Furiosus. J.Mol.Biol. V. 284 101 1998.
ISSN: ISSN 0022-2836
PubMed: 9811545
DOI: 10.1006/JMBI.1998.2146