Cobalt in PDB 5yr7: Human Methionine Aminopeptidase Type 1B (F309L Mutant)

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

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant), PDB code: 5yr7 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)	23.69 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.414, 77.193, 48.220, 90.00, 92.03, 90.00
R / Rfree (%)	19.6 / 26.6

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) 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) (pdb code 5yr7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Human Methionine Aminopeptidase Type 1B (F309L Mutant), PDB code: 5yr7:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:27.5 occ:1.00 OE1 A:GLU367 2.0 24.5 1.0 OD1 A:ASP240 2.0 22.4 1.0 OD1 A:ASP229 2.2 24.8 1.0 O A:MET406 2.3 22.4 0.5 N A:MET406 2.3 21.6 0.5 OD2 A:ASP229 2.4 22.9 1.0 CG A:ASP229 2.6 21.2 1.0 CA A:MET406 2.9 24.4 0.5 C A:MET406 2.9 24.6 0.5 CG A:ASP240 2.9 24.2 1.0 CD A:GLU367 3.0 25.4 1.0 CO A:CO402 3.1 24.1 1.0 OD2 A:ASP240 3.2 17.0 1.0 OE2 A:GLU367 3.4 26.1 1.0 OXT A:MET406 4.1 25.7 0.5 CB A:ASP229 4.1 23.0 1.0 OG1 A:THR231 4.2 24.9 0.7 CG2 A:THR231 4.2 24.6 0.3 O A:HOH503 4.3 23.6 1.0 ND2 A:ASN242 4.3 26.6 1.0 CG A:GLU367 4.3 24.9 1.0 CB A:MET406 4.3 26.7 0.5 OE2 A:GLU336 4.3 28.6 1.0 CB A:ASP240 4.4 24.6 1.0 OE1 A:GLU336 4.4 22.8 1.0 O A:LEU241 4.4 22.6 1.0 O A:HOH545 4.5 14.0 0.5 N A:LEU241 4.5 25.6 1.0 CD A:GLU336 4.7 24.0 1.0 O A:ILE230 4.7 26.0 1.0 C A:LEU241 4.7 24.5 1.0 CB A:GLU367 4.7 24.3 1.0 C A:ASP240 4.8 26.0 1.0 CB A:ASN242 4.8 25.5 1.0 CA A:ASP240 4.8 25.4 1.0 CA A:ASP229 4.9 20.6 1.0 CA A:LEU241 4.9 25.8 1.0

Cobalt binding site 2 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:24.1 occ:1.00 O A:MET406 1.8 22.4 0.5 OE1 A:GLU336 1.9 22.8 1.0 OE2 A:GLU367 2.0 26.1 1.0 OD2 A:ASP240 2.1 17.0 1.0 NE2 A:HIS303 2.2 27.1 1.0 CD A:GLU367 2.8 25.4 1.0 C A:MET406 2.9 24.6 0.5 CD A:GLU336 2.9 24.0 1.0 CG A:ASP240 3.0 24.2 1.0 OE1 A:GLU367 3.1 24.5 1.0 CO A:CO401 3.1 27.5 1.0 CD2 A:HIS303 3.2 28.0 1.0 CE1 A:HIS303 3.2 33.5 1.0 OXT A:MET406 3.3 25.7 0.5 OE2 A:GLU336 3.3 28.6 1.0 OD1 A:ASP240 3.5 22.4 1.0 OG1 A:THR334 3.6 28.6 1.0 CG2 A:THR334 3.9 25.2 1.0 CB A:THR334 4.1 27.9 1.0 CA A:MET406 4.1 24.4 0.5 CG A:GLU367 4.2 24.9 1.0 CG A:GLU336 4.2 24.8 1.0 N A:MET406 4.2 21.6 0.5 CB A:ASP240 4.3 24.6 1.0 ND1 A:HIS303 4.3 29.5 1.0 CG A:HIS303 4.3 29.3 1.0 CB A:GLU336 4.7 26.5 1.0 O A:HOH545 4.8 14.0 0.5 NE2 A:HIS310 4.8 54.0 1.0

Cobalt binding site 3 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:47.7 occ:0.50 NE2 A:HIS212 2.2 35.5 1.0 O A:HOH545 2.4 14.0 0.5 O A:HOH561 2.4 23.1 0.5 OXT A:MET406 2.5 25.7 0.5 CE1 A:HIS212 2.9 32.6 1.0 C A:MET406 3.0 24.6 0.5 CD2 A:HIS212 3.3 35.7 1.0 CA A:MET406 3.5 24.4 0.5 CG A:MET406 3.6 27.2 0.5 CB A:MET406 3.6 26.7 0.5 O A:MET406 3.8 22.4 0.5 NE2 A:HIS310 4.0 54.0 1.0 ND1 A:HIS212 4.1 31.1 1.0 OE2 A:GLU336 4.3 28.6 1.0 CG A:HIS212 4.3 31.7 1.0 CE1 A:HIS310 4.5 56.8 1.0 O A:HOH503 4.6 23.6 1.0 N A:MET406 5.0 21.6 0.5

Cobalt binding site 4 out of 4 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co404 b:40.8 occ:0.50 O A:HOH564 2.1 21.4 0.5 NE2 A:HIS99 2.2 41.5 1.0 O A:HOH568 2.3 31.9 0.5 CE1 A:HIS99 3.1 41.1 1.0 CD2 A:HIS99 3.2 37.5 1.0 ND1 A:HIS99 4.2 39.3 1.0 CG A:HIS99 4.3 37.4 1.0 O A:HOH559 4.4 35.5 1.0

V.Pillalamarri, T.Arya, A.Addlagatta. Differential Inhibition of Sub-Type 1 Methionine Aminopeptidases By Ovalicin To Be Published.