Magnesium in PDB 9j89: ZBP1 Nucleic Acid Complex

The structure of ZBP1 Nucleic Acid Complex, PDB code: 9j89 was solved by A.M.Gao, C.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.57 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.24, 173.95, 30.44, 90, 94.42, 90
R / Rfree (%)	21.2 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the ZBP1 Nucleic Acid Complex (pdb code 9j89). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the ZBP1 Nucleic Acid Complex, PDB code: 9j89:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:12.5 occ:1.00 N7 C:DA206 1.8 26.4 1.0 O C:HOH414 2.1 32.2 1.0 O C:HOH401 2.2 32.0 1.0 C8 C:DA206 2.7 25.6 1.0 C5 C:DA206 2.9 23.8 1.0 N6 C:DA206 3.4 20.7 1.0 C6 C:DA206 3.6 22.5 1.0 N9 C:DA206 3.9 28.3 1.0 C4 C:DA206 4.0 26.2 1.0 N1 C:DA206 4.9 23.6 1.0

Magnesium binding site 2 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:50.0 occ:1.00 O C:HOH402 2.1 44.1 1.0 N7 C:DA202 2.2 19.8 1.0 C8 C:DA202 3.0 18.9 1.0 C5 C:DA202 3.4 17.2 1.0 N6 C:DA202 3.8 19.6 1.0 OP2 C:DC201 3.8 26.4 1.0 O C:HOH412 4.0 38.4 1.0 C6 C:DA202 4.1 18.2 1.0 N9 C:DA202 4.3 15.4 1.0 O C:HOH416 4.4 21.6 1.0 C4 C:DA202 4.5 18.3 1.0 O C:HOH421 4.9 47.4 1.0

Magnesium binding site 3 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:13.0 occ:1.00 N7 G:DA206 2.0 26.2 1.0 O G:HOH408 2.1 38.1 1.0 O G:HOH407 2.1 34.5 1.0 C8 G:DA206 2.9 28.2 1.0 C5 G:DA206 3.1 29.3 1.0 N6 G:DA206 3.4 25.9 1.0 C6 G:DA206 3.7 27.8 1.0 OP1 G:DC205 3.9 26.9 1.0 OP2 G:DC205 4.1 30.1 1.0 N9 G:DA206 4.2 33.3 1.0 C4 G:DA206 4.2 30.0 1.0 P G:DC205 4.5 27.0 1.0

Magnesium binding site 4 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:50.0 occ:1.00 N7 G:DA202 2.2 17.4 1.0 C8 G:DA202 3.0 19.5 1.0 C5 G:DA202 3.3 18.3 1.0 N6 G:DA202 3.6 18.8 1.0 O G:HOH410 3.8 23.7 1.0 C6 G:DA202 3.9 17.1 1.0 N9 G:DA202 4.3 17.9 1.0 OP2 G:DC201 4.4 27.4 1.0 C4 G:DA202 4.4 16.5 1.0 N4 G:DC203 4.5 17.4 1.0

Magnesium binding site 5 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:50.0 occ:1.00 NE2 D:HIS13 1.8 19.6 1.0 O D:HOH241 2.2 25.1 1.0 CE1 D:HIS13 2.6 25.6 1.0 CD2 D:HIS13 3.0 16.9 1.0 ND1 D:HIS13 3.8 25.0 1.0 CG D:HIS13 4.0 16.6 1.0 OE1 D:GLN16 4.8 28.1 1.0 O D:HOH225 4.8 17.1 1.0

Magnesium binding site 6 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:50.0 occ:1.00 NE2 F:HIS13 2.0 18.7 1.0 CE1 F:HIS13 2.9 18.7 1.0 CD2 F:HIS13 3.1 15.8 1.0 ND1 F:HIS13 4.0 19.3 1.0 CG F:HIS13 4.1 15.2 1.0 OE1 F:GLN16 4.9 27.5 1.0

Magnesium binding site 7 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:50.0 occ:1.00 NE2 A:HIS13 2.0 25.7 1.0 O A:HOH230 2.2 22.8 1.0 O A:HOH231 2.4 21.0 1.0 CE1 A:HIS13 2.9 26.4 1.0 CD2 A:HIS13 3.1 24.1 1.0 O A:HOH237 4.0 40.4 1.0 ND1 A:HIS13 4.1 25.4 1.0 CG A:HIS13 4.2 23.9 1.0

Magnesium binding site 8 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:16.2 occ:1.00 N7 E:G6 1.9 29.7 1.0 O E:HOH210 2.3 33.4 1.0 C8 E:G6 2.7 32.0 1.0 C5 E:G6 3.1 29.6 1.0 O6 E:G6 3.7 26.1 1.0 C6 E:G6 3.7 27.8 1.0 OP1 E:U5 3.9 28.3 1.0 N9 E:G6 3.9 33.4 1.0 O E:HOH206 4.1 35.0 1.0 C4 E:G6 4.1 31.8 1.0 P E:U5 4.9 31.4 1.0 OP2 E:U5 4.9 36.2 1.0

Magnesium binding site 9 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:50.0 occ:1.00 N7 E:G2 2.2 28.4 1.0 O E:HOH209 2.5 37.5 1.0 C8 E:G2 3.1 28.1 1.0 C5 E:G2 3.3 24.4 1.0 O6 E:G2 3.6 26.8 1.0 C6 E:G2 3.8 25.3 1.0 OP1 E:U1 4.0 44.9 1.0 O E:HOH208 4.1 24.0 1.0 O E:HOH215 4.2 37.1 1.0 N9 E:G2 4.3 22.9 1.0 C4 E:G2 4.4 26.6 1.0 N4 E:C3 4.5 23.8 1.0

Magnesium binding site 10 out of 11 in the ZBP1 Nucleic Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of ZBP1 Nucleic Acid Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:15.2 occ:1.00 N7 B:G6 2.1 28.9 1.0 O B:HOH225 2.2 35.6 1.0 C8 B:G6 3.0 30.6 1.0 C5 B:G6 3.2 28.8 1.0 O6 B:G6 3.7 28.3 1.0 C6 B:G6 3.8 27.4 1.0 O B:HOH226 4.0 35.0 1.0 N9 B:G6 4.2 31.8 1.0 C4 B:G6 4.3 30.6 1.0 O B:HOH203 4.4 30.9 1.0

J.He, Y.Zhu, Z.Tian, M.Liu, A.Gao, W.Fu, F.Lu, Y.Sun, Y.Guo, R.Pan, Y.Ji, J.Chen, H.Lu, J.Lin, X.Liang, C.Kim, C.Zhou, H.Jiao. ZBP1 Senses Spliceosome Stress Through Z-Rna:Dna Hybrid Recognition. Mol.Cell V. 85 1790 2025.
ISSN: ISSN 1097-2765
PubMed: 40267921
DOI: 10.1016/J.MOLCEL.2025.04.004