Magnesium in PDB 5zki: Human Exog-H140A in Complex with Duplex Dna

The structure of Human Exog-H140A in Complex with Duplex Dna, PDB code: 5zki was solved by C.C.Wu, J.L.J.Lin, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.497, 91.123, 129.451, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.8

The structure of Human Exog-H140A in Complex with Duplex Dna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Human Exog-H140A in Complex with Duplex Dna (pdb code 5zki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Exog-H140A in Complex with Duplex Dna, PDB code: 5zki:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Exog-H140A in Complex with Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Exog-H140A in Complex with Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:40.7 occ:1.00 O A:HOH518 2.1 37.5 1.0 OD1 A:ASN171 2.1 43.0 1.0 O A:HOH515 2.1 42.1 1.0 O A:HOH507 2.1 41.0 1.0 OP1 C:DG3 2.3 44.5 1.0 O3' C:DG2 2.3 56.0 1.0 P C:DG3 2.8 51.1 1.0 CG A:ASN171 3.2 41.2 1.0 H A:ALA140 3.3 52.9 1.0 HD21 A:ASN171 3.4 56.2 1.0 H4' C:DG2 3.5 57.4 1.0 HD1 A:TRP175 3.5 54.8 1.0 C3' C:DG2 3.6 47.8 1.0 HA2 A:GLY139 3.6 54.3 1.0 ND2 A:ASN171 3.7 46.8 1.0 O5' C:DG3 3.7 38.0 1.0 N A:ALA140 3.9 44.1 1.0 H2'' C:DG2 3.9 55.7 1.0 H5'' C:DG2 3.9 55.9 1.0 OE1 A:GLU179 4.0 52.4 1.0 C4' C:DG2 4.0 47.8 1.0 O A:ALA140 4.0 41.4 1.0 O A:ASN171 4.0 43.6 1.0 HB3 A:ALA140 4.0 57.6 1.0 OE2 A:GLU179 4.1 46.0 1.0 OP2 C:DG3 4.1 41.5 1.0 O C:HOH204 4.2 53.6 1.0 HA A:ASN171 4.2 55.1 1.0 OE1 A:GLN166 4.2 42.2 1.0 H3' C:DG2 4.3 57.4 1.0 C2' C:DG2 4.3 46.5 1.0 CD1 A:TRP175 4.4 45.7 1.0 CD A:GLU179 4.4 49.8 1.0 CA A:GLY139 4.4 45.2 1.0 CB A:ASN171 4.5 45.1 1.0 HA3 A:GLY139 4.5 54.3 1.0 C5' C:DG2 4.5 46.6 1.0 HD22 A:ASN171 4.5 56.2 1.0 C A:GLY139 4.6 44.9 1.0 C A:ASN171 4.6 50.5 1.0 CA A:ASN171 4.6 45.9 1.0 HE22 A:GLN166 4.7 51.4 1.0 HE1 A:TRP175 4.7 57.1 1.0 CA A:ALA140 4.7 49.4 1.0 CB A:ALA140 4.8 48.0 1.0 C A:ALA140 4.8 52.1 1.0 H2' C:DG2 4.9 55.7 1.0 NE1 A:TRP175 4.9 47.6 1.0 HB2 A:ASN171 5.0 54.1 1.0 CD A:GLN166 5.0 50.6 1.0

Magnesium binding site 2 out of 3 in the Human Exog-H140A in Complex with Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Exog-H140A in Complex with Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:44.1 occ:1.00 O B:HOH525 2.1 39.1 1.0 OD1 B:ASN171 2.1 42.6 1.0 O B:HOH504 2.1 37.6 1.0 O B:HOH513 2.1 34.5 1.0 OP1 E:DG3 2.2 44.9 1.0 O3' E:DG2 2.4 42.8 1.0 P E:DG3 2.9 43.9 1.0 CG B:ASN171 3.1 41.7 1.0 H B:ALA140 3.2 45.5 1.0 HD21 B:ASN171 3.3 51.8 1.0 HD1 B:TRP175 3.4 52.7 1.0 HA2 B:GLY139 3.6 55.7 1.0 H4' E:DG2 3.6 55.5 1.0 ND2 B:ASN171 3.6 43.2 1.0 O5' E:DG3 3.7 33.8 1.0 C3' E:DG2 3.7 43.8 1.0 N B:ALA140 3.8 37.9 1.0 HB3 B:ALA140 3.8 55.7 1.0 OE2 B:GLU179 3.9 43.3 1.0 O B:ALA140 3.9 42.2 1.0 H2'' E:DG2 4.0 52.5 1.0 O B:ASN171 4.1 41.2 1.0 H5'' E:DG2 4.1 51.2 1.0 C4' E:DG2 4.1 46.2 1.0 OE1 B:GLU179 4.1 48.3 1.0 OE1 B:GLN166 4.1 42.1 1.0 OP2 E:DG3 4.2 33.1 1.0 HA B:ASN171 4.2 44.1 1.0 CD1 B:TRP175 4.2 43.9 1.0 O E:HOH203 4.3 49.0 1.0 H3' E:DG2 4.4 52.5 1.0 CD B:GLU179 4.4 44.6 1.0 CA B:GLY139 4.4 46.4 1.0 C2' E:DG2 4.4 43.8 1.0 CB B:ASN171 4.4 42.0 1.0 HD22 B:ASN171 4.5 51.8 1.0 C B:GLY139 4.5 45.5 1.0 HE1 B:TRP175 4.5 56.1 1.0 HA3 B:GLY139 4.6 55.7 1.0 CA B:ALA140 4.6 49.6 1.0 CB B:ALA140 4.6 46.4 1.0 HE22 B:GLN166 4.6 46.9 1.0 CA B:ASN171 4.6 36.7 1.0 C5' E:DG2 4.6 42.7 1.0 C B:ASN171 4.7 46.4 1.0 C B:ALA140 4.7 48.4 1.0 NE1 B:TRP175 4.8 46.8 1.0 CD B:GLN166 4.9 44.0 1.0 HB2 B:ALA140 4.9 55.7 1.0 H2' E:DG2 5.0 52.5 1.0 HB2 B:ASN171 5.0 50.4 1.0

Magnesium binding site 3 out of 3 in the Human Exog-H140A in Complex with Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Exog-H140A in Complex with Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:68.4 occ:1.00 O B:HOH553 2.2 67.2 1.0 O B:HOH540 2.2 62.7 1.0 O F:HOH103 2.2 62.4 1.0 O F:HOH102 2.2 77.5 1.0 HD2 B:ARG324 2.9 82.4 1.0 HB3 B:ARG324 3.3 69.7 1.0 HA B:ALA319 3.4 72.3 1.0 CD B:ARG324 3.8 68.6 1.0 HD3 B:ARG324 4.1 82.4 1.0 HE2 B:LYS315 4.1 61.5 1.0 HD11 B:ILE328 4.2 65.3 1.0 CB B:ARG324 4.2 58.1 1.0 CA B:ALA319 4.3 60.2 1.0 O B:GLY318 4.3 65.3 1.0 HG3 B:ARG324 4.4 75.5 1.0 CG B:ARG324 4.4 62.9 1.0 H B:ARG320 4.5 85.4 1.0 OP2 F:DC11 4.5 52.5 1.0 N B:ALA319 4.6 60.5 1.0 C B:GLY318 4.6 65.6 1.0 HB2 B:ALA319 4.7 71.6 1.0 HB3 B:LYS315 4.7 59.8 1.0 H5 F:DC11 4.7 53.7 1.0 H3' F:DC10 4.7 65.1 1.0 HB2 B:ARG324 4.7 69.7 1.0 OP2 F:DC10 4.9 62.0 1.0 NE B:ARG324 4.9 80.2 1.0 HE B:ARG324 4.9 96.2 1.0 O B:ARG324 4.9 59.2 1.0 O B:LYS315 4.9 54.2 1.0 CB B:ALA319 5.0 59.7 1.0

C.C.Wu, J.L.J.Lin, H.F.Yang-Yen, H.S.Yuan. A Unique Exonuclease Exog Cleaves Between Rna and Dna in Mitochondrial Dna Replication. Nucleic Acids Res. V. 47 5405 2019.
ISSN: ESSN 1362-4962
PubMed: 30949702
DOI: 10.1093/NAR/GKZ241