Zinc in PDB 7pdv: Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna

The structure of Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna, PDB code: 7pdv was solved by K.Soni, P.K.A.Jagtap, M.Sattler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.45 / 3.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.23, 65.89, 94.91, 90, 90.05, 90
R / Rfree (%)	33.7 / 39

The binding sites of Zinc atom in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna (pdb code 7pdv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna, PDB code: 7pdv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:28.8 occ:1.00 SG A:CYS110 2.2 50.2 1.0 CB A:CYS99 2.4 34.1 1.0 SG A:CYS99 2.5 32.6 1.0 SG A:CYS96 2.7 37.1 1.0 CB A:CYS110 3.1 49.9 1.0 CB A:CYS96 3.2 37.0 1.0 CA A:CYS99 3.5 32.5 1.0 N A:CYS99 3.6 34.0 1.0 CB A:LEU101 3.9 30.4 1.0 CB A:ARG112 4.0 50.6 1.0 C A:CYS99 4.0 32.5 1.0 N A:LEU101 4.1 30.4 1.0 N A:GLY100 4.2 33.0 1.0 N A:CYS113 4.5 50.2 1.0 CA A:LEU101 4.5 30.4 1.0 N A:ARG112 4.6 50.3 1.0 CA A:CYS110 4.6 49.8 1.0 O A:LEU101 4.6 30.5 1.0 CA A:CYS96 4.7 36.9 1.0 C A:LYS98 4.7 30.2 1.0 CA A:ARG112 4.8 50.4 1.0 SG A:CYS113 4.8 50.1 1.0 O A:CYS99 4.9 32.5 1.0 N A:PHE111 5.0 50.0 1.0 ND2 A:ASN103 5.0 30.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:32.8 occ:1.00 CB C:CYS99 2.3 45.2 1.0 SG C:CYS110 2.3 42.2 1.0 SG C:CYS99 2.4 41.5 1.0 SG C:CYS96 2.4 42.3 1.0 CB C:CYS96 2.7 42.3 1.0 CB C:CYS110 3.4 42.0 1.0 CA C:CYS99 3.4 41.7 1.0 N C:CYS99 3.5 41.6 1.0 CB C:LEU101 3.8 41.8 1.0 C C:CYS99 3.9 41.7 1.0 N C:LEU101 4.1 41.9 1.0 CA C:CYS96 4.1 42.3 1.0 N C:GLY100 4.1 46.0 1.0 CA C:LEU101 4.5 41.9 1.0 C C:CYS96 4.5 42.4 1.0 O C:LEU101 4.6 41.8 1.0 O C:CYS96 4.6 46.1 1.0 CB C:ARG112 4.6 47.2 1.0 C C:LYS98 4.6 46.3 1.0 OD1 C:ASN103 4.7 47.0 1.0 O C:CYS99 4.7 45.4 1.0 CA C:CYS110 4.8 41.8 1.0 N C:ARG112 4.9 46.8 1.0 CD2 C:LEU101 4.9 41.8 1.0 N C:CYS96 4.9 42.4 1.0 N C:PHE111 4.9 42.5 1.0 CG C:LEU101 5.0 41.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:16.9 occ:1.00 SG E:CYS110 2.2 26.8 1.0 SG E:CYS99 2.3 19.6 1.0 SG E:CYS96 2.5 24.4 1.0 CB E:CYS110 2.5 26.9 1.0 CB E:CYS96 3.0 24.5 1.0 CB E:CYS99 3.2 19.9 1.0 SG E:CYS113 3.5 26.1 1.0 N E:CYS113 3.8 26.3 1.0 CA E:CYS110 4.0 27.1 1.0 N E:GLY114 4.1 18.9 1.0 CB E:CYS113 4.3 26.2 1.0 N E:CYS99 4.3 20.7 1.0 CA E:CYS99 4.4 20.5 1.0 CB E:ARG112 4.4 31.4 1.0 N E:ARG112 4.5 31.1 1.0 CA E:CYS113 4.5 26.2 1.0 CA E:CYS96 4.5 24.7 1.0 C E:CYS110 4.6 27.1 1.0 CB E:LEU101 4.7 26.5 1.0 C E:ARG112 4.8 31.0 1.0 CA E:ARG112 4.8 31.4 1.0 N E:CYS110 4.8 27.0 1.0 N E:PHE111 4.8 30.5 1.0 C E:CYS113 4.9 26.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:21.6 occ:1.00 CB G:CYS110 2.3 35.0 1.0 SG G:CYS99 2.3 16.9 1.0 SG G:CYS110 2.4 34.9 1.0 SG G:CYS96 3.0 23.2 1.0 SG G:CYS113 3.1 42.3 1.0 N G:GLY114 3.5 40.1 1.0 CB G:CYS99 3.5 15.8 1.0 CB G:CYS96 3.6 23.0 1.0 N G:CYS113 3.7 44.7 1.0 CA G:CYS110 3.8 35.0 1.0 CB G:CYS113 4.0 44.0 1.0 CA G:CYS113 4.2 44.1 1.0 CA G:GLY114 4.3 39.5 1.0 C G:CYS113 4.4 42.6 1.0 N G:CYS110 4.4 35.1 1.0 C G:CYS110 4.5 35.0 1.0 N G:CYS99 4.6 15.9 1.0 C G:GLY114 4.6 38.5 1.0 N G:ARG112 4.6 46.2 1.0 CA G:CYS99 4.7 15.8 1.0 CB G:ARG112 4.8 46.1 1.0 C G:ARG112 4.8 45.6 1.0 N G:PHE111 4.8 40.6 1.0 CA G:ARG112 5.0 45.7 1.0

K.Soni, P.K.A.Jagtap, M.Sattler. Crystal Structure of RBM5 RRM1-Zinc Finger in Complex with Rna To Be Published.