Magnesium in PDB 6iid: Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex

The structure of Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex, PDB code: 6iid 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)	29.83 / 2.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.710, 75.953, 81.152, 72.96, 90.01, 70.75
R / Rfree (%)	19.9 / 25.2

The binding sites of Magnesium atom in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex (pdb code 6iid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex, PDB code: 6iid:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex


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 Rna-Dna Chimeric Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:40.8 occ:1.00 OP1 G:DG3 2.1 40.3 1.0 OD1 B:ASN171 2.1 41.7 1.0 O B:HOH501 2.2 50.4 1.0 O B:HOH503 2.2 43.5 1.0 O3' G:G2 2.3 66.6 1.0 P G:DG3 2.7 49.0 1.0 HD21 B:ASN171 3.0 59.1 1.0 CG B:ASN171 3.1 48.2 1.0 HA2 B:GLY139 3.1 49.2 1.0 HO2' G:G2 3.1 62.7 1.0 H B:ALA140 3.3 62.5 1.0 ND2 B:ASN171 3.4 49.2 1.0 O5' G:DG3 3.6 48.3 1.0 C3' G:G2 3.6 55.6 1.0 H4' G:G2 3.6 67.7 1.0 N B:ALA140 3.7 52.1 1.0 OE2 B:GLU179 3.8 52.4 1.0 O2' G:G2 3.8 52.2 1.0 HD1 B:TRP175 3.9 62.4 1.0 CA B:GLY139 3.9 41.0 1.0 O B:ALA140 3.9 48.5 1.0 OP2 G:DG3 4.0 52.3 1.0 HA3 B:GLY139 4.0 49.2 1.0 C4' G:G2 4.0 56.4 1.0 HB3 B:ALA140 4.1 57.7 1.0 H5'' G:G2 4.1 67.2 1.0 C B:GLY139 4.1 47.9 1.0 H3' G:G2 4.2 66.8 1.0 HD22 B:ASN171 4.2 59.1 1.0 OE1 B:GLN166 4.2 38.5 1.0 O B:ASN171 4.3 58.7 1.0 C2' G:G2 4.3 54.2 1.0 CB B:ASN171 4.5 51.2 1.0 HA B:ASN171 4.5 61.0 1.0 OE1 B:GLU179 4.5 61.1 1.0 HE1 B:TRP175 4.5 61.6 1.0 CD B:GLU179 4.5 59.4 1.0 CD1 B:TRP175 4.6 52.0 1.0 CA B:ALA140 4.6 46.6 1.0 C5' G:G2 4.6 56.0 1.0 O B:ARG138 4.7 47.0 1.0 C B:ALA140 4.7 40.5 1.0 H2' G:G2 4.8 65.1 1.0 CB B:ALA140 4.8 48.0 1.0 C5' G:DG3 4.8 46.4 1.0 CA B:ASN171 4.9 50.9 1.0 C B:ASN171 4.9 55.4 1.0 HB2 B:ASN171 4.9 61.5 1.0 NE1 B:TRP175 4.9 51.4 1.0 H5' G:DG3 4.9 55.7 1.0

Magnesium binding site 2 out of 4 in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex


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 Rna-Dna Chimeric Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:35.3 occ:1.00 OP1 I:DG3 2.1 43.6 1.0 OD1 C:ASN171 2.1 38.5 1.0 O C:HOH501 2.2 40.5 1.0 O3' I:G2 2.2 47.7 1.0 O C:HOH503 2.2 48.8 1.0 P I:DG3 2.6 44.5 1.0 HD21 C:ASN171 2.8 49.3 1.0 CG C:ASN171 3.0 43.8 1.0 H C:ALA140 3.1 53.6 1.0 ND2 C:ASN171 3.2 41.0 1.0 HO2' I:G2 3.2 54.9 1.0 HA2 C:GLY139 3.4 47.8 1.0 C3' I:G2 3.5 46.6 1.0 O5' I:DG3 3.5 42.8 1.0 H4' I:G2 3.6 61.7 1.0 N C:ALA140 3.7 44.7 1.0 O C:ALA140 3.8 49.4 1.0 HD1 C:TRP175 3.9 41.4 1.0 HB3 C:ALA140 3.9 41.1 1.0 OP2 I:DG3 3.9 49.7 1.0 H5'' I:G2 3.9 52.4 1.0 O2' I:G2 3.9 45.7 1.0 C4' I:G2 4.0 51.4 1.0 HD22 C:ASN171 4.0 49.3 1.0 H3' I:G2 4.1 56.0 1.0 CA C:GLY139 4.2 39.8 1.0 OE1 C:GLU179 4.3 55.4 1.0 C C:GLY139 4.3 45.6 1.0 O C:ASN171 4.3 46.2 1.0 C2' I:G2 4.3 47.7 1.0 OE2 C:GLU179 4.3 52.3 1.0 HA3 C:GLY139 4.3 47.8 1.0 OE1 C:GLN166 4.3 38.5 1.0 CB C:ASN171 4.4 47.0 1.0 HA C:ASN171 4.5 55.1 1.0 C5' I:G2 4.5 43.6 1.0 CA C:ALA140 4.5 45.7 1.0 C C:ALA140 4.6 42.8 1.0 CB C:ALA140 4.6 34.2 1.0 CD1 C:TRP175 4.7 34.5 1.0 CD C:GLU179 4.7 54.5 1.0 H2' I:G2 4.8 57.2 1.0 CA C:ASN171 4.8 45.9 1.0 C5' I:DG3 4.8 41.7 1.0 C C:ASN171 4.9 44.9 1.0 HB3 C:ASN171 4.9 56.4 1.0 HE1 C:TRP175 4.9 36.0 1.0 HB2 C:ASN171 4.9 56.4 1.0 HB2 C:ALA140 4.9 41.1 1.0 H5' I:DG3 4.9 50.1 1.0

Magnesium binding site 3 out of 4 in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex


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 Rna-Dna Chimeric Duplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:40.3 occ:1.00 OP1 E:DG3 2.0 49.9 1.0 O3' E:G2 2.1 61.0 1.0 O E:HOH201 2.1 41.5 1.0 OD1 A:ASN171 2.1 44.9 1.0 O A:HOH406 2.1 53.8 1.0 O A:HOH403 2.2 56.1 1.0 P E:DG3 2.6 51.4 1.0 HD21 A:ASN171 3.0 67.6 1.0 H A:ALA140 3.0 52.9 1.0 HO2' E:G2 3.1 59.1 1.0 CG A:ASN171 3.1 50.3 1.0 ND2 A:ASN171 3.4 56.3 1.0 C3' E:G2 3.4 60.1 1.0 HA2 A:GLY139 3.5 63.8 1.0 O5' E:DG3 3.5 51.2 1.0 H4' E:G2 3.6 68.3 1.0 HD1 A:TRP175 3.6 51.7 1.0 N A:ALA140 3.8 44.1 1.0 OP2 E:DG3 3.8 46.6 1.0 O2' E:G2 3.9 49.2 1.0 H5'' E:G2 3.9 78.7 1.0 C4' E:G2 3.9 56.9 1.0 H3' E:G2 4.0 72.2 1.0 OE1 A:GLU179 4.0 61.4 1.0 HB3 A:ALA140 4.0 59.9 1.0 O A:ALA140 4.1 49.2 1.0 O A:ASN171 4.2 49.0 1.0 C2' E:G2 4.2 58.5 1.0 CA A:GLY139 4.2 53.2 1.0 HD22 A:ASN171 4.2 67.6 1.0 OE1 A:GLN166 4.2 38.7 1.0 HA3 A:GLY139 4.3 63.8 1.0 CD1 A:TRP175 4.4 43.0 1.0 C5' E:G2 4.4 65.5 1.0 C A:GLY139 4.4 49.8 1.0 CB A:ASN171 4.5 48.5 1.0 OE2 A:GLU179 4.5 60.1 1.0 HA A:ASN171 4.6 63.1 1.0 HE1 A:TRP175 4.6 55.9 1.0 CA A:ALA140 4.6 53.8 1.0 CD A:GLU179 4.7 69.8 1.0 H2' E:G2 4.7 70.2 1.0 C A:ASN171 4.7 51.8 1.0 CB A:ALA140 4.7 49.9 1.0 C A:ALA140 4.8 52.6 1.0 C5' E:DG3 4.8 58.6 1.0 CA A:ASN171 4.9 52.6 1.0 NE1 A:TRP175 4.9 46.6 1.0 H5' E:DG3 5.0 70.4 1.0 HB2 A:ASN171 5.0 58.1 1.0

Magnesium binding site 4 out of 4 in the Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Exog-H140A in Complex with Rna-Dna Chimeric Duplex within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg101 b:50.4 occ:1.00 OD1 D:ASN171 2.1 47.6 1.0 O D:HOH404 2.1 42.5 1.0 OP1 K:DG3 2.2 46.0 1.0 O3' K:G2 2.2 55.4 1.0 O D:HOH406 2.2 41.5 1.0 P K:DG3 2.7 42.8 1.0 HD21 D:ASN171 3.0 65.6 1.0 H D:ALA140 3.1 42.9 1.0 CG D:ASN171 3.1 42.2 1.0 ND2 D:ASN171 3.4 54.7 1.0 H4' K:G2 3.5 75.8 1.0 C3' K:G2 3.5 56.8 1.0 HA2 D:GLY139 3.6 57.8 1.0 O5' K:DG3 3.6 47.8 1.0 HD1 D:TRP175 3.7 47.8 1.0 N D:ALA140 3.8 35.7 1.0 HO2' K:G2 3.8 73.3 1.0 O2' K:G2 3.8 61.1 1.0 H5'' K:G2 3.9 70.8 1.0 C4' K:G2 3.9 63.1 1.0 OP2 K:DG3 3.9 64.9 1.0 O D:ALA140 3.9 53.1 1.0 OE2 D:GLU179 3.9 49.7 1.0 OE1 D:GLU179 4.1 49.9 1.0 H3' K:G2 4.1 68.1 1.0 O D:ASN171 4.1 48.6 1.0 HB3 D:ALA140 4.1 46.4 1.0 C2' K:G2 4.3 60.7 1.0 HD22 D:ASN171 4.3 65.6 1.0 CA D:GLY139 4.3 48.2 1.0 OE1 D:GLN166 4.3 39.0 1.0 HA3 D:GLY139 4.3 57.8 1.0 CD D:GLU179 4.4 55.2 1.0 HA D:ASN171 4.4 65.9 1.0 C5' K:G2 4.4 59.0 1.0 CB D:ASN171 4.4 40.6 1.0 C D:GLY139 4.5 50.3 1.0 CD1 D:TRP175 4.5 39.8 1.0 CA D:ALA140 4.7 41.8 1.0 C D:ASN171 4.7 59.4 1.0 C D:ALA140 4.7 43.6 1.0 CA D:ASN171 4.7 54.9 1.0 H2' K:G2 4.8 72.9 1.0 HH12 D:ARG109 4.8 83.3 1.0 HE1 D:TRP175 4.8 51.7 1.0 CB D:ALA140 4.8 38.6 1.0 C5' K:DG3 4.9 56.4 1.0 HB2 D:ASN171 4.9 48.7 1.0 HB3 D:ASN171 5.0 48.7 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