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Zinc in PDB 4msx: Crystal Structure of An Essential Yeast Splicing Factor

Protein crystallography data

The structure of Crystal Structure of An Essential Yeast Splicing Factor, PDB code: 4msx was solved by H.Hadjivassiliou, C.Guthrie, O.S.Rosenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 1.87
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.315, 139.315, 86.737, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Essential Yeast Splicing Factor (pdb code 4msx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of An Essential Yeast Splicing Factor, PDB code: 4msx:

Zinc binding site 1 out of 1 in 4msx

Go back to Zinc Binding Sites List in 4msx
Zinc binding site 1 out of 1 in the Crystal Structure of An Essential Yeast Splicing Factor


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 An Essential Yeast Splicing Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:32.9
occ:1.00
NE2 A:HIS79 2.0 34.7 1.0
ND1 A:HIS85 2.2 35.3 1.0
SG A:CYS60 2.3 30.1 1.0
SG A:CYS63 2.4 34.0 1.0
CE1 A:HIS79 3.0 32.4 1.0
H A:CYS63 3.0 34.9 1.0
HB2 A:HIS85 3.0 38.4 1.0
CG A:HIS85 3.1 31.3 1.0
HB3 A:HIS85 3.1 38.4 1.0
CD2 A:HIS79 3.1 34.2 1.0
HE1 A:HIS79 3.1 38.8 1.0
HB3 A:CYS60 3.1 36.1 1.0
HB3 A:CYS63 3.1 40.4 1.0
CB A:CYS60 3.2 30.2 1.0
CB A:HIS85 3.3 32.0 1.0
CE1 A:HIS85 3.3 39.3 1.0
HD2 A:HIS79 3.3 40.9 1.0
CB A:CYS63 3.3 33.8 1.0
HB2 A:CYS60 3.4 36.1 1.0
HB A:VAL62 3.5 43.7 1.0
HE1 A:HIS85 3.5 47.1 1.0
N A:CYS63 3.7 29.2 1.0
HE2 A:TYR67 3.9 34.8 1.0
CA A:CYS63 4.1 31.4 1.0
ND1 A:HIS79 4.1 32.4 1.0
HB2 A:CYS63 4.2 40.4 1.0
CG A:HIS79 4.2 33.3 1.0
O A:HOH727 4.2 44.1 1.0
HH A:TYR67 4.3 38.0 1.0
CD2 A:HIS85 4.3 35.5 1.0
H A:VAL62 4.3 29.9 1.0
NE2 A:HIS85 4.3 41.1 1.0
CB A:VAL62 4.4 36.5 1.0
HB2 A:GLU83 4.4 50.4 1.0
H A:GLY64 4.4 37.3 1.0
CA A:CYS60 4.6 29.4 1.0
H A:HIS65 4.6 39.7 1.0
CE2 A:TYR67 4.6 29.0 1.0
C A:VAL62 4.7 31.8 1.0
HB3 A:GLU83 4.7 50.4 1.0
HB2 A:HIS65 4.8 37.6 1.0
HG12 A:VAL62 4.8 41.8 1.0
CA A:HIS85 4.8 31.7 1.0
C A:CYS63 4.8 32.5 1.0
HA A:CYS63 4.9 37.6 1.0
HD1 A:HIS79 4.9 38.8 1.0
N A:GLY64 4.9 31.2 1.0
CA A:VAL62 4.9 26.9 1.0
N A:VAL62 4.9 24.9 1.0
OH A:TYR67 4.9 31.7 1.0
C A:CYS60 4.9 30.1 1.0
HA A:CYS60 5.0 35.2 1.0

Reference:

H.Hadjivassiliou, O.S.Rosenberg, C.Guthrie. The Crystal Structure of S. Cerevisiae SAD1, A Catalytically Inactive Deubiquitinase That Is Broadly Required For Pre-Mrna Splicing. Rna V. 20 656 2014.
ISSN: ISSN 1355-8382
PubMed: 24681967
DOI: 10.1261/RNA.042838.113
Page generated: Wed Dec 16 05:35:50 2020

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