Magnesium in PDB 8yfk: Crystal Structure of FIP200 Claw/TNIP1_FIR_PS123

The structure of Crystal Structure of FIP200 Claw/TNIP1_FIR_PS123, PDB code: 8yfk was solved by M.Q.Lv, S.M.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.80 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.812, 45.936, 72.951, 81.2, 89.67, 88.74
R / Rfree (%)	18.3 / 22

The binding sites of Magnesium atom in the Crystal Structure of FIP200 Claw/TNIP1_FIR_PS123 (pdb code 8yfk). 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 FIP200 Claw/TNIP1_FIR_PS123, PDB code: 8yfk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of FIP200 Claw/TNIP1_FIR_PS123


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 FIP200 Claw/TNIP1_FIR_PS123 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:36.4 occ:1.00 NH1 A:ARG1584 2.9 49.2 1.0 OG A:SER1532 3.0 52.6 1.0 N A:SER1532 3.1 27.9 1.0 CB A:SER1532 3.4 40.2 1.0 NH1 A:ARG1573 3.5 57.2 1.0 CD A:ARG1584 3.6 48.0 1.0 CA A:SER1532 3.9 30.4 1.0 CZ A:PHE1574 3.9 46.5 1.0 CZ A:ARG1584 4.0 47.1 1.0 C A:HIS1531 4.1 32.8 1.0 CD A:ARG1573 4.1 45.5 1.0 CA A:HIS1531 4.1 26.2 1.0 ND1 A:HIS1531 4.2 37.9 1.0 CG A:ARG1584 4.2 50.4 1.0 NE A:ARG1584 4.2 47.8 1.0 CE1 A:PHE1574 4.3 39.1 1.0 CG A:HIS1531 4.4 31.6 1.0 CE1 A:HIS1531 4.4 37.8 1.0 CZ A:ARG1573 4.6 54.5 1.0 O A:LEU1530 4.7 32.5 1.0 CD2 A:HIS1531 4.8 34.2 1.0 NE2 A:HIS1531 4.8 37.2 1.0 NE A:ARG1573 4.8 42.2 1.0 CB A:HIS1531 4.8 29.5 1.0 CE2 A:PHE1574 4.9 52.8 1.0 CZ B:PHE106 5.0 54.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of FIP200 Claw/TNIP1_FIR_PS123


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 FIP200 Claw/TNIP1_FIR_PS123 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1601 b:44.0 occ:1.00 NH1 C:ARG1573 2.5 86.4 1.0 NH1 C:ARG1584 2.7 63.6 1.0 OG C:SER1532 2.9 64.7 1.0 N C:SER1532 3.2 37.5 1.0 CB C:SER1532 3.5 56.0 1.0 CZ C:ARG1573 3.7 86.0 1.0 CD C:ARG1584 3.8 53.8 1.0 CZ C:PHE1574 3.8 51.8 1.0 CZ C:ARG1584 3.9 59.7 1.0 CA C:SER1532 4.0 43.2 1.0 ND1 C:HIS1531 4.1 40.5 1.0 CA C:HIS1531 4.2 33.8 1.0 C C:HIS1531 4.2 38.5 1.0 CE1 C:HIS1531 4.2 44.5 1.0 CG C:ARG1584 4.3 46.6 1.0 CG C:HIS1531 4.3 33.7 1.0 NE C:ARG1584 4.3 55.1 1.0 CZ D:PHE106 4.4 85.5 1.0 NE2 C:HIS1531 4.5 42.6 1.0 CD C:ARG1573 4.5 76.7 1.0 CE1 C:PHE1574 4.5 45.8 1.0 NH2 C:ARG1573 4.5 84.1 1.0 NE C:ARG1573 4.5 85.2 1.0 CD2 C:HIS1531 4.5 35.6 1.0 CE2 C:PHE1574 4.8 59.0 1.0 CB C:HIS1531 4.8 34.6 1.0 CE2 D:PHE106 4.9 86.5 1.0 O C:LEU1530 4.9 34.4 1.0

S.Wu, M.Li, L.Wang, L.Yang, J.Cui, F.Li, Q.Wang, Y.Shi, M.Lv. Structural Basis For TNIP1 Binding to FIP200 During Mitophagy. J.Biol.Chem. 07605 2024.
ISSN: ESSN 1083-351X
PubMed: 39059492
DOI: 10.1016/J.JBC.2024.107605