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Zinc in PDB 6cvp: Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex

Enzymatic activity of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex

All present enzymatic activity of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex:
3.1.11.7; 3.1.12.2;

Protein crystallography data

The structure of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvp was solved by M.J.Schellenberg, R.S.Williams, P.S.Tumbale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.62 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.507, 121.105, 122.314, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.4

Other elements in 6cvp:

The structure of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex (pdb code 6cvp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex, PDB code: 6cvp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6cvp

Go back to Zinc Binding Sites List in 6cvp
Zinc binding site 1 out of 2 in the Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.8
occ:1.00
NE2 A:HIS335 2.0 26.3 1.0
NE2 A:HIS339 2.1 24.4 1.0
SG A:CYS322 2.2 28.9 1.0
SG A:CYS319 2.3 27.4 1.0
CE1 A:HIS335 2.9 30.3 1.0
CD2 A:HIS339 3.0 24.4 1.0
CE1 A:HIS339 3.1 27.1 1.0
CD2 A:HIS335 3.1 24.5 1.0
CB A:CYS319 3.2 25.6 1.0
CB A:CYS322 3.3 34.4 1.0
N A:CYS322 3.7 27.0 1.0
ND1 A:HIS335 4.0 27.6 1.0
CA A:CYS322 4.0 29.1 1.0
CG A:HIS335 4.1 27.6 1.0
ND1 A:HIS339 4.2 27.7 1.0
CG A:HIS339 4.2 23.1 1.0
CB A:GLU321 4.5 31.5 1.0
C A:GLU321 4.5 29.2 1.0
CA A:CYS319 4.6 23.9 1.0
C A:CYS322 4.7 30.3 1.0
CB A:GLN324 4.8 27.5 1.0
N A:GLU321 4.8 26.3 1.0
CA A:GLU321 4.9 28.4 1.0
N A:GLN323 4.9 32.5 1.0

Zinc binding site 2 out of 2 in 6cvp

Go back to Zinc Binding Sites List in 6cvp
Zinc binding site 2 out of 2 in the Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Aprataxin (Aptx) R199H Bound to Rna-Dna, Amp and Zn Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:25.9
occ:1.00
NE2 B:HIS335 2.0 36.8 1.0
NE2 B:HIS339 2.1 32.5 1.0
SG B:CYS319 2.3 27.3 1.0
SG B:CYS322 2.3 28.8 1.0
CE1 B:HIS335 3.0 35.8 1.0
CD2 B:HIS335 3.0 33.2 1.0
CE1 B:HIS339 3.0 33.9 1.0
CB B:CYS319 3.0 26.3 1.0
CD2 B:HIS339 3.1 32.8 1.0
CB B:CYS322 3.4 29.3 1.0
N B:CYS322 3.7 30.5 1.0
ND1 B:HIS335 4.1 33.5 1.0
CA B:CYS322 4.1 28.4 1.0
CG B:HIS335 4.1 29.3 1.0
ND1 B:HIS339 4.1 35.0 1.0
CG B:HIS339 4.2 36.3 1.0
CB B:GLU321 4.4 32.9 1.0
CA B:CYS319 4.5 25.4 1.0
C B:GLU321 4.6 29.0 1.0
N B:GLU321 4.7 27.2 1.0
C B:CYS322 4.7 27.6 1.0
CB B:GLN324 4.8 49.1 1.0
CA B:GLU321 4.8 29.5 1.0
N B:GLN323 4.9 26.7 1.0
C B:CYS319 4.9 25.4 1.0

Reference:

P.Tumbale, M.J.Schellenberg, G.A.Mueller, E.Fairweather, M.Watson, J.N.Little, J.Krahn, I.Waddell, R.E.London, R.S.Williams. Mechanism of Aptx Nicked Dna Sensing and Pleiotropic Inactivation in Neurodegenerative Disease. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 29934293
DOI: 10.15252/EMBJ.201798875
Page generated: Mon Oct 28 19:10:54 2024

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