Magnesium in PDB 9l55: Plastid Localized Exonuclease 1 (D249A) Complexed with Dna

The structure of Plastid Localized Exonuclease 1 (D249A) Complexed with Dna, PDB code: 9l55 was solved by G.Shi, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.38 / 2.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.45, 104.4, 117.35, 90, 90, 90
R / Rfree (%)	26.9 / 31.5

The binding sites of Magnesium atom in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna (pdb code 9l55). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna, PDB code: 9l55:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plastid Localized Exonuclease 1 (D249A) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:98.3 occ:1.00 HB3 A:GLU224 2.6 86.0 1.0 OP2 F:DA1 2.7 119.3 1.0 H A:ASP226 2.8 97.8 1.0 O A:HOH604 2.8 70.1 1.0 H A:ALA225 3.1 78.8 1.0 OD1 A:ASP226 3.1 118.1 1.0 OD2 A:ASP155 3.2 86.2 1.0 OD1 A:ASP155 3.3 69.3 1.0 OE1 A:GLU224 3.3 86.9 1.0 CG A:ASP226 3.3 93.5 1.0 HB2 A:ASP226 3.5 88.2 1.0 HB3 A:ALA225 3.5 67.7 1.0 N A:ASP226 3.5 80.8 1.0 CB A:GLU224 3.5 71.0 1.0 N A:ALA225 3.6 65.0 1.0 CG A:ASP155 3.6 68.7 1.0 OD2 A:ASP226 3.7 81.2 1.0 O A:HOH606 3.8 118.8 1.0 CB A:ASP226 3.8 72.8 1.0 O A:HOH609 3.9 102.8 1.0 O A:HOH603 3.9 79.5 1.0 HB2 A:GLU224 4.0 86.0 1.0 P F:DA1 4.0 146.7 1.0 HA A:GLU224 4.0 81.0 1.0 CD A:GLU224 4.1 73.2 1.0 CA A:GLU224 4.2 66.8 1.0 C A:GLU224 4.2 60.2 1.0 CA A:ASP226 4.3 65.5 1.0 CB A:ALA225 4.3 55.7 1.0 CA A:ALA225 4.3 45.5 1.0 OP3 F:DA1 4.4 90.2 1.0 C A:ALA225 4.4 69.3 1.0 CG A:GLU224 4.4 82.1 1.0 HB3 A:ASP226 4.7 88.2 1.0 HB2 A:ALA225 4.7 67.7 1.0 OP1 F:DA1 4.8 131.0 1.0 HA A:ASP226 4.8 79.5 1.0 HG3 A:GLU224 4.8 99.4 1.0 OE2 A:GLU224 5.0 89.5 1.0 HB1 A:ALA225 5.0 67.7 1.0 H A:ASP227 5.0 77.3 1.0

Magnesium binding site 2 out of 4 in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plastid Localized Exonuclease 1 (D249A) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:95.9 occ:1.00 OD2 A:ASP304 2.1 93.0 1.0 O A:HOH601 2.3 93.0 1.0 O A:HOH611 2.4 65.3 1.0 O A:HOH602 2.4 96.6 1.0 O A:HOH605 2.6 100.0 1.0 OD1 A:ASP251 2.8 94.8 1.0 CG A:ASP304 3.2 80.2 1.0 OD2 A:ASP251 3.3 105.5 1.0 CG A:ASP251 3.4 85.2 1.0 OD2 A:ASP301 3.5 89.4 1.0 OD1 A:ASP304 3.8 65.1 1.0 CG A:ASP301 4.2 103.6 1.0 O A:HOH606 4.2 118.8 1.0 HB2 A:ASP304 4.4 89.7 1.0 CB A:ASP304 4.4 74.0 1.0 H5' F:DA1 4.6 130.0 1.0 HB3 A:ASP301 4.6 99.5 1.0 OP2 F:DT2 4.7 89.5 1.0 CB A:ASP251 4.8 68.8 1.0 O A:HOH609 4.8 102.8 1.0 HB3 A:ASP304 4.8 89.7 1.0 O5' F:DA1 4.8 110.3 1.0 OD1 A:ASP301 4.8 108.9 1.0 CB A:ASP301 4.9 82.2 1.0 HB2 A:ASP301 4.9 99.5 1.0 HA A:ASP251 5.0 85.2 1.0

Magnesium binding site 3 out of 4 in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plastid Localized Exonuclease 1 (D249A) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:92.7 occ:1.00 O B:HOH609 2.1 123.5 1.0 O B:HOH602 2.1 92.5 1.0 OD1 B:ASP226 2.1 97.2 1.0 O B:HOH608 2.2 68.4 1.0 O B:HOH610 2.2 110.6 1.0 OD2 B:ASP226 2.7 97.9 1.0 CG B:ASP226 2.7 96.5 1.0 O B:HOH611 3.3 81.8 1.0 HB2 B:ALA249 3.8 160.3 1.0 OD2 B:ASP98 3.9 86.3 1.0 H B:ASP226 4.0 90.7 1.0 HG3 B:GLU224 4.1 109.9 1.0 OD2 B:ASP155 4.1 100.6 1.0 HG2 B:GLU224 4.2 109.9 1.0 CB B:ASP226 4.2 85.6 1.0 HB3 B:ALA225 4.4 64.9 1.0 HB1 B:ALA249 4.5 160.3 1.0 CB B:ALA249 4.5 132.9 1.0 HB2 B:ASP226 4.6 103.5 1.0 N B:ASP226 4.6 74.9 1.0 CG B:GLU224 4.6 90.9 1.0 HB3 B:ALA249 4.7 160.3 1.0 HB3 B:ASP226 4.7 103.5 1.0 HZ1 B:LYS189 4.8 128.6 1.0 CG B:ASP98 4.9 96.5 1.0 CA B:ASP226 4.9 53.3 1.0 HG B:SER101 5.0 112.5 1.0 HA B:ASP226 5.0 64.8 1.0 HZ2 B:LYS189 5.0 128.6 1.0

Magnesium binding site 4 out of 4 in the Plastid Localized Exonuclease 1 (D249A) Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Plastid Localized Exonuclease 1 (D249A) Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:143.9 occ:1.00 OD2 B:ASP251 2.1 114.0 1.0 O B:HOH606 2.2 95.4 1.0 OD2 B:ASP304 2.2 121.4 1.0 O B:HOH601 2.3 113.2 1.0 O B:HOH612 2.3 72.0 1.0 CG B:ASP251 2.9 105.0 1.0 O B:HOH603 2.9 100.2 1.0 OD1 B:ASP251 3.1 88.9 1.0 CG B:ASP304 3.4 112.6 1.0 OD1 B:ASP304 4.1 112.6 1.0 HD11 B:ILE306 4.2 102.3 1.0 HB2 B:ASP304 4.3 122.1 1.0 HD12 B:ILE306 4.3 102.3 1.0 CB B:ASP251 4.3 85.9 1.0 CB B:ASP304 4.3 101.0 1.0 HB3 B:ASP304 4.5 122.1 1.0 HB3 B:ASP251 4.5 103.9 1.0 HA B:ALA360 4.5 105.8 1.0 OD2 B:ASP301 4.5 123.2 1.0 HA B:ASP251 4.7 115.7 1.0 HZ1 B:LYS189 4.7 128.6 1.0 H B:ASP251 4.7 132.1 1.0 CD1 B:ILE306 4.7 84.5 1.0 OH B:TYR188 4.9 89.8 1.0 HZ3 B:LYS189 4.9 128.6 1.0 HB2 B:ASP251 4.9 103.9 1.0 CA B:ASP251 4.9 95.7 1.0 HE1 B:TYR188 5.0 105.4 1.0

X.Huang, G.Shi, Q.Xiao, J.Feng, Y.Huang, H.Shi, Q.Wang, Y.Su, J.Wang, X.Wu, Y.Cao, H.Wang, W.Wang, Y.Zhang, Y.Wu. PEN1 Catalyses Rna Primer Removal During Plastid Dna Replication in Maize. Nat.Plants 2025.
ISSN: ESSN 2055-0278
PubMed: 40562815
DOI: 10.1038/S41477-025-02027-4