Calcium in PDB 5zyv: Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+

The structure of Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+, PDB code: 5zyv 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)	28.30 / 2.72
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.282, 106.151, 33.391, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.4

The binding sites of Calcium atom in the Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+ (pdb code 5zyv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+, PDB code: 5zyv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:40.0 occ:1.00 OD1 A:ASP251 2.2 39.4 1.0 O A:HOH509 2.3 37.3 1.0 O A:HOH503 2.3 41.7 1.0 O A:ACT403 2.4 46.8 1.0 O A:TRP252 2.4 33.7 1.0 OD2 A:ASP238 2.4 42.8 1.0 CG A:ASP238 3.3 46.0 1.0 CG A:ASP251 3.5 37.6 1.0 C A:TRP252 3.5 30.8 1.0 C A:ACT403 3.5 47.6 1.0 OD1 A:ASP238 3.6 59.0 1.0 N A:TRP252 3.6 27.1 1.0 OXT A:ACT403 3.9 42.3 1.0 CA A:TRP252 4.1 27.1 1.0 C A:ASP251 4.1 30.0 1.0 OD2 A:ASP251 4.1 46.6 1.0 NZ A:LYS253 4.2 37.4 1.0 C5' E:DA5 4.3 29.6 1.0 OP1 E:DA5 4.4 35.9 1.0 CA A:ASP251 4.4 28.5 1.0 CD A:LYS253 4.4 35.4 1.0 CB A:ASP238 4.5 42.8 1.0 CB A:ASP251 4.5 27.5 1.0 OP2 E:DC6 4.6 29.2 1.0 CB A:TRP252 4.6 32.6 1.0 N A:LYS253 4.6 28.3 1.0 CE A:LYS253 4.7 37.9 1.0 O A:HOH502 4.7 16.4 1.0 CH3 A:ACT403 4.7 47.7 1.0 O A:ASP251 4.8 28.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human MGME1 with Single Strand DNA2 and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:80.1 occ:1.00 O A:TYR285 2.6 68.3 1.0 O A:ASP282 2.6 80.0 1.0 C A:TYR285 3.4 72.8 1.0 O A:MET279 3.5 67.7 1.0 C A:ASP282 3.5 78.2 1.0 CB A:TYR285 3.6 68.7 1.0 N A:TYR285 3.6 66.0 1.0 CA A:TYR285 3.7 71.7 1.0 O A:ASN280 3.9 67.3 1.0 N A:ASP282 4.1 65.3 1.0 CB A:ASP282 4.1 67.9 1.0 CA A:ASP282 4.1 70.5 1.0 O A:PHE287 4.2 70.4 1.0 C A:ASN280 4.5 61.5 1.0 N A:SER286 4.5 73.9 1.0 N A:THR283 4.6 81.7 1.0 CG A:TYR285 4.6 61.6 1.0 N A:ASN284 4.6 75.1 1.0 CD2 A:TYR285 4.7 57.0 1.0 C A:THR283 4.7 83.3 1.0 C A:MET279 4.7 57.0 1.0 CA A:ASN280 4.8 43.3 1.0 C A:ASN284 4.8 63.4 1.0 CA A:THR283 4.9 84.1 1.0 O A:THR283 5.0 88.1 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