Manganese in PDB 9l56: Plastid-Localized Exonuclease 1

The structure of Plastid-Localized Exonuclease 1, PDB code: 9l56 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)	31.18 / 2.42
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.147, 107.147, 132.433, 90, 90, 120
R / Rfree (%)	23 / 26.1

The binding sites of Manganese atom in the Plastid-Localized Exonuclease 1 (pdb code 9l56). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Plastid-Localized Exonuclease 1, PDB code: 9l56:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Plastid-Localized Exonuclease 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Plastid-Localized Exonuclease 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:73.7 occ:1.00 OD2 A:ASP301 2.1 70.2 1.0 OD2 A:ASP304 2.2 73.2 1.0 OD1 A:ASP251 2.3 64.8 1.0 OD2 A:ASP251 2.6 51.8 1.0 CG A:ASP251 2.8 55.7 1.0 CG A:ASP304 3.2 70.1 1.0 CG A:ASP301 3.3 68.6 1.0 HB2 A:ASP304 3.4 65.0 1.0 CB A:ASP304 3.8 65.0 1.0 OD1 A:ASP301 3.9 74.8 1.0 O A:HOH623 4.0 53.8 1.0 O A:HOH603 4.0 55.4 1.0 OD1 A:ASP304 4.1 70.7 1.0 MN A:MN502 4.1 54.2 1.0 CB A:ASP251 4.3 50.0 1.0 HB3 A:ASP304 4.3 65.0 1.0 CB A:ASP301 4.4 65.2 1.0 HB3 A:ASP301 4.4 65.2 1.0 OD1 A:ASP249 4.5 52.2 1.0 HB3 A:ALA303 4.6 69.0 1.0 HD12 A:ILE306 4.6 61.7 1.0 HB2 A:ASP301 4.6 65.2 1.0 H A:ASP304 4.6 67.5 1.0 HB3 A:ASP251 4.7 50.0 1.0 HA A:ASP251 4.8 56.6 1.0 HB2 A:ASP251 4.8 50.0 1.0 HD11 A:ILE306 4.8 61.7 1.0 H A:ASP251 4.8 59.4 1.0 O A:HOH636 4.9 56.0 1.0 N A:ASP304 5.0 67.5 1.0

Manganese binding site 2 out of 4 in the Plastid-Localized Exonuclease 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Plastid-Localized Exonuclease 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:54.2 occ:1.00 OD2 A:ASP249 2.1 59.3 1.0 OD2 A:ASP226 2.2 62.6 1.0 OD2 A:ASP251 2.2 51.8 1.0 O A:HOH603 2.3 55.4 1.0 O A:HOH623 2.4 53.8 1.0 O A:HOH635 2.8 52.6 1.0 CG A:ASP249 3.1 60.9 1.0 CG A:ASP226 3.2 61.2 1.0 CG A:ASP251 3.3 55.7 1.0 OD1 A:ASP249 3.5 52.2 1.0 HB2 A:ASP251 3.5 50.0 1.0 OD1 A:ASP226 3.6 59.7 1.0 HZ1 A:LYS189 3.7 73.2 1.0 OD2 A:ASP304 3.7 73.2 1.0 O A:HOH611 3.9 54.9 1.0 OE1 A:GLU224 3.9 65.4 1.0 CB A:ASP251 3.9 50.0 1.0 MN A:MN501 4.1 73.7 1.0 HB3 A:ASP251 4.2 50.0 1.0 O A:HOH636 4.2 56.0 1.0 OD1 A:ASP251 4.3 64.8 1.0 O A:HOH629 4.3 67.8 1.0 CB A:ASP249 4.5 52.2 1.0 HE2 A:LYS189 4.5 65.9 1.0 CB A:ASP226 4.5 59.7 1.0 NZ A:LYS189 4.5 73.2 1.0 HB2 A:ASP249 4.6 52.2 1.0 HB2 A:ASP226 4.6 59.7 1.0 CG A:ASP304 4.6 70.1 1.0 HB3 A:ASP249 4.7 52.2 1.0 OD1 A:ASP304 4.7 70.7 1.0 HE3 A:LYS189 4.7 65.9 1.0 HB3 A:ASP226 4.7 59.7 1.0 HH22 A:ARG192 4.7 81.6 1.0 H A:ASP251 4.8 59.4 1.0 CE A:LYS189 4.8 65.9 1.0 HH21 A:ARG192 4.8 81.6 1.0 HZ3 A:LYS189 4.9 73.2 1.0 O A:HOH630 4.9 72.3 1.0

Manganese binding site 3 out of 4 in the Plastid-Localized Exonuclease 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Plastid-Localized Exonuclease 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:72.2 occ:1.00 OD2 B:ASP304 2.2 76.1 1.0 OD2 B:ASP301 2.2 83.1 1.0 OD1 B:ASP251 2.2 63.5 1.0 OD2 B:ASP251 2.5 57.6 1.0 CG B:ASP251 2.7 61.6 1.0 CG B:ASP304 3.2 77.3 1.0 CG B:ASP301 3.4 81.8 1.0 O B:HOH624 3.6 70.0 1.0 HB2 B:ASP304 3.7 73.8 1.0 OD1 B:ASP304 4.0 79.9 1.0 O B:HOH601 4.0 62.0 1.0 CB B:ASP304 4.0 73.8 1.0 MN B:MN502 4.1 67.5 1.0 OD1 B:ASP301 4.1 90.4 1.0 CB B:ASP251 4.2 60.7 1.0 OD1 B:ASP249 4.2 57.5 1.0 CB B:ASP301 4.5 77.7 1.0 HB3 B:ASP301 4.5 77.7 1.0 HB2 B:ASP301 4.5 77.7 1.0 HB3 B:ASP304 4.6 73.8 1.0 HB3 B:ASP251 4.6 60.7 1.0 HB3 B:ALA303 4.6 85.5 1.0 HB2 B:ASP251 4.6 60.7 1.0 HA B:ASP251 4.7 57.8 1.0 HD12 B:ILE306 4.7 68.3 1.0 H B:ASP251 4.7 63.7 1.0 H B:ASP304 4.8 85.2 1.0 CA B:ASP251 4.9 57.8 1.0 OD2 B:ASP249 4.9 67.0 1.0 HD11 B:ILE306 4.9 68.3 1.0

Manganese binding site 4 out of 4 in the Plastid-Localized Exonuclease 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Plastid-Localized Exonuclease 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:67.5 occ:1.00 OD2 B:ASP226 2.1 54.4 1.0 OD2 B:ASP249 2.1 67.0 1.0 OD2 B:ASP251 2.3 57.6 1.0 O B:HOH624 2.4 70.0 1.0 O B:HOH601 2.5 62.0 1.0 CG B:ASP226 3.1 57.6 1.0 CG B:ASP249 3.2 62.4 1.0 O B:HOH641 3.3 67.1 1.0 CG B:ASP251 3.4 61.6 1.0 HZ1 B:LYS189 3.5 80.5 1.0 O B:HOH605 3.5 56.1 1.0 OD1 B:ASP226 3.5 60.4 1.0 HB2 B:ASP251 3.6 60.7 1.0 OD1 B:ASP249 3.6 57.5 1.0 OE1 B:GLU224 3.9 76.3 1.0 OD2 B:ASP304 4.0 76.1 1.0 CB B:ASP251 4.0 60.7 1.0 MN B:MN501 4.1 72.2 1.0 HB3 B:ASP251 4.3 60.7 1.0 OD1 B:ASP251 4.3 63.5 1.0 NZ B:LYS189 4.4 80.5 1.0 CB B:ASP226 4.4 54.0 1.0 CB B:ASP249 4.5 63.1 1.0 O B:HOH640 4.5 60.8 1.0 HB2 B:ASP226 4.5 54.0 1.0 OD1 B:ASP304 4.6 79.9 1.0 HB2 B:ASP249 4.6 63.1 1.0 HB3 B:ASP249 4.6 63.1 1.0 HB3 B:ASP226 4.7 54.0 1.0 CG B:ASP304 4.7 77.3 1.0 HZ2 B:LYS189 4.7 80.5 1.0 HZ3 B:LYS189 4.7 80.5 1.0 HE3 B:LYS189 4.9 69.4 1.0 HE2 B:LYS189 4.9 69.4 1.0 H B:ASP251 4.9 63.7 1.0 HH22 B:ARG192 4.9 106.7 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