Zinc in PDB 4pjo: Minimal U1 Snrnp

The structure of Minimal U1 Snrnp, PDB code: 4pjo was solved by Y.Kondo, C.Oubridge, A.M.Van Roon, K.Nagai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.359, 172.627, 256.322, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.5

The structure of Minimal U1 Snrnp also contains other interesting chemical elements:

Magnesium	(Mg)	20 atoms
Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Minimal U1 Snrnp (pdb code 4pjo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Minimal U1 Snrnp, PDB code: 4pjo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn201 b:83.8 occ:1.00 NE2 L:HIS24 1.9 58.9 1.0 ND1 L:HIS30 2.1 92.5 1.0 SG L:CYS9 2.2 97.6 1.0 SG L:CYS6 2.3 86.3 1.0 CE1 L:HIS30 2.7 84.9 1.0 CE1 L:HIS24 2.9 58.8 1.0 CD2 L:HIS24 3.0 62.7 1.0 CG L:HIS30 3.1 99.2 1.0 CB L:CYS6 3.3 81.3 1.0 CB L:CYS9 3.4 85.5 1.0 NE2 L:HIS30 3.8 89.9 1.0 CB L:HIS30 3.8 0.5 1.0 N L:CYS9 3.9 78.6 1.0 CD2 L:HIS30 4.0 91.5 1.0 ND1 L:HIS24 4.0 63.2 1.0 CG L:HIS24 4.1 64.9 1.0 CA L:CYS9 4.3 84.0 1.0 CA L:HIS30 4.3 97.8 1.0 CB L:TYR8 4.5 83.3 1.0 CA L:CYS6 4.6 82.0 1.0 C L:TYR8 4.9 80.8 1.0 CG2 L:THR11 4.9 91.3 1.0

Zinc binding site 2 out of 4 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ l:Zn201 b:98.6 occ:1.00 SG l:CYS9 1.9 0.5 1.0 NE2 l:HIS24 2.0 64.3 1.0 ND1 l:HIS30 2.2 0.7 1.0 SG l:CYS6 2.4 76.4 1.0 CE1 l:HIS24 2.8 69.2 1.0 CE1 l:HIS30 2.9 0.6 1.0 CD2 l:HIS24 3.1 69.3 1.0 CG l:HIS30 3.2 0.8 1.0 CB l:CYS9 3.2 0.5 1.0 CB l:CYS6 3.4 62.6 1.0 CB l:HIS30 3.7 0.1 1.0 N l:CYS9 3.9 99.5 1.0 NE2 l:HIS30 4.0 0.4 1.0 ND1 l:HIS24 4.0 71.4 1.0 CD2 l:HIS30 4.1 0.5 1.0 CA l:HIS30 4.1 1.0 1.0 CA l:CYS9 4.1 0.9 1.0 CG l:HIS24 4.2 70.8 1.0 CB l:TYR8 4.5 0.1 1.0 CA l:CYS6 4.8 67.4 1.0 CG2 l:THR11 4.8 0.7 1.0 C l:TYR8 4.8 99.4 1.0

Zinc binding site 3 out of 4 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn201 b:0.9 occ:1.00 ND1 M:HIS30 2.0 0.8 1.0 NE2 M:HIS24 2.1 0.5 1.0 SG M:CYS9 2.2 0.6 1.0 SG M:CYS6 2.2 0.5 1.0 CE1 M:HIS30 2.6 96.5 1.0 CE1 M:HIS24 3.0 99.1 1.0 CG M:HIS30 3.1 0.6 1.0 CD2 M:HIS24 3.2 97.7 1.0 CB M:CYS6 3.3 0.5 1.0 CB M:CYS9 3.4 0.4 1.0 NE2 M:HIS30 3.7 0.6 1.0 CB M:HIS30 3.8 0.8 1.0 N M:CYS9 3.9 0.1 1.0 CD2 M:HIS30 3.9 0.2 1.0 ND1 M:HIS24 4.2 0.1 1.0 CA M:HIS30 4.3 0.7 1.0 CG M:HIS24 4.3 0.7 1.0 CA M:CYS9 4.3 0.8 1.0 CB M:TYR8 4.4 0.7 1.0 CA M:CYS6 4.6 0.6 1.0 C M:TYR8 4.8 0.6 1.0

Zinc binding site 4 out of 4 in the Minimal U1 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Minimal U1 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ m:Zn201 b:0.1 occ:1.00 NE2 m:HIS24 1.8 0.6 1.0 ND1 m:HIS30 2.0 0.4 1.0 SG m:CYS9 2.3 0.4 1.0 SG m:CYS6 2.5 0.8 1.0 CE1 m:HIS30 2.6 0.9 1.0 CD2 m:HIS24 2.8 0.0 1.0 CE1 m:HIS24 2.8 0.0 1.0 CG m:HIS30 3.0 1.0 1.0 CB m:CYS6 3.5 0.4 1.0 CB m:HIS30 3.6 0.5 1.0 CB m:CYS9 3.6 0.5 1.0 NE2 m:HIS30 3.6 1.0 1.0 CD2 m:HIS30 3.8 0.1 1.0 ND1 m:HIS24 3.9 1.0 1.0 CG m:HIS24 3.9 0.1 1.0 CA m:HIS30 4.2 0.2 1.0 N m:CYS9 4.2 0.7 1.0 CA m:CYS9 4.5 0.3 1.0 CB m:TYR8 4.7 0.4 1.0 CA m:CYS6 4.8 0.5 1.0 O m:HIS24 4.9 1.0 1.0

Y.Kondo, C.Oubridge, A.M.Van Roon, K.Nagai. Crystal Structure of Human U1 Snrnp, A Small Nuclear Ribonucleoprotein Particle, Reveals the Mechanism of 5' Splice Site Recognition. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 25555158
DOI: 10.7554/ELIFE.04986