Magnesium in PDB 7uk1: Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna

The structure of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna, PDB code: 7uk1 was solved by I.B.Lomakin, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.87 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.451, 64.658, 68.837, 90, 97.79, 90
R / Rfree (%)	20 / 29.1

The binding sites of Magnesium atom in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna (pdb code 7uk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna, PDB code: 7uk1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:141.4 occ:1.00 O A:HOH701 2.2 141.8 1.0 O A:HOH714 2.2 141.0 1.0 O A:HOH713 2.2 154.0 1.0 O A:HOH709 2.2 151.6 1.0 O A:HOH710 2.2 141.2 1.0 O A:HOH715 2.2 148.4 1.0 OE1 A:GLU389 4.3 149.7 1.0 OE2 A:GLU389 4.6 156.8 1.0 CD A:GLU389 4.9 141.4 1.0

Magnesium binding site 2 out of 5 in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:124.3 occ:1.00 OE2 A:GLU310 3.1 168.3 1.0 OD1 A:ASP311 3.3 131.8 1.0 CD A:GLU310 3.4 170.9 1.0 OE1 A:GLU310 3.8 173.0 1.0 CG A:GLU310 3.9 164.3 1.0 CB A:GLU310 4.2 155.3 1.0 CG A:ASP311 4.3 133.6 1.0 OD2 A:ASP311 4.5 134.6 1.0

Magnesium binding site 3 out of 5 in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:136.7 occ:1.00 OE2 A:GLU310 3.3 168.3 1.0 OE1 A:GLU310 3.3 173.0 1.0 CD A:GLU310 3.6 170.9 1.0

Magnesium binding site 4 out of 5 in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:152.7 occ:1.00 O B:HOH702 2.2 149.0 1.0 O B:HOH705 2.2 148.2 1.0 O B:HOH710 2.2 153.3 1.0 O B:HOH713 2.2 158.6 1.0 O B:HOH707 2.2 144.8 1.0 O B:HOH712 2.2 151.0 1.0 OE1 B:GLU461 4.0 131.0 1.0 OH B:TYR470 4.3 185.0 1.0 CD B:GLU461 4.4 130.2 1.0 OE2 B:GLU461 4.4 134.1 1.0 O B:HOH701 4.8 99.7 1.0

Magnesium binding site 5 out of 5 in the Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) with Murine Virus-Like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:105.0 occ:1.00 OE1 B:GLU501 2.7 107.3 1.0 O A:HOH711 3.0 97.9 1.0 CD B:GLU501 3.2 98.3 1.0 OE2 A:GLU509 3.3 129.1 1.0 OE2 B:GLU501 3.3 104.0 1.0 CG A:GLU509 3.4 121.6 1.0 NH1 B:ARG505 3.8 159.6 1.0 CD A:GLU509 3.8 130.9 1.0 CG B:GLU501 4.5 91.3 1.0 O A:HOH704 4.7 94.4 1.0 CB A:GLU509 4.7 108.4 1.0

J.Wang, A.Sachpatzidis, T.D.Christian, I.B.Lomakin, A.Garen, W.H.Konigsberg. Insight Into the Tumor Suppression Mechanism From the Structure of Human Polypyrimidine Splicing Factor (Psf/Sfpq) Complexed with A 30MER Rna From Murine Virus-Like 30S Transcript-1. Biochemistry V. 61 1723 2022.
ISSN: ISSN 0006-2960
PubMed: 35998361
DOI: 10.1021/ACS.BIOCHEM.2C00192