Manganese in PDB 5zyw: The Crystal Structure of Apo-HSMGME1 with MN2+

The structure of The Crystal Structure of Apo-HSMGME1 with MN2+, PDB code: 5zyw was solved by C.Yang, J.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.997, 67.997, 114.841, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.2

The binding sites of Manganese atom in the The Crystal Structure of Apo-HSMGME1 with MN2+ (pdb code 5zyw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of Apo-HSMGME1 with MN2+, PDB code: 5zyw:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.6 occ:1.00 O A:HOH554 2.0 17.0 1.0 OD1 A:ASP238 2.1 20.2 1.0 OE2 A:GLU344 2.1 18.0 1.0 O1 A:TLA404 2.2 17.8 1.0 O A:HOH511 2.2 20.2 1.0 O A:HOH528 2.3 19.9 1.0 CD A:GLU344 3.1 18.6 1.0 CG A:ASP238 3.2 21.4 1.0 C1 A:TLA404 3.2 18.2 1.0 OE1 A:GLU344 3.5 19.1 1.0 OD2 A:ASP238 3.7 21.3 1.0 C2 A:TLA404 3.7 18.1 1.0 MN A:MN402 3.9 19.3 1.0 O A:LEU236 4.0 22.6 1.0 CD2 A:HIS180 4.0 20.5 1.0 C3 A:TLA404 4.1 18.3 1.0 OE1 A:GLU223 4.2 25.6 1.0 NE2 A:HIS180 4.2 20.5 1.0 OE2 A:GLU223 4.2 24.6 1.0 OD2 A:ASP251 4.3 20.7 1.0 O11 A:TLA404 4.3 18.6 1.0 O A:HOH588 4.3 20.7 1.0 CG A:GLU344 4.3 18.8 1.0 CB A:ASP238 4.4 22.2 1.0 N A:ASP238 4.5 22.6 1.0 CA A:ASP238 4.5 23.0 1.0 CB A:GLU344 4.6 19.0 1.0 CD A:GLU223 4.6 25.2 1.0 OD1 A:ASP251 4.8 21.5 1.0 O3 A:TLA404 4.8 18.0 1.0 CG A:ASP251 4.9 21.2 1.0 C A:LEU237 4.9 22.3 1.0 CG A:HIS180 5.0 20.9 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:19.3 occ:1.00 OD2 A:ASP238 2.1 21.3 1.0 O A:TRP252 2.1 19.4 1.0 OD1 A:ASP251 2.2 21.5 1.0 O1 A:TLA404 2.3 17.8 1.0 NE2 A:HIS180 2.3 20.5 1.0 O11 A:TLA404 2.4 18.6 1.0 C1 A:TLA404 2.7 18.2 1.0 CG A:ASP238 3.1 21.4 1.0 CG A:ASP251 3.1 21.2 1.0 C A:TRP252 3.2 19.8 1.0 CE1 A:HIS180 3.3 20.3 1.0 N A:TRP252 3.3 20.6 1.0 CD2 A:HIS180 3.3 20.5 1.0 OD1 A:ASP238 3.4 20.2 1.0 OD2 A:ASP251 3.6 20.7 1.0 CA A:TRP252 3.7 20.6 1.0 MN A:MN401 3.9 20.6 1.0 C A:ASP251 3.9 20.9 1.0 CB A:TRP252 4.1 21.3 1.0 NZ A:LYS253 4.1 18.8 1.0 C2 A:TLA404 4.2 18.1 1.0 CB A:ASP251 4.2 21.3 1.0 CA A:ASP251 4.2 21.6 1.0 O A:HOH554 4.3 17.0 1.0 N A:LYS253 4.4 19.0 1.0 ND1 A:HIS180 4.4 20.2 1.0 CD A:LYS253 4.4 18.9 1.0 CE A:LYS253 4.4 18.8 1.0 CB A:ASP238 4.4 22.2 1.0 CG A:HIS180 4.5 20.9 1.0 O A:ASP251 4.7 20.3 1.0 CA A:LYS253 4.8 18.7 1.0 O3 A:TLA404 4.8 18.0 1.0 CD1 A:TRP252 4.9 22.5 1.0 O A:HOH528 4.9 19.9 1.0 O2 A:TLA404 4.9 18.3 1.0 CG A:TRP252 4.9 22.1 1.0 O A:HOH587 5.0 17.9 1.0 C3 A:TLA404 5.0 18.3 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:55.3 occ:1.00 OG A:SER343 2.3 18.3 1.0 O A:HOH550 2.4 30.4 1.0 OG1 A:THR134 2.5 18.3 1.0 O A:HOH501 2.7 21.6 1.0 CB A:THR134 3.3 18.5 1.0 CB A:SER343 3.6 19.0 1.0 NZ A:LYS259 3.7 24.4 1.0 N A:GLU344 4.0 18.8 1.0 CA A:SER343 4.2 19.4 1.0 CG2 A:THR134 4.3 18.6 1.0 C A:THR134 4.4 19.8 1.0 N A:ARG135 4.4 21.0 1.0 OXT A:GLU344 4.4 18.9 1.0 CA A:THR134 4.4 19.1 1.0 C A:SER343 4.5 19.3 1.0 O A:HOH564 4.5 29.1 1.0 OG A:SER132 4.6 20.5 1.0 O A:HOH565 4.7 28.7 1.0 O4 A:TLA404 4.7 18.0 1.0 O41 A:TLA404 4.8 18.2 1.0 O A:THR134 4.8 20.8 1.0 OE1 A:GLN138 5.0 26.7 1.0

C.Yang, R.Wu, H.Liu, Y.Chen, Y.Gao, X.Chen, Y.Li, J.Ma, J.Li, J.Gan. Structural Insights Into Dna Degradation By Human Mitochondrial Nuclease MGME1 Nucleic Acids Res. V. 46 11075 2018.
ISSN: ESSN 1362-4962
PubMed: 30247721
DOI: 10.1093/NAR/GKY855