Magnesium in PDB 9hjo: Fancm-FAAP24-Dsdna Complex

All present enzymatic activity of Fancm-FAAP24-Dsdna Complex:
3.6.4.13;

The structure of Fancm-FAAP24-Dsdna Complex, PDB code: 9hjo was solved by R.J.Coulthard-Graf, D.C.Briggs, N.Q.Mcdonald, A.Deans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.72 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.008, 69.975, 86.76, 91.63, 89.93, 115.95
R / Rfree (%)	21.5 / 26.5

The binding sites of Magnesium atom in the Fancm-FAAP24-Dsdna Complex (pdb code 9hjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Fancm-FAAP24-Dsdna Complex, PDB code: 9hjo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Fancm-FAAP24-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fancm-FAAP24-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:52.1 occ:1.00 OP2 F:DC17 2.3 58.5 1.0 O B:GLN164 2.4 45.4 1.0 O B:VAL169 2.6 50.9 1.0 O B:ILE166 2.7 54.7 1.0 HA B:PRO167 3.2 52.5 1.0 P F:DC17 3.3 56.7 1.0 OP1 F:DC17 3.4 47.7 1.0 H B:VAL169 3.4 55.2 1.0 C B:GLN164 3.5 44.8 1.0 C B:ILE166 3.6 49.6 1.0 C B:VAL169 3.7 47.1 1.0 H B:GLY168 3.9 58.9 1.0 HA B:GLN164 3.9 44.4 1.0 N B:VAL169 4.0 56.8 1.0 HB B:VAL169 4.0 47.3 1.0 CA B:PRO167 4.0 52.4 1.0 HA B:GLN165 4.0 46.5 1.0 C B:GLN165 4.1 48.7 1.0 N B:PRO167 4.1 50.1 1.0 N B:ILE166 4.2 49.4 1.0 N B:GLY168 4.3 57.9 1.0 CA B:GLN164 4.3 43.5 1.0 CA B:VAL169 4.3 50.0 1.0 HA2 B:GLY170 4.3 45.7 1.0 N B:GLN165 4.4 45.0 1.0 H3' F:DG16 4.4 53.7 1.0 CA B:GLN165 4.4 45.3 1.0 H B:ILE166 4.4 48.1 1.0 HB3 B:GLN164 4.4 47.2 1.0 O3' F:DG16 4.5 55.9 1.0 O5' F:DC17 4.5 57.1 1.0 C B:PRO167 4.5 55.1 1.0 O B:GLN165 4.5 56.7 1.0 CA B:ILE166 4.6 48.6 1.0 CB B:VAL169 4.7 47.0 1.0 N B:GLY170 4.7 46.9 1.0 C B:GLY168 4.8 60.2 1.0 C3' F:DG16 4.9 52.9 1.0 CB B:GLN164 4.9 46.7 1.0

Magnesium binding site 2 out of 4 in the Fancm-FAAP24-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fancm-FAAP24-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:73.3 occ:1.00 O B:LEU85 2.3 99.3 1.0 O B:SER82 2.5 104.6 1.0 O B:ARG80 2.6 77.6 1.0 HA B:ARG80 2.8 79.1 0.5 O B:VAL79 2.9 78.5 1.0 HA B:ARG80 2.9 78.7 0.5 HH11 B:ARG80 3.1 71.3 0.5 O B:HOH404 3.2 59.4 1.0 HD2 B:ARG80 3.2 73.2 0.5 C B:ARG80 3.3 81.6 1.0 HD3 B:LYS86 3.4 109.0 1.0 C B:LEU85 3.5 97.8 1.0 CA B:ARG80 3.5 80.8 0.5 CA B:ARG80 3.5 80.5 0.5 HA B:LYS86 3.5 87.0 1.0 C B:SER82 3.7 105.7 1.0 O B:HOH411 3.8 59.4 1.0 C B:VAL79 3.9 81.7 1.0 HZ2 B:LYS86 3.9 117.2 1.0 H B:LEU85 4.0 113.0 1.0 NH1 B:ARG80 4.0 70.7 0.5 HB2 B:SER82 4.1 94.3 1.0 HB3 B:LEU85 4.1 107.8 1.0 N B:ARG80 4.2 80.8 1.0 CD B:ARG80 4.2 71.8 0.5 H B:SER82 4.2 97.2 1.0 HA B:ASN83 4.3 119.7 1.0 N B:SER82 4.3 100.2 1.0 HG2 B:LYS86 4.3 101.8 1.0 N B:LYS86 4.3 90.3 1.0 CA B:LYS86 4.4 87.6 1.0 CD B:LYS86 4.4 109.8 1.0 HH12 B:ARG80 4.4 72.3 0.5 HD3 B:ARG80 4.4 70.7 0.5 HZ1 B:LYS86 4.4 117.9 1.0 N B:ASN81 4.4 85.6 1.0 CA B:SER82 4.5 100.5 1.0 CA B:LEU85 4.5 105.5 1.0 NZ B:LYS86 4.6 117.3 1.0 N B:LEU85 4.6 114.2 1.0 HB2 B:ARG80 4.6 75.9 0.5 CB B:ARG80 4.7 77.3 0.5 CB B:SER82 4.7 95.6 1.0 HD2 B:ARG80 4.8 75.7 0.5 N B:ASN83 4.8 115.3 1.0 HG11 B:VAL79 4.8 79.0 1.0 CB B:LEU85 4.8 108.2 1.0 HG12 B:VAL79 4.8 76.3 1.0 CG B:LYS86 4.8 100.5 1.0 CB B:ARG80 4.8 76.7 0.5 C B:ASN81 4.9 96.1 1.0 CZ B:ARG80 4.9 69.2 0.5 HD2 B:LYS86 4.9 106.7 1.0 H B:GLY87 4.9 77.3 1.0 CA B:ASN83 5.0 123.7 1.0 NE B:ARG80 5.0 69.9 0.5

Magnesium binding site 3 out of 4 in the Fancm-FAAP24-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fancm-FAAP24-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:69.9 occ:1.00 O D:LEU85 2.3 99.6 1.0 O D:ARG80 2.6 75.3 1.0 O D:SER82 2.7 112.5 1.0 O D:VAL79 2.8 78.8 1.0 HA D:ARG80 2.8 80.9 1.0 C D:ARG80 3.3 80.2 1.0 O D:HOH408 3.3 80.7 1.0 O D:HOH406 3.4 59.8 1.0 HA D:LYS86 3.4 87.5 1.0 CA D:ARG80 3.4 83.4 1.0 C D:LEU85 3.4 98.5 1.0 C D:VAL79 3.7 81.6 1.0 C D:SER82 3.8 112.1 1.0 HE3 D:LYS86 3.9 109.8 1.0 N D:ARG80 4.0 79.2 1.0 HG2 D:LYS86 4.1 102.7 1.0 HB3 D:LEU85 4.1 109.3 1.0 HB2 D:SER82 4.1 96.6 1.0 H D:LEU85 4.1 115.3 1.0 H D:SER82 4.2 98.2 1.0 CA D:LYS86 4.2 88.1 1.0 N D:LYS86 4.2 91.8 1.0 N D:SER82 4.3 100.3 1.0 HG2 D:ARG80 4.4 91.2 1.0 HA D:ASN83 4.4 124.5 1.0 N D:ASN81 4.4 83.6 1.0 CA D:LEU85 4.5 107.2 1.0 CA D:SER82 4.5 103.5 1.0 HG11 D:VAL79 4.5 80.8 1.0 HG12 D:VAL79 4.6 78.1 1.0 N D:LEU85 4.7 117.2 1.0 HD2 D:ARG80 4.7 102.4 1.0 HE2 D:LYS86 4.7 108.5 1.0 CE D:LYS86 4.7 110.8 1.0 H D:GLY87 4.7 74.3 1.0 CB D:ARG80 4.7 85.8 1.0 CB D:LEU85 4.8 109.3 1.0 CB D:SER82 4.8 98.5 1.0 CG D:LYS86 4.9 101.9 1.0 N D:ASN83 4.9 124.3 1.0 H D:ARG80 4.9 80.4 1.0 C D:ASN81 4.9 96.9 1.0 CG D:ARG80 5.0 92.0 1.0

Magnesium binding site 4 out of 4 in the Fancm-FAAP24-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fancm-FAAP24-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:50.0 occ:1.00 OP2 H:DC17 2.4 59.0 1.0 O D:GLN164 2.6 45.3 1.0 O D:ILE166 2.7 50.5 1.0 O D:VAL169 2.7 49.8 1.0 OP1 H:DC17 2.9 48.1 1.0 HA D:PRO167 3.0 50.1 1.0 P H:DC17 3.1 53.1 1.0 H D:VAL169 3.4 53.2 1.0 C D:ILE166 3.5 48.1 1.0 C D:GLN164 3.7 45.4 1.0 H D:GLY168 3.7 54.7 1.0 C D:VAL169 3.8 49.2 1.0 CA D:PRO167 3.8 50.3 1.0 N D:VAL169 4.0 54.6 1.0 N D:PRO167 4.0 46.4 1.0 HB D:VAL169 4.1 47.4 1.0 HA D:GLN165 4.1 44.4 1.0 N D:GLY168 4.1 53.8 1.0 C D:GLN165 4.2 48.1 1.0 HA D:GLN164 4.2 46.1 1.0 N D:ILE166 4.2 47.0 1.0 O3' H:DG16 4.3 52.8 1.0 O5' H:DC17 4.3 50.2 1.0 C D:PRO167 4.3 52.6 1.0 CA D:VAL169 4.4 50.9 1.0 O D:GLN165 4.4 55.0 1.0 H3' H:DG16 4.4 50.9 1.0 HA2 D:GLY170 4.5 51.4 1.0 CA D:GLN165 4.5 43.2 1.0 H D:ILE166 4.5 46.6 1.0 N D:GLN165 4.5 43.0 1.0 CA D:GLN164 4.5 45.5 1.0 CA D:ILE166 4.6 47.7 1.0 HB3 D:GLN164 4.7 49.0 1.0 CB D:VAL169 4.8 47.6 1.0 C D:GLY168 4.8 55.9 1.0 N D:GLY170 4.8 51.6 1.0 C3' H:DG16 4.9 49.7 1.0 HB3 D:PRO167 4.9 51.0 1.0 CB D:PRO167 5.0 50.4 1.0

R.Bythell-Douglas, S.Van Twest, L.Abbouche, E.Dunn, R.J.Coulthard, D.C.Briggs, V.Murphy, X.Zhang, W.Tan, S.S.Henrikus, D.Qian, Y.Wu, J.Wolf, L.Rigoreau, S.Shakeel, K.L.Chapman, N.Q.Mcdonald, A.J.Deans. Structural Basis of Fanconi Anemia Pathway Activation By Fancm. Embo J. 2025.
ISSN: ESSN 1460-2075
PubMed: 40447800
DOI: 10.1038/S44318-025-00468-3