Magnesium in PDB 5gkp: Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna

The structure of Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna, PDB code: 5gkp was solved by J.L.Lin, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.672, 72.562, 127.914, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna (pdb code 5gkp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna, PDB code: 5gkp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.3 occ:1.00 O A:HOH532 2.2 29.8 1.0 OD1 A:ASN180 2.3 31.1 1.0 O A:HOH505 2.4 23.4 1.0 OP1 C:DT-1 2.4 33.9 1.0 O A:HOH530 2.5 32.0 1.0 O3' C:DT-2 2.8 45.0 1.0 H A:ALA148 3.2 25.5 1.0 P C:DT-1 3.2 47.7 1.0 CG A:ASN180 3.4 29.0 1.0 HD1 A:TRP184 3.6 28.0 1.0 HD21 A:ASN180 3.6 45.9 1.0 H4' C:DT-2 3.7 70.7 1.0 HA2 A:GLY147 3.7 29.8 1.0 OE2 A:GLU188 3.7 25.6 1.0 O A:ALA148 3.8 26.9 1.0 N A:ALA148 3.9 21.2 1.0 ND2 A:ASN180 3.9 38.3 1.0 OE1 A:GLN174 3.9 34.5 1.0 O5' C:DT-1 4.0 44.1 1.0 C3' C:DT-2 4.1 59.4 1.0 OE1 A:GLU188 4.1 32.7 1.0 C4' C:DT-2 4.3 58.9 1.0 CD A:GLU188 4.3 28.6 1.0 O A:ASN180 4.4 36.1 1.0 CA A:GLY147 4.4 24.8 1.0 CD1 A:TRP184 4.4 23.4 1.0 HA3 A:GLY147 4.4 29.8 1.0 O C:HOH201 4.4 31.0 1.0 OP2 C:DT-1 4.5 51.4 1.0 C A:GLY147 4.5 25.0 1.0 HE1 A:TRP184 4.5 31.7 1.0 H5'' C:DT-2 4.6 68.8 1.0 H2'' C:DT-2 4.6 69.8 1.0 HA A:ASN180 4.6 30.4 1.0 CB A:ASN180 4.7 25.4 1.0 C A:ALA148 4.7 26.9 1.0 CA A:ALA148 4.7 25.7 1.0 H3' C:DT-2 4.7 71.3 1.0 HD22 A:ASN180 4.8 45.9 1.0 CB A:ALA148 4.8 20.2 1.0 C5' C:DT-2 4.8 57.3 1.0 HB2 A:ASN180 4.9 30.4 1.0 NE1 A:TRP184 4.9 26.4 1.0 C2' C:DT-2 5.0 58.1 1.0 O5' C:DT-2 5.0 61.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Endog Worm Homologue Cps-6 H148A/F122A in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.4 occ:1.00 O B:HOH516 2.2 19.3 1.0 OD1 B:ASN180 2.3 25.4 1.0 OP1 D:DT-1 2.3 26.6 1.0 O B:HOH513 2.4 24.2 1.0 O B:HOH566 2.4 32.3 1.0 O3' D:DT-2 2.7 35.1 1.0 P D:DT-1 3.1 30.4 1.0 H B:ALA148 3.3 25.1 1.0 CG B:ASN180 3.4 24.6 1.0 HD21 B:ASN180 3.4 28.6 1.0 HD1 B:TRP184 3.5 35.8 1.0 HA2 B:GLY147 3.7 27.7 1.0 H4' D:DT-2 3.7 60.9 1.0 ND2 B:ASN180 3.8 23.9 1.0 H2'' D:DT-2 3.8 62.9 1.0 O B:ALA148 3.9 19.1 1.0 OE2 B:GLU188 3.9 28.3 1.0 O5' D:DT-1 3.9 26.6 1.0 C3' D:DT-2 3.9 44.8 1.0 N B:ALA148 3.9 20.9 1.0 OE1 B:GLN174 4.1 21.8 1.0 O B:HOH588 4.2 25.0 1.0 HE1 B:TRP184 4.2 31.9 1.0 CD1 B:TRP184 4.2 29.9 1.0 OE1 B:GLU188 4.3 29.7 1.0 O B:ASN180 4.3 23.9 1.0 C4' D:DT-2 4.3 50.7 1.0 CA B:GLY147 4.4 23.1 1.0 C2' D:DT-2 4.4 52.4 1.0 OP2 D:DT-1 4.4 34.0 1.0 HA3 B:GLY147 4.4 27.7 1.0 CD B:GLU188 4.5 35.7 1.0 HA B:ASN180 4.5 27.8 1.0 C B:GLY147 4.6 24.0 1.0 NE1 B:TRP184 4.6 26.5 1.0 HD22 B:ASN180 4.7 28.6 1.0 H3' D:DT-2 4.7 53.7 1.0 CB B:ASN180 4.7 24.6 1.0 CA B:ALA148 4.7 16.5 1.0 C B:ALA148 4.7 22.7 1.0 CB B:ALA148 4.8 21.3 1.0 H2' D:DT-2 5.0 62.9 1.0 CA B:ASN180 5.0 23.2 1.0 C B:ASN180 5.0 29.5 1.0

J.L.Lin, C.C.Wu, W.Z.Yang, H.S.Yuan. Crystal Structure of Endonuclease G in Complex with Dna Reveals How It Nonspecifically Degrades Dna As A Homodimer. Nucleic Acids Res. V. 44 10480 2016.
ISSN: ESSN 1362-4962
PubMed: 27738134
DOI: 10.1093/NAR/GKW931