Calcium in PDB 8xa9: Human MGME1 in Complex with 5'-Overhang Dna

The structure of Human MGME1 in Complex with 5'-Overhang Dna, PDB code: 8xa9 was solved by C.C.Wu, E.Y.C.Mao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.46 / 2.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.756, 56.193, 114.445, 90, 113.02, 90
R / Rfree (%)	25.8 / 27.8

The binding sites of Calcium atom in the Human MGME1 in Complex with 5'-Overhang Dna (pdb code 8xa9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human MGME1 in Complex with 5'-Overhang Dna, PDB code: 8xa9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human MGME1 in Complex with 5'-Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human MGME1 in Complex with 5'-Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:53.9 occ:1.00 OD2 A:ASP238 2.3 53.1 1.0 NE2 A:HIS180 2.3 56.8 1.0 OP1 E:DT4 2.3 61.8 1.0 O A:TRP252 2.3 57.6 1.0 O E:HOH201 2.4 58.4 1.0 OD1 A:ASP251 2.4 66.6 1.0 CE1 A:HIS180 3.1 59.6 1.0 CG A:ASP238 3.3 60.2 1.0 CD2 A:HIS180 3.4 58.2 1.0 C A:TRP252 3.5 56.6 1.0 OD1 A:ASP238 3.6 59.3 1.0 CG A:ASP251 3.6 54.9 1.0 P E:DT4 3.7 51.4 1.0 CA E:CA101 3.8 78.3 1.0 N A:TRP252 3.8 54.4 1.0 C A:ASP251 4.2 57.2 1.0 CA A:TRP252 4.2 53.3 1.0 O E:HOH204 4.2 56.1 1.0 O5' E:DT4 4.3 59.6 1.0 ND1 A:HIS180 4.3 62.5 1.0 OP2 E:DT5 4.3 63.6 1.0 OD2 A:ASP251 4.4 55.1 1.0 NZ A:LYS253 4.4 56.0 1.0 CA A:ASP251 4.4 50.5 1.0 CG A:HIS180 4.5 60.4 1.0 C5' E:DT4 4.5 58.0 1.0 N A:LYS253 4.5 54.3 1.0 CB A:LYS253 4.5 60.6 1.0 OP2 E:DT4 4.6 62.1 1.0 CB A:ASP251 4.6 54.7 1.0 CB A:ASP238 4.6 53.5 1.0 CA A:LYS253 4.7 58.6 1.0 O3' E:DT3 4.7 62.3 1.0 CB A:TRP252 4.8 57.4 1.0 O A:ASP251 4.8 55.5 1.0

Calcium binding site 2 out of 4 in the Human MGME1 in Complex with 5'-Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human MGME1 in Complex with 5'-Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:43.6 occ:1.00 OP1 C:DT4 2.3 44.2 1.0 NE2 B:HIS180 2.3 41.2 1.0 O B:TRP252 2.3 47.4 1.0 OD2 B:ASP238 2.3 38.7 1.0 O B:HOH522 2.4 46.0 1.0 OD1 B:ASP251 2.4 54.1 1.0 CE1 B:HIS180 3.2 43.8 1.0 CD2 B:HIS180 3.4 44.6 1.0 CG B:ASP238 3.4 43.5 1.0 C B:TRP252 3.5 44.3 1.0 CG B:ASP251 3.6 52.0 1.0 P C:DT4 3.7 39.9 1.0 OD1 B:ASP238 3.7 42.7 1.0 N B:TRP252 3.8 39.6 1.0 CA C:CA101 3.8 61.0 1.0 CA B:TRP252 4.2 42.3 1.0 C B:ASP251 4.2 46.3 1.0 NZ B:LYS253 4.2 47.6 1.0 O5' C:DT4 4.2 46.5 1.0 ND1 B:HIS180 4.3 43.6 1.0 OD2 B:ASP251 4.4 47.4 1.0 CA B:ASP251 4.4 42.7 1.0 OP2 C:DT5 4.4 48.6 1.0 O B:HOH529 4.4 38.6 1.0 C5' C:DT4 4.4 44.8 1.0 OP2 C:DT4 4.4 44.5 1.0 CG B:HIS180 4.5 47.5 1.0 N B:LYS253 4.5 43.6 1.0 CB B:ASP251 4.6 42.4 1.0 CB B:TRP252 4.7 48.1 1.0 CB B:LYS253 4.7 42.6 1.0 CB B:ASP238 4.7 38.4 1.0 O3' C:DT3 4.7 46.1 1.0 CA B:LYS253 4.7 46.7 1.0 O B:HOH514 4.9 50.4 1.0 O B:ASP251 4.9 41.2 1.0

Calcium binding site 3 out of 4 in the Human MGME1 in Complex with 5'-Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human MGME1 in Complex with 5'-Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:61.0 occ:1.00 OD1 B:ASP238 2.3 42.7 1.0 O3' C:DT3 2.4 46.1 1.0 O B:HOH529 2.4 38.6 1.0 OP1 C:DT4 2.4 44.2 1.0 O B:HOH537 2.5 49.4 1.0 O B:HOH534 2.5 44.7 1.0 P C:DT4 3.0 39.9 1.0 CG B:ASP238 3.4 43.5 1.0 C3' C:DT3 3.5 43.0 1.0 C4' C:DT3 3.7 48.5 1.0 CD2 B:HIS180 3.8 44.6 1.0 OD2 B:ASP238 3.8 38.7 1.0 CA B:CA401 3.8 43.6 1.0 C5' C:DT4 3.9 44.8 1.0 O5' C:DT4 4.0 46.5 1.0 NE2 B:HIS180 4.0 41.2 1.0 OE2 B:GLU223 4.0 50.5 1.0 O B:LEU236 4.1 41.4 1.0 OP2 C:DT4 4.2 44.5 1.0 C5' C:DT3 4.3 45.4 1.0 O C:HOH202 4.6 55.0 1.0 OE1 B:GLU223 4.6 54.3 1.0 C2' C:DT3 4.7 48.2 1.0 CB B:ASP238 4.7 38.4 1.0 CD B:GLU223 4.7 56.1 1.0 CG B:HIS180 4.8 47.5 1.0 N B:ASP238 4.8 42.5 1.0 CA B:ASP238 4.9 46.0 1.0 O4' C:DT3 4.9 42.1 1.0

Calcium binding site 4 out of 4 in the Human MGME1 in Complex with 5'-Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human MGME1 in Complex with 5'-Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca101 b:78.3 occ:1.00 O3' E:DT3 2.3 62.3 1.0 OD1 A:ASP238 2.4 59.3 1.0 O E:HOH204 2.4 56.1 1.0 O A:HOH512 2.5 51.3 1.0 O A:HOH517 2.5 60.2 1.0 OP1 E:DT4 2.5 61.8 1.0 P E:DT4 3.0 51.4 1.0 CG A:ASP238 3.4 60.2 1.0 C3' E:DT3 3.5 60.5 1.0 C4' E:DT3 3.7 60.8 1.0 C5' E:DT4 3.8 58.0 1.0 CD2 A:HIS180 3.8 58.2 1.0 OD2 A:ASP238 3.8 53.1 1.0 CA A:CA401 3.8 53.9 1.0 O5' E:DT4 3.9 59.6 1.0 NE2 A:HIS180 4.0 56.8 1.0 OP2 E:DT4 4.2 62.1 1.0 O A:LEU236 4.2 50.1 1.0 C5' E:DT3 4.3 59.4 1.0 OE2 A:GLU223 4.4 66.1 1.0 OE1 A:GLU223 4.5 61.1 1.0 C2' E:DT3 4.6 60.1 1.0 CB A:ASP238 4.7 53.5 1.0 CG A:HIS180 4.7 60.4 1.0 N A:ASP238 4.9 54.6 1.0 CD A:GLU223 4.9 63.0 1.0 CE1 A:HIS180 4.9 59.6 1.0 O4' E:DT3 4.9 51.3 1.0 CA A:ASP238 4.9 59.3 1.0

E.Y.C.Mao, H.Y.Yen, C.C.Wu. Structural Basis of How MGME1 Processes Dna 5' Ends to Maintain Mitochondrial Genome Integrity. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38471810
DOI: 10.1093/NAR/GKAE186