Magnesium in PDB 9cdv: Crystal Structure of Rhombotarget A

The structure of Crystal Structure of Rhombotarget A, PDB code: 9cdv was solved by A.K.Bera, S.Rettie, A.Kang, G.Bhardwaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.71 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.156, 106.477, 71.305, 90, 107.04, 90
R / Rfree (%)	19.5 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of Rhombotarget A (pdb code 9cdv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Rhombotarget A, PDB code: 9cdv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Rhombotarget A


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 Rhombotarget A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.1 occ:1.00 OD1 A:ASN17 2.3 27.0 1.0 O A:HIS48 2.3 27.0 1.0 OE2 A:GLU13 2.4 27.4 1.0 OE1 A:GLU24 2.4 25.8 1.0 OE2 A:GLU24 2.5 27.5 1.0 O A:VAL15 2.5 29.2 1.0 O A:VAL19 2.6 26.0 1.0 CD A:GLU24 2.8 27.2 1.0 CG A:ASN17 3.3 30.0 1.0 C A:HIS48 3.6 28.6 1.0 CD A:GLU13 3.6 31.2 1.0 C A:VAL19 3.7 28.7 1.0 C A:VAL15 3.8 28.9 1.0 ND2 A:ASN17 3.8 28.5 1.0 N A:ASN17 4.0 31.1 1.0 CG A:GLU13 4.2 28.2 1.0 CB A:HIS48 4.2 29.0 1.0 N A:VAL15 4.2 29.3 1.0 CG2 A:VAL19 4.3 29.9 1.0 CG A:GLU24 4.3 24.0 1.0 CA A:GLY49 4.4 29.5 1.0 N A:GLY49 4.4 29.0 1.0 N A:VAL19 4.5 28.6 1.0 CA A:HIS48 4.5 29.3 1.0 OE1 A:GLU13 4.5 32.0 1.0 CB A:ASN17 4.5 26.1 1.0 CA A:VAL15 4.5 30.0 1.0 N A:CYS20 4.6 29.4 1.0 CA A:VAL19 4.6 30.8 1.0 O A:ASN17 4.6 27.6 1.0 CA A:ASN17 4.6 28.6 1.0 C A:ASN17 4.6 29.5 1.0 CA A:CYS20 4.7 26.9 1.0 N A:ASP16 4.7 29.3 1.0 C A:ASP16 4.9 29.3 1.0 CA A:ASP16 4.9 28.2 1.0 N A:SER21 4.9 25.2 1.0 CB A:VAL15 5.0 30.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Rhombotarget A


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 Rhombotarget A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:18.3 occ:1.00 O B:HOH713 2.2 28.3 1.0 O B:HOH627 2.2 28.5 1.0 O B:HOH643 2.3 28.6 1.0 O B:HOH633 2.3 27.3 1.0 OD1 B:ASP116 2.3 29.4 1.0 OE2 B:GLU152 2.4 27.4 1.0 OE1 B:GLU152 2.9 23.4 1.0 CD B:GLU152 3.0 27.0 1.0 CG B:ASP116 3.2 29.0 1.0 OD2 B:ASP116 3.6 30.4 1.0 OD1 B:ASP115 4.1 31.1 1.0 N B:ASP116 4.3 29.3 1.0 O B:LYS121 4.4 36.0 1.0 CA B:SER123 4.4 29.2 1.0 O B:HIS151 4.5 23.0 1.0 CG B:GLU152 4.5 25.9 1.0 O B:HOH657 4.5 31.2 1.0 N B:SER118 4.5 32.0 1.0 O B:SER118 4.5 32.5 1.0 CB B:ASP116 4.5 30.3 1.0 N B:GLU117 4.6 29.3 1.0 OG B:SER123 4.6 29.8 1.0 O B:ALA122 4.6 31.6 1.0 O B:THR184 4.7 31.4 1.0 CE2 B:PHE124 4.7 27.4 1.0 CD2 B:PHE124 4.8 28.7 1.0 CB B:SER118 4.8 34.0 1.0 CA B:ASP116 4.8 30.2 1.0 N B:SER123 4.8 29.7 1.0 C B:ALA122 4.9 33.9 1.0 CB B:THR184 4.9 28.7 1.0 CB B:SER123 5.0 27.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Rhombotarget A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rhombotarget A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.4 occ:1.00 OD1 B:ASN17 2.4 27.0 1.0 OE2 B:GLU13 2.4 25.8 1.0 OE1 B:GLU24 2.4 25.3 1.0 O B:HIS48 2.4 24.8 1.0 O B:VAL19 2.5 22.5 1.0 OE2 B:GLU24 2.5 25.5 1.0 O B:VAL15 2.5 24.9 1.0 CD B:GLU24 2.7 23.4 1.0 CG B:ASN17 3.3 23.8 1.0 CD B:GLU13 3.5 23.0 1.0 C B:VAL19 3.6 22.0 1.0 C B:HIS48 3.7 27.0 1.0 C B:VAL15 3.7 25.0 1.0 ND2 B:ASN17 3.8 24.9 1.0 N B:ASN17 4.1 26.3 1.0 CG B:GLU13 4.1 21.6 1.0 CG2 B:VAL19 4.1 25.1 1.0 N B:VAL15 4.2 23.2 1.0 CG B:GLU24 4.2 21.1 1.0 CB B:HIS48 4.3 26.2 1.0 N B:VAL19 4.4 24.6 1.0 CA B:VAL15 4.4 25.4 1.0 OE1 B:GLU13 4.5 24.0 1.0 CA B:VAL19 4.5 25.9 1.0 N B:CYS20 4.5 24.1 1.0 N B:GLY49 4.5 29.1 1.0 CA B:GLY49 4.5 28.7 1.0 CB B:ASN17 4.6 24.2 1.0 CA B:HIS48 4.6 29.2 1.0 CA B:CYS20 4.6 22.6 1.0 C B:ASN17 4.7 28.1 1.0 CA B:ASN17 4.7 25.7 1.0 N B:ASP16 4.7 25.6 1.0 O B:ASN17 4.8 29.4 1.0 CB B:VAL15 4.8 23.6 1.0 N B:SER21 4.8 22.2 1.0 C B:ASP16 4.9 28.9 1.0 CA B:ASP16 4.9 25.9 1.0 CB B:VAL19 4.9 23.8 1.0 CB B:GLU24 5.0 19.6 1.0

S.A.Rettie, D.Juergens, V.Adebomi, Y.F.Bueso, Q.Zhao, A.N.Leveille, A.Liu, A.K.Bera, J.A.Wilms, A.Uffing, A.Kang, E.Brackenbrough, M.Lamb, S.R.Gerben, A.Murray, P.M.Levine, M.Schneider, V.Vasireddy, S.Ovchinnikov, O.H.Weiergraber, D.Willbold, J.A.Kritzer, J.D.Mougous, D.Baker, F.Dimaio, G.Bhardwaj. Accurate De Novo Design of High-Affinity Protein-Binding Macrocycles Using Deep Learning. Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469
PubMed: 40542165
DOI: 10.1038/S41589-025-01929-W