Cobalt in PDB 5yr5: Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin:
3.4.11.18;

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin, PDB code: 5yr5 was solved by V.Pillalamarri, T.Arya, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.24 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.392, 77.339, 47.464, 90.00, 87.95, 90.00
R / Rfree (%)	17.7 / 20.1

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin (pdb code 5yr5). 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 Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin, PDB code: 5yr5:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:18.1 occ:1.00 O A:HOH455 2.0 18.5 1.0 NE2 A:HIS303 2.0 16.3 1.0 OE2 A:GLU367 2.0 16.5 1.0 OD2 A:ASP240 2.0 16.6 1.0 OE1 A:GLU336 2.2 18.3 1.0 CE1 A:HIS303 2.9 18.8 1.0 CG A:ASP240 2.9 17.7 1.0 CD A:GLU367 3.0 19.1 1.0 CD A:GLU336 3.0 17.6 1.0 CD2 A:HIS303 3.1 20.0 1.0 CO A:CO402 3.2 18.4 1.0 OE2 A:GLU336 3.3 18.9 1.0 OE1 A:GLU367 3.3 16.7 1.0 OD1 A:ASP240 3.4 17.1 1.0 O11 A:OVA405 3.5 20.3 1.0 O A:HOH438 3.6 20.8 1.0 OG1 A:THR334 3.6 17.1 1.0 CG2 A:THR334 3.9 17.8 1.0 ND1 A:HIS303 4.1 19.4 1.0 CB A:THR334 4.1 17.2 1.0 CB A:ASP240 4.1 18.0 1.0 CG A:HIS303 4.2 18.4 1.0 O A:HOH447 4.2 19.5 1.0 CG A:GLU367 4.3 18.8 1.0 CG A:GLU336 4.4 15.7 1.0 C1 A:OVA405 4.7 19.2 1.0 C5 A:OVA405 4.7 20.6 1.0 CB A:GLU336 4.9 16.1 1.0 OD2 A:ASP229 4.9 18.6 1.0 C6 A:OVA405 5.0 19.5 1.0

Cobalt binding site 2 out of 3 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:18.4 occ:1.00 OD1 A:ASP240 2.0 17.1 1.0 O A:HOH455 2.1 18.5 1.0 O A:HOH447 2.1 19.5 1.0 OE1 A:GLU367 2.1 16.7 1.0 OD2 A:ASP229 2.2 18.6 1.0 OD1 A:ASP229 2.3 18.3 1.0 CG A:ASP229 2.5 16.0 1.0 CG A:ASP240 2.9 17.7 1.0 CD A:GLU367 3.1 19.1 1.0 CO A:CO401 3.2 18.1 1.0 OD2 A:ASP240 3.2 16.6 1.0 OE2 A:GLU367 3.3 16.5 1.0 O A:HOH438 3.8 20.8 1.0 CB A:ASP229 4.0 15.7 1.0 O A:HOH493 4.0 23.9 0.8 OE2 A:GLU336 4.1 18.9 1.0 ND2 A:ASN242 4.1 15.5 1.0 CG2 A:THR231 4.1 19.2 0.7 OG1 A:THR231 4.2 19.6 0.3 O A:HOH430 4.2 18.6 1.0 O11 A:OVA405 4.3 20.3 1.0 CB A:ASP240 4.3 18.0 1.0 CG A:GLU367 4.5 18.8 1.0 O A:HOH506 4.5 22.8 1.0 O A:LEU241 4.5 16.4 1.0 OE1 A:GLU336 4.6 18.3 1.0 N A:LEU241 4.6 15.9 1.0 CD A:GLU336 4.7 17.6 1.0 C A:LEU241 4.8 17.9 1.0 C A:ASP240 4.9 16.5 1.0 CA A:ASP240 4.9 18.1 1.0 CA A:ASP229 4.9 15.3 1.0 CB A:ASN242 4.9 16.7 1.0 CB A:GLU367 5.0 16.5 1.0 O A:ILE230 5.0 15.5 1.0

Cobalt binding site 3 out of 3 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with Ovalicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:36.4 occ:0.40 OE1 A:GLU128 1.8 41.1 0.4 O A:HOH613 2.0 29.3 0.4 OH A:TYR195 2.0 31.8 1.0 O A:HOH612 2.3 36.0 0.4 NE2 A:HIS310 2.3 35.7 1.0 O A:HOH612 2.4 30.6 0.5 OE1 A:GLU128 2.7 46.4 0.6 CD A:GLU128 2.8 39.9 0.4 CZ A:TYR195 3.2 29.5 1.0 CD2 A:HIS310 3.2 33.5 1.0 OE2 A:GLU128 3.3 38.4 0.4 CE1 A:HIS310 3.4 33.9 1.0 CE1 A:TYR196 3.6 27.5 0.2 CE1 A:TYR196 3.7 42.8 0.8 CE2 A:TYR195 3.7 25.5 1.0 CD A:GLU128 3.8 41.3 0.6 CG A:GLU128 4.1 36.6 0.4 CE1 A:TYR195 4.2 29.8 1.0 CD1 A:TYR196 4.2 27.1 0.2 CZ A:TYR196 4.3 27.5 0.2 OE2 A:GLU128 4.3 35.1 0.6 CD1 A:TYR196 4.4 37.9 0.8 CZ A:TYR196 4.4 39.9 0.8 CG A:HIS310 4.4 27.1 1.0 OH A:TYR196 4.4 27.6 0.2 OH A:TYR196 4.4 50.6 0.8 ND1 A:HIS310 4.5 34.3 1.0 O A:HOH611 4.8 30.1 0.8

V.Pillalamarri, T.Arya, N.Haque, S.C.Bala, A.K.Marapaka, A.Addlagatta. Discovery of Natural Product Ovalicin Sensitive Type 1 Methionine Aminopeptidases: Molecular and Structural Basis. Biochem. J. V. 476 991 2019.
ISSN: ESSN 1470-8728
PubMed: 30837307
DOI: 10.1042/BCJ20180874