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Zinc in PDB 7q3z: Dna/Rna Binding Protein

Protein crystallography data

The structure of Dna/Rna Binding Protein, PDB code: 7q3z was solved by E.Huber, K.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.88, 64.04, 104.58, 90, 93, 90
R / Rfree (%) 18.8 / 21.3

Other elements in 7q3z:

The structure of Dna/Rna Binding Protein also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna/Rna Binding Protein (pdb code 7q3z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna/Rna Binding Protein, PDB code: 7q3z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7q3z

Go back to Zinc Binding Sites List in 7q3z
Zinc binding site 1 out of 2 in the Dna/Rna Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna/Rna Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:30.9
occ:0.83
ND1 B:HIS266 1.9 25.6 1.0
SG B:CYS303 2.3 38.8 1.0
SG B:CYS268 2.3 38.0 1.0
SG B:CYS302 2.4 36.9 1.0
CE1 B:HIS266 2.7 37.9 1.0
CG B:HIS266 3.0 38.1 1.0
CB B:CYS303 3.3 35.7 1.0
CB B:CYS268 3.4 35.6 1.0
CB B:CYS302 3.5 27.6 1.0
CB B:HIS266 3.5 43.9 1.0
N B:CYS303 3.8 28.5 1.0
CA B:HIS266 3.9 39.5 1.0
NE2 B:HIS266 3.9 33.3 1.0
CD2 B:HIS266 4.0 34.5 1.0
N B:CYS268 4.1 47.7 1.0
C B:CYS302 4.2 28.9 1.0
CA B:CYS303 4.2 34.9 1.0
N B:PHE267 4.3 33.8 1.0
CA B:CYS268 4.4 40.1 1.0
CA B:CYS302 4.4 30.3 1.0
CD B:PRO272 4.4 37.1 1.0
CA B:ARG271 4.6 39.7 1.0
C B:HIS266 4.6 41.6 1.0
O B:HOH547 4.8 51.2 1.0
N B:ARG271 4.8 44.7 1.0
O B:CYS302 4.9 33.8 1.0
CE2 B:PHE301 4.9 35.1 1.0

Zinc binding site 2 out of 2 in 7q3z

Go back to Zinc Binding Sites List in 7q3z
Zinc binding site 2 out of 2 in the Dna/Rna Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna/Rna Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:30.0
occ:0.84
ND1 A:HIS266 2.0 26.5 1.0
SG A:CYS303 2.3 35.9 1.0
SG A:CYS302 2.3 34.5 1.0
SG A:CYS268 2.4 35.7 1.0
CE1 A:HIS266 2.9 35.8 1.0
CG A:HIS266 3.2 35.6 1.0
CB A:CYS303 3.2 32.0 1.0
CB A:CYS302 3.3 27.3 1.0
CB A:CYS268 3.5 38.1 1.0
CB A:HIS266 3.6 30.6 1.0
N A:CYS303 3.7 29.2 1.0
CA A:HIS266 3.9 29.6 1.0
NE2 A:HIS266 4.0 33.1 1.0
C A:CYS302 4.1 33.2 1.0
CA A:CYS303 4.1 34.0 1.0
N A:CYS268 4.1 41.0 1.0
CD2 A:HIS266 4.2 29.1 1.0
N A:PHE267 4.3 37.2 1.0
CA A:CYS302 4.3 29.5 1.0
CD A:PRO272 4.4 34.6 1.0
CA A:CYS268 4.4 38.6 1.0
C A:HIS266 4.6 35.8 1.0
CA A:ARG271 4.7 38.6 1.0
O A:CYS302 4.8 37.7 1.0
N A:CYS302 4.9 27.4 1.0
N A:ARG271 4.9 41.0 1.0
CE2 A:PHE301 5.0 29.1 1.0

Reference:

F.J.Metzner, E.Huber, K.P.Hopfner, K.Lammens. Structural and Biochemical Characterization of Human Schlafen 5. Nucleic Acids Res. V. 50 1147 2022.
ISSN: ESSN 1362-4962
PubMed: 35037067
DOI: 10.1093/NAR/GKAB1278
Page generated: Wed Oct 30 09:33:52 2024

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