Manganese in PDB 3c0s: Uvde 3 Metals

The structure of Uvde 3 Metals, PDB code: 3c0s was solved by E.M.Meulenbroek, K.Paspaleva, E.A.J.Thomassen, J.P.Abrahams, N.Goosen, N.S.Pannu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.41 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.137, 47.562, 48.250, 99.50, 111.39, 109.02
R / Rfree (%)	20.2 / 27.5

The structure of Uvde 3 Metals also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Uvde 3 Metals (pdb code 3c0s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Uvde 3 Metals, PDB code: 3c0s:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Uvde 3 Metals


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Uvde 3 Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn281 b:16.6 occ:1.00 O A:HOH525 2.0 16.5 1.0 OD2 A:ASP200 2.1 14.3 1.0 OE2 A:GLU175 2.2 18.4 1.0 OE1 A:GLU269 2.2 18.5 1.0 ND1 A:HIS231 2.3 18.4 1.0 O A:HOH521 2.5 22.9 1.0 CD A:GLU269 3.1 20.5 1.0 CD A:GLU175 3.2 23.3 1.0 CG A:ASP200 3.2 14.7 1.0 CE1 A:HIS231 3.2 17.6 1.0 MN A:MN282 3.2 40.3 1.0 OE2 A:GLU269 3.2 21.1 1.0 CG A:HIS231 3.3 18.8 1.0 CB A:HIS231 3.5 13.2 1.0 OE1 A:GLU175 3.6 24.4 1.0 CB A:ASP200 3.7 15.5 1.0 CE1 A:HIS203 3.8 22.7 1.0 ND1 A:HIS203 4.2 17.4 1.0 OD1 A:ASP200 4.2 13.2 1.0 NE2 A:HIS231 4.3 17.3 1.0 CG A:GLU175 4.4 16.6 1.0 CD2 A:HIS231 4.4 16.9 1.0 NE2 A:HIS203 4.4 19.0 1.0 MN A:MN283 4.4 31.1 1.0 CG A:GLU269 4.5 18.8 1.0 CE1 A:HIS143 4.9 35.7 1.0 CA A:ASP200 4.9 14.6 1.0

Manganese binding site 2 out of 3 in the Uvde 3 Metals


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Uvde 3 Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn282 b:40.3 occ:1.00 OE1 A:GLU175 1.7 24.4 1.0 O A:HOH525 2.1 16.5 1.0 NE2 A:HIS101 2.3 26.9 1.0 CD A:GLU175 2.4 23.3 1.0 OE2 A:GLU175 2.6 18.4 1.0 NE2 A:HIS143 2.7 31.1 1.0 CE1 A:HIS143 2.9 35.7 1.0 CD2 A:HIS101 3.1 24.0 1.0 MN A:MN281 3.2 16.6 1.0 CE1 A:HIS101 3.3 27.7 1.0 CD2 A:HIS143 3.6 32.9 1.0 CE1 A:HIS231 3.8 17.6 1.0 CG A:GLU175 3.8 16.6 1.0 ND1 A:HIS143 3.9 31.6 1.0 O A:HOH521 4.0 22.9 1.0 ND1 A:HIS231 4.0 18.4 1.0 CG A:HIS101 4.2 24.8 1.0 CG A:HIS143 4.3 26.3 1.0 ND1 A:HIS101 4.3 23.9 1.0 CB A:GLU175 4.3 16.0 1.0 OE2 A:GLU269 4.3 21.1 1.0 CE1 A:HIS203 4.4 22.7 1.0 O A:HOH515 4.5 43.1 1.0 CG1 A:VAL141 4.7 15.3 1.0 OE1 A:GLU269 4.9 18.5 1.0 OD2 A:ASP200 5.0 14.3 1.0

Manganese binding site 3 out of 3 in the Uvde 3 Metals


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Uvde 3 Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn283 b:31.1 occ:1.00 O A:HOH521 2.2 22.9 1.0 O A:HOH509 2.3 23.5 1.0 NE2 A:HIS203 2.3 19.0 1.0 NE2 A:HIS244 2.4 25.9 1.0 O A:HOH473 2.5 28.6 1.0 CE1 A:HIS203 3.2 22.7 1.0 CD2 A:HIS203 3.3 20.9 1.0 CE1 A:HIS244 3.3 28.0 1.0 CD2 A:HIS244 3.5 25.7 1.0 O A:GLY242 4.1 18.6 1.0 OD2 A:ASP200 4.1 14.3 1.0 OE1 A:GLU178 4.2 26.4 1.0 ND1 A:HIS203 4.3 17.4 1.0 CG A:HIS203 4.3 15.3 1.0 MN A:MN281 4.4 16.6 1.0 ND1 A:HIS244 4.5 26.3 1.0 O A:HOH525 4.6 16.5 1.0 OE1 A:GLU269 4.6 18.5 1.0 CG A:HIS244 4.6 21.1 1.0 OE2 A:GLU178 4.7 22.1 1.0 CD A:GLU178 4.8 28.1 1.0 CG A:ASP200 4.9 14.7 1.0 OD1 A:ASP200 4.9 13.2 1.0

E.M.Meulenbroek, K.Paspaleva, E.A.Thomassen, J.P.Abrahams, N.Goosen, N.S.Pannu. Involvement of A Carboxylated Lysine in Uv Damage Endonuclease Protein Sci. V. 18 549 2009.
ISSN: ISSN 0961-8368
PubMed: 19241382
DOI: 10.1002/PRO.54