Cobalt in PDB 4n8m: Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1

The structure of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1, PDB code: 4n8m was solved by D.Mitrea, G.Royappa, M.Buljan, M.Yun, N.Pytel, J.Satumba, A.Nourse, C.Park, M.M.Babu, S.W.White, R.W.Kriwacki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.26 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.675, 69.794, 88.630, 90.00, 99.87, 90.00
R / Rfree (%)	16.3 / 19

The binding sites of Cobalt atom in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 (pdb code 4n8m). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1, PDB code: 4n8m:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co601 b:76.6 occ:1.00 NE2 A:HIS30 2.3 34.1 1.0 OD2 A:ASP28 2.4 44.5 1.0 OD1 A:ASP28 2.8 34.7 1.0 CG A:ASP28 2.9 33.6 1.0 CD2 A:HIS30 3.2 38.1 1.0 CE1 A:HIS30 3.3 43.7 1.0 O A:HOH735 4.3 44.0 1.0 ND1 A:HIS30 4.4 42.5 1.0 CG A:HIS30 4.4 34.6 1.0 CB A:ASP28 4.4 26.2 1.0

Cobalt binding site 2 out of 5 in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:39.7 occ:1.00 OD2 B:ASP28 2.1 25.0 1.0 O B:HOH357 2.1 40.5 1.0 NE2 B:HIS30 2.2 24.0 1.0 O B:HOH358 2.4 53.5 1.0 O B:HOH355 2.5 37.7 1.0 CG B:ASP28 2.8 27.2 1.0 OD1 B:ASP28 2.8 24.9 1.0 CD2 B:HIS30 3.1 26.9 1.0 CE1 B:HIS30 3.2 28.9 1.0 O B:HOH354 3.7 28.8 1.0 CB B:ASP28 4.2 19.1 1.0 CG B:HIS30 4.3 22.5 1.0 ND1 B:HIS30 4.3 22.8 1.0 NH1 B:ARG101 4.4 47.9 1.0 O B:HOH326 4.7 55.0 1.0 CG1 B:VAL99 4.7 17.8 1.0 O B:HOH356 4.9 45.6 1.0 O B:HOH325 5.0 32.9 1.0

Cobalt binding site 3 out of 5 in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co201 b:58.1 occ:1.00 NE2 C:HIS30 2.2 40.5 1.0 OD2 C:ASP28 2.3 36.1 1.0 CG C:ASP28 3.0 32.7 1.0 OD1 C:ASP28 3.0 31.8 1.0 CE1 C:HIS30 3.1 42.0 1.0 CD2 C:HIS30 3.2 36.3 1.0 O C:HOH338 3.8 42.9 1.0 ND1 C:HIS30 4.2 41.3 1.0 CG C:HIS30 4.3 36.4 1.0 CB C:ASP28 4.4 19.1 1.0 CG1 C:VAL99 4.9 18.9 1.0

Cobalt binding site 4 out of 5 in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co201 b:64.5 occ:1.00 NE2 D:HIS30 2.2 46.9 1.0 OD2 D:ASP28 2.2 37.0 1.0 CG D:ASP28 3.0 35.7 1.0 OD1 D:ASP28 3.1 36.8 1.0 CE1 D:HIS30 3.1 47.4 1.0 CD2 D:HIS30 3.2 42.3 1.0 ND1 D:HIS30 4.3 43.6 1.0 CG D:HIS30 4.4 40.8 1.0 CB D:ASP28 4.4 22.7 1.0 CG1 D:VAL99 4.9 25.9 1.0

Cobalt binding site 5 out of 5 in the Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Co201 b:86.0 occ:1.00 OD2 E:ASP28 2.4 59.2 1.0 NE2 E:HIS30 2.4 49.4 1.0 CG E:ASP28 3.1 51.4 1.0 OD1 E:ASP28 3.1 52.2 1.0 CE1 E:HIS30 3.3 54.2 1.0 CD2 E:HIS30 3.4 44.6 1.0 ND1 E:HIS30 4.5 48.2 1.0 CB E:ASP28 4.5 33.8 1.0 CG E:HIS30 4.5 36.7 1.0 CG1 E:VAL99 4.7 32.2 1.0

D.M.Mitrea, C.R.Grace, M.Buljan, M.K.Yun, N.J.Pytel, J.Satumba, A.Nourse, C.G.Park, M.Madan Babu, S.W.White, R.W.Kriwacki. Structural Polymorphism in the N-Terminal Oligomerization Domain of NPM1. Proc.Natl.Acad.Sci.Usa V. 111 4466 2014.
ISSN: ISSN 0027-8424
PubMed: 24616519
DOI: 10.1073/PNAS.1321007111