Sodium in PDB 7s4e: Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex

The structure of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex, PDB code: 7s4e was solved by D.J.Macpherson, W.Sherman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.92 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.14, 116.57, 122.32, 90, 90, 90
R / Rfree (%)	21.9 / 25.9

The structure of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex (pdb code 7s4e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex, PDB code: 7s4e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1504 b:59.1 occ:1.00 O A:VAL1429 2.8 50.6 1.0 OH A:TYR1421 2.8 47.2 1.0 ND2 A:ASN1459 3.1 49.4 1.0 N A:VAL1429 3.1 49.8 1.0 CB A:ASN1459 3.5 43.9 1.0 C42 B:87A308 3.5 43.2 1.0 C A:VAL1429 3.7 50.9 1.0 CA A:PRO1428 3.8 50.2 1.0 CG A:ASN1459 3.8 46.4 1.0 CD2 A:LEU1412 3.9 53.1 1.0 C A:PRO1428 3.9 50.8 1.0 CZ A:TYR1421 3.9 46.4 1.0 CA A:VAL1429 3.9 50.9 1.0 CG1 A:VAL1429 4.0 49.4 1.0 C41 B:87A308 4.1 47.4 1.0 CE1 A:TYR1421 4.2 44.7 1.0 CA A:LEU1456 4.3 45.8 1.0 O A:LEU1456 4.3 49.3 1.0 C43 B:87A308 4.4 44.3 1.0 O7 B:87A308 4.5 43.5 1.0 CB A:PRO1428 4.5 52.3 1.0 O A:LYS1427 4.6 50.0 1.0 CB A:VAL1429 4.6 51.2 1.0 CG2 A:ILE1425 4.6 47.8 1.0 CG A:LEU1412 4.7 54.8 1.0 CG A:LEU1456 4.7 46.0 1.0 C A:LEU1456 4.8 47.6 1.0 CD1 A:LEU1412 4.8 56.5 1.0 CA A:ASN1459 4.9 42.9 1.0 N A:PRO1428 4.9 51.8 1.0 N A:ASP1430 4.9 52.4 1.0 CB A:LEU1456 5.0 46.0 1.0 OD1 A:ASN1459 5.0 44.4 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:54.4 occ:1.00 NE2 B:HIS115 2.9 37.2 1.0 O4 B:87A308 2.9 38.8 1.0 OD1 B:ASN67 3.1 45.6 1.0 N B:ARG69 3.4 44.2 1.0 N B:SER68 3.5 45.5 1.0 CE1 B:HIS115 3.5 36.6 1.0 CA B:ASN67 3.5 47.1 1.0 C19 B:87A308 3.6 41.0 1.0 C B:ASN67 3.7 47.2 1.0 C20 B:87A308 3.8 41.2 1.0 C17 B:87A308 3.9 37.4 1.0 CE1 B:PHE91 3.9 52.8 1.0 CZ B:PHE91 3.9 52.2 1.0 O B:VAL66 4.0 44.5 1.0 CG B:ASN67 4.0 47.2 1.0 CA B:ARG69 4.0 43.3 1.0 CD2 B:HIS115 4.1 37.6 1.0 CG B:TYR112 4.1 41.3 1.0 CB B:TYR112 4.1 41.9 1.0 C18 B:87A308 4.2 37.0 1.0 CB B:ASN67 4.3 47.9 1.0 OG B:SER68 4.3 43.1 1.0 CG B:ARG69 4.4 45.2 1.0 C B:SER68 4.4 45.9 1.0 CA B:SER68 4.5 45.7 1.0 CD1 B:TYR112 4.5 40.8 1.0 CD2 B:TYR112 4.5 41.9 1.0 N B:ASN67 4.5 46.8 1.0 O B:ASN67 4.5 50.8 1.0 C B:VAL66 4.7 45.9 1.0 ND1 B:HIS115 4.7 36.3 1.0 CB B:ARG69 4.8 44.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:63.2 occ:1.00 O B:SER111 2.9 40.6 1.0 O B:HOH403 2.9 46.1 1.0 CB B:PRO71 3.3 42.9 1.0 CD2 B:HIS110 3.3 44.7 1.0 CA B:PRO71 3.5 42.0 1.0 CB B:HIS110 3.6 43.8 1.0 N B:SER72 3.8 42.4 1.0 CG B:HIS110 3.8 45.2 1.0 CE2 B:TYR112 3.8 41.2 1.0 CZ B:TYR112 4.0 40.9 1.0 N B:SER111 4.0 40.7 1.0 C B:SER111 4.0 38.9 1.0 C B:PRO71 4.1 42.4 1.0 CD2 B:TYR112 4.2 41.9 1.0 CG B:PRO71 4.2 43.1 1.0 CA B:HIS110 4.2 42.0 1.0 O B:SER72 4.3 41.2 1.0 OH B:TYR112 4.3 41.6 1.0 C B:HIS110 4.3 42.0 1.0 O A:GLU1466 4.4 50.2 1.0 CE1 B:TYR112 4.5 39.9 1.0 NE2 B:HIS110 4.6 45.3 1.0 CA B:SER111 4.6 39.8 1.0 C A:GLY1467 4.7 50.8 1.0 CG B:TYR112 4.7 41.3 1.0 C B:SER72 4.7 41.9 1.0 N B:PRO71 4.7 42.8 1.0 CD1 B:TYR112 4.8 40.8 1.0 N A:SER1468 4.8 48.6 1.0 O A:GLY1467 4.8 55.0 1.0 CA B:SER72 4.9 43.5 1.0 CA A:GLY1467 5.0 51.1 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na307 b:58.9 occ:1.00 O C:HOH205 2.6 49.5 1.0 OH C:TYR79 2.7 45.5 1.0 O B:PRO154 3.0 49.1 1.0 CD2 B:TYR156 3.4 47.9 1.0 N B:TYR156 3.6 50.1 1.0 CZ C:TYR79 3.7 44.4 1.0 CE2 C:TYR79 3.8 43.0 1.0 CA B:VAL155 4.0 51.3 1.0 C B:PRO154 4.1 49.1 1.0 CG B:TYR156 4.1 48.0 1.0 CB B:TYR156 4.2 49.6 1.0 CE2 B:TYR156 4.2 48.7 1.0 C B:VAL155 4.3 50.8 1.0 N C:PHE93 4.4 48.8 1.0 N B:VAL155 4.5 49.2 1.0 CA B:TYR156 4.5 49.4 1.0 CD1 B:LEU153 4.5 51.5 1.0 O C:PRO91 4.6 45.4 1.0 CB B:LEU153 4.6 47.5 1.0 CB C:PHE93 4.7 45.9 1.0 CG2 C:ILE90 4.8 59.3 1.0 OE2 C:GLU92 4.8 53.7 1.0 O B:TYR156 4.9 52.8 1.0 CE1 C:TYR79 4.9 44.8 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ligand ACBI1 in Complex with Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Na303 b:56.8 occ:1.00 OH G:TYR79 2.6 45.5 1.0 O G:HOH306 2.8 41.9 1.0 O F:PRO154 2.9 44.6 1.0 CD2 F:TYR156 3.3 47.1 1.0 N F:TYR156 3.4 46.8 1.0 CZ G:TYR79 3.6 44.7 1.0 CE2 G:TYR79 3.8 44.3 1.0 CA F:VAL155 3.8 47.0 1.0 CG F:TYR156 3.9 47.8 1.0 CB F:TYR156 4.0 48.4 1.0 C F:PRO154 4.0 44.7 1.0 CE2 F:TYR156 4.1 46.5 1.0 C F:VAL155 4.1 47.9 1.0 CA F:TYR156 4.3 47.5 1.0 N F:VAL155 4.4 44.6 1.0 CD1 F:LEU153 4.6 45.1 1.0 N G:PHE93 4.6 47.5 1.0 CB F:LEU153 4.7 43.1 1.0 CG2 G:ILE90 4.7 56.7 1.0 O G:PRO91 4.7 43.6 1.0 O F:TYR156 4.7 50.1 1.0 CB G:PHE93 4.8 48.4 1.0 CE1 G:TYR79 4.9 45.6 1.0 CB F:VAL155 5.0 48.7 1.0

B.Mostofian, T.Dixon, D.J.Macpherson, T.Dauzhenka, S.Lotz, D.Mcgee, S.Shechter, U.Shrestha, R.Wiewiora, Z.Mcdargh, F.Pei, J.Vieira-Ribeiro, T.Wilkerson, V.Sachdeva, N.Gao, J.Shourya, S.Sparks, Y.Li, A.Vinitsky, X.Zhang, J.Imbriglio, A.Evdokimov, L.Bergeron, A.Dickson, H.Xu, W.Sherman, J.A.Izaguirre. Atomic-Resolution Prediction Ofdegrader-Mediated Ternary Complex Structuresby Combining Molecular Simulations Withhydrogen Deuterium Exchange To Be Published.