Magnesium in PDB 8k0q: The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State

The binding sites of Magnesium atom in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State (pdb code 8k0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State, PDB code: 8k0q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:16.7 occ:1.00 OP1 A:U583 1.8 44.7 1.0 OP2 A:C585 2.1 52.6 1.0 P A:U583 3.0 9.7 1.0 P A:C585 3.4 3.0 1.0 OP2 A:U583 3.6 47.3 1.0 O3' A:G582 3.7 44.9 1.0 OP1 A:C585 3.8 37.4 1.0 C5' F:DT7 4.1 45.2 1.0 MG A:MG702 4.1 26.5 1.0 O5' A:C585 4.2 37.9 1.0 O5' A:U583 4.3 43.1 1.0 OP2 A:G567 4.4 25.4 1.0 O5' F:DT7 4.5 51.5 1.0 O3' A:A584 4.6 158.3 1.0 OP1 A:G567 4.6 30.3 1.0 C5' A:C585 4.7 43.9 1.0 O3' F:DT6 4.7 51.5 1.0 OP1 F:DT7 4.8 51.7 1.0 C4' F:DT6 4.8 47.9 1.0 C3' A:A584 4.8 159.4 1.0 C5' A:U583 4.9 47.9 1.0 C5' A:A584 4.9 161.1 1.0 C3' A:G582 4.9 46.9 1.0 P A:G567 5.0 0.0 1.0

Magnesium binding site 2 out of 4 in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:26.5 occ:1.00 O3' A:U633 1.8 22.7 1.0 O2' A:U633 2.0 29.9 1.0 OP1 A:C585 2.1 37.4 1.0 OP1 A:C566 2.5 21.3 1.0 C2' A:U633 2.7 22.1 1.0 C3' A:U633 2.7 22.9 1.0 OP2 A:G567 2.8 25.4 1.0 C1' A:U633 3.3 24.3 1.0 P A:C585 3.4 3.0 1.0 O5' F:DT7 3.6 51.5 1.0 OP2 A:C585 3.8 52.6 1.0 C4' A:U633 3.9 19.4 1.0 P A:C566 3.9 3.6 1.0 MG A:MG701 4.1 16.7 1.0 O4' A:U633 4.1 18.8 1.0 C5' F:DT7 4.2 45.2 1.0 OP1 F:DT7 4.2 51.7 1.0 P A:G567 4.3 0.0 1.0 O5' A:C585 4.4 37.9 1.0 O3' A:A584 4.4 158.3 1.0 N1 A:U633 4.4 17.4 1.0 C5' A:C566 4.5 27.7 1.0 O5' A:C566 4.5 26.7 1.0 O2 A:U633 4.5 13.6 1.0 P F:DT7 4.6 63.3 1.0 O3' A:C565 4.8 3.2 1.0 C2 A:U633 4.9 13.8 1.0 OP2 A:C566 4.9 24.7 1.0 O5' A:G567 5.0 0.0 1.0

Magnesium binding site 3 out of 4 in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:16.7 occ:1.00 OP1 C:U583 1.8 44.7 1.0 OP2 C:C585 2.1 52.6 1.0 P C:U583 3.0 9.7 1.0 P C:C585 3.4 3.0 1.0 OP2 C:U583 3.6 47.3 1.0 O3' C:G582 3.7 44.9 1.0 OP1 C:C585 3.8 37.4 1.0 C5' E:DT7 4.1 45.2 1.0 MG C:MG702 4.1 26.5 1.0 O5' C:C585 4.2 37.9 1.0 O5' C:U583 4.3 43.1 1.0 OP2 C:G567 4.4 25.4 1.0 O5' E:DT7 4.5 51.5 1.0 O3' C:A584 4.6 158.3 1.0 OP1 C:G567 4.6 30.3 1.0 C5' C:C585 4.7 43.9 1.0 O3' E:DT6 4.7 51.5 1.0 OP1 E:DT7 4.8 51.7 1.0 C4' E:DT6 4.8 47.9 1.0 C3' C:A584 4.8 159.4 1.0 C5' C:U583 4.9 47.9 1.0 C5' C:A584 4.9 161.1 1.0 C3' C:G582 4.9 46.9 1.0 P C:G567 5.0 0.0 1.0

Magnesium binding site 4 out of 4 in the The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Anoxybacillus Pushchinoensis Orf-Less Group Iic Intron HYER1 at Symmetric Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:26.5 occ:1.00 O3' C:U633 1.8 22.7 1.0 O2' C:U633 2.0 29.9 1.0 OP1 C:C585 2.1 37.4 1.0 OP1 C:C566 2.5 21.3 1.0 C2' C:U633 2.7 22.1 1.0 C3' C:U633 2.7 22.9 1.0 OP2 C:G567 2.8 25.4 1.0 C1' C:U633 3.3 24.3 1.0 P C:C585 3.4 3.0 1.0 O5' E:DT7 3.6 51.5 1.0 OP2 C:C585 3.8 52.6 1.0 C4' C:U633 3.9 19.4 1.0 P C:C566 3.9 3.6 1.0 MG C:MG701 4.1 16.7 1.0 O4' C:U633 4.1 18.8 1.0 C5' E:DT7 4.2 45.2 1.0 OP1 E:DT7 4.2 51.7 1.0 P C:G567 4.3 0.0 1.0 O5' C:C585 4.4 37.9 1.0 O3' C:A584 4.4 158.3 1.0 N1 C:U633 4.4 17.4 1.0 C5' C:C566 4.5 27.7 1.0 O5' C:C566 4.5 26.7 1.0 O2 C:U633 4.5 13.6 1.0 P E:DT7 4.6 63.3 1.0 O3' C:C565 4.8 3.2 1.0 C2 C:U633 4.9 13.8 1.0 OP2 C:C566 4.9 24.7 1.0 O5' C:G567 5.0 0.0 1.0

Z.X.Liu, S.Zhang, H.Z.Zhu, Z.H.Chen, Y.Yang, L.Q.Li, Y.Lei, Y.Liu, D.Y.Li, A.Sun, C.P.Li, S.Q.Tan, G.L.Wang, J.Y.Shen, S.Jin, C.Gao, J.G.Liu. Hydrolytic Endonucleolytic Ribozyme (Hyer) Is Programmable For Sequence-Specific Dna Cleavage. Science V. 383 H4859 2024.
ISSN: ESSN 1095-9203
PubMed: 38301022
DOI: 10.1126/SCIENCE.ADH4859