Magnesium in PDB 5zkj: Human Exog-H140A in Complex with Rna/Dna Hybrid Duplex

The structure of Human Exog-H140A in Complex with Rna/Dna Hybrid Duplex, PDB code: 5zkj 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)	28.43 / 2.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	167.576, 167.576, 105.438, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 22.7

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

Chlorine

(Cl)

1 atom

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

Magnesium binding site 1 out of 2 in the Human Exog-H140A in Complex with Rna/Dna Hybrid 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 Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:89.4 occ:1.00 O A:HOH507 2.1 63.8 1.0 O A:HOH508 2.1 62.1 1.0 OD1 A:ASN171 2.4 83.5 1.0 O3' E:G2 2.5 89.1 1.0 OP1 E:G3 2.6 86.0 1.0 P E:G3 3.1 75.4 1.0 HO2' E:G2 3.1 99.7 1.0 H A:ALA140 3.3 80.9 1.0 OE2 A:GLU179 3.3 87.5 1.0 HD1 A:TRP175 3.4 80.5 1.0 CG A:ASN171 3.5 74.3 1.0 H4' E:G2 3.6 0.9 1.0 HD21 A:ASN171 3.6 89.0 1.0 HA2 A:GLY139 3.6 78.3 1.0 C3' E:G2 3.7 87.1 1.0 O A:ALA140 3.8 62.9 1.0 ND2 A:ASN171 3.9 74.2 1.0 N A:ALA140 3.9 67.4 1.0 O2' E:G2 3.9 83.0 1.0 H5'' E:G2 4.0 0.5 1.0 OP2 E:G3 4.0 79.0 1.0 C4' E:G2 4.0 91.6 1.0 OE1 A:GLU179 4.0 81.7 1.0 CD A:GLU179 4.1 80.6 1.0 HB3 A:ALA140 4.2 69.5 1.0 CD1 A:TRP175 4.2 67.1 1.0 O A:HOH522 4.3 71.5 1.0 O5' E:G3 4.3 89.5 1.0 HE1 A:TRP175 4.3 75.6 1.0 CA A:GLY139 4.3 65.2 1.0 HA A:ASN171 4.4 90.3 1.0 H3' E:G2 4.4 0.5 1.0 HA3 A:GLY139 4.4 78.3 1.0 O A:ASN171 4.4 81.4 1.0 C2' E:G2 4.4 92.7 1.0 OE1 A:GLN166 4.5 61.7 1.0 C A:GLY139 4.5 59.3 1.0 C5' E:G2 4.6 87.1 1.0 NE1 A:TRP175 4.6 63.0 1.0 C A:ALA140 4.7 70.2 1.0 CA A:ALA140 4.7 58.8 1.0 CB A:ASN171 4.7 73.0 1.0 HD22 A:ASN171 4.7 89.0 1.0 C A:ASN171 4.8 82.7 1.0 HE22 A:GLN166 4.8 92.5 1.0 CA A:ASN171 4.8 75.3 1.0 CB A:ALA140 4.9 57.9 1.0 H2' E:G2 4.9 0.2 1.0 H5' E:G3 5.0 95.4 1.0

Magnesium binding site 2 out of 2 in the Human Exog-H140A in Complex with Rna/Dna Hybrid 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 Hybrid Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:58.9 occ:1.00 O B:HOH522 2.1 53.7 1.0 O B:HOH508 2.1 53.0 1.0 O B:HOH513 2.1 53.3 1.0 OD1 B:ASN171 2.2 53.1 1.0 O3' C:G2 2.3 56.6 1.0 OP1 C:G3 2.6 56.2 1.0 HO2' C:G2 2.9 67.2 1.0 P C:G3 3.0 56.3 1.0 CG B:ASN171 3.2 43.8 1.0 H B:ALA140 3.3 71.7 1.0 HD21 B:ASN171 3.4 68.7 1.0 H4' C:G2 3.4 61.4 1.0 HA2 B:GLY139 3.5 69.5 1.0 HD1 B:TRP175 3.6 52.9 1.0 C3' C:G2 3.6 50.5 1.0 O5' C:G3 3.6 50.2 1.0 ND2 B:ASN171 3.7 57.2 1.0 O2' C:G2 3.8 56.0 1.0 N B:ALA140 3.9 59.8 1.0 C4' C:G2 3.9 51.1 1.0 O B:ALA140 3.9 52.3 1.0 O B:ASN171 4.0 55.4 1.0 H5'' C:G2 4.0 66.2 1.0 OE2 B:GLU179 4.1 65.4 1.0 HA B:ASN171 4.2 57.6 1.0 OE1 B:GLU179 4.2 56.0 1.0 CA B:GLY139 4.2 58.0 1.0 HB3 B:ALA140 4.3 54.1 1.0 O C:HOH202 4.3 57.1 1.0 H3' C:G2 4.3 60.5 1.0 C2' C:G2 4.3 46.5 1.0 OP2 C:G3 4.3 52.1 1.0 HA3 B:GLY139 4.3 69.5 1.0 CD1 B:TRP175 4.4 44.1 1.0 C B:GLY139 4.5 51.1 1.0 CB B:ASN171 4.5 50.5 1.0 C5' C:G2 4.5 55.1 1.0 OE1 B:GLN166 4.5 48.2 1.0 CD B:GLU179 4.5 63.3 1.0 HD22 B:ASN171 4.5 68.7 1.0 C B:ASN171 4.6 56.6 1.0 CA B:ASN171 4.6 48.0 1.0 HE22 B:GLN166 4.7 56.6 1.0 CA B:ALA140 4.8 49.1 1.0 C B:ALA140 4.8 50.4 1.0 H2' C:G2 4.8 55.8 1.0 HE1 B:TRP175 4.9 56.1 1.0 HB2 B:ASN171 4.9 60.5 1.0 CB B:ALA140 5.0 45.0 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