Zinc in PDB 7jl5: Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains

All present enzymatic activity of Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains:
4.2.99.18;

The structure of Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains, PDB code: 7jl5 was solved by A.A.Rodriguez, J.L.Wojtaszek, R.S.Williams, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.95 / 2.60
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	93.494, 93.494, 63.646, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.6

The binding sites of Zinc atom in the Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains (pdb code 7jl5). 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 Human NEIL3 Tandem Zinc Finger Grf Domains, PDB code: 7jl5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains


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 Human NEIL3 Tandem Zinc Finger Grf Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:39.6 occ:1.00 ND1 A:HIS510 2.3 63.1 1.0 SG A:CYS507 2.3 46.9 1.0 SG A:CYS541 2.3 35.7 1.0 SG A:CYS533 2.4 33.8 1.0 CE1 A:HIS510 3.0 37.3 1.0 HE1 A:HIS510 3.1 44.0 1.0 CB A:CYS507 3.2 45.9 1.0 CG A:HIS510 3.3 67.9 1.0 HB2 A:HIS510 3.3 79.7 1.0 H A:HIS510 3.3 78.6 1.0 CB A:CYS541 3.5 45.7 1.0 CB A:CYS533 3.5 32.4 1.0 HD2 A:PRO534 3.7 0.0 1.0 CB A:HIS510 3.8 66.3 1.0 N A:CYS541 4.0 64.9 1.0 N A:HIS510 4.1 65.4 1.0 NE2 A:HIS510 4.1 70.0 1.0 HG A:LEU535 4.2 58.5 1.0 CD2 A:HIS510 4.2 69.7 1.0 CA A:CYS533 4.3 37.7 1.0 CA A:CYS541 4.4 56.5 1.0 O A:HIS510 4.4 72.5 1.0 CA A:HIS510 4.4 62.9 1.0 HB2 A:PHE543 4.5 42.5 1.0 HD12 A:LEU535 4.5 44.5 1.0 CD A:PRO534 4.5 0.2 1.0 HB3 A:HIS510 4.6 79.7 1.0 CA A:CYS507 4.6 44.0 1.0 HD11 A:LEU535 4.6 44.5 1.0 HD3 A:PRO534 4.7 0.0 1.0 HB2 A:ARG512 4.7 76.3 1.0 HE2 A:HIS510 4.8 84.2 1.0 C A:HIS510 4.8 68.3 1.0 CB A:LYS509 4.9 56.9 1.0 CD1 A:LEU535 4.9 37.8 1.0 H A:LYS509 4.9 61.5 1.0 HB3 A:PHE543 5.0 42.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains


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 Human NEIL3 Tandem Zinc Finger Grf Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:27.8 occ:1.00 ND1 A:HIS556 2.2 43.6 1.0 SG A:CYS579 2.3 30.1 1.0 SG A:CYS554 2.4 30.1 1.0 SG A:CYS587 2.4 28.4 1.0 HB3 A:CYS587 2.8 33.6 1.0 H A:HIS556 2.8 42.0 1.0 HB2 A:HIS556 2.9 58.6 1.0 HB2 A:CYS579 3.0 53.1 1.0 H A:CYS587 3.0 35.4 1.0 CB A:CYS587 3.2 28.7 1.0 CG A:HIS556 3.2 42.4 1.0 CE1 A:HIS556 3.2 40.3 1.0 CB A:CYS579 3.2 44.1 1.0 HG A:CYS579 3.3 36.2 1.0 CB A:CYS554 3.3 26.2 1.0 HE1 A:HIS556 3.4 48.5 1.0 CB A:HIS556 3.4 48.7 1.0 N A:HIS556 3.5 34.9 1.0 H A:ASN555 3.7 30.2 1.0 HA A:CYS579 3.7 44.3 1.0 HD2 A:PRO580 3.7 47.8 1.0 N A:CYS587 3.8 29.5 1.0 HB2 A:CYS587 3.9 33.6 1.0 HB3 A:CYS579 4.0 53.1 1.0 N A:ASN555 4.0 25.9 1.0 CA A:CYS587 4.1 29.8 1.0 CA A:CYS579 4.1 36.8 1.0 HD12 A:LEU581 4.1 56.5 1.0 CA A:HIS556 4.1 43.4 1.0 HB3 A:HIS556 4.3 58.6 1.0 NE2 A:HIS556 4.3 44.3 1.0 CD2 A:HIS556 4.3 41.8 1.0 HB2 A:ASN555 4.4 41.2 1.0 C A:CYS554 4.4 31.7 1.0 CA A:CYS554 4.5 27.2 1.0 HG A:LEU581 4.5 52.3 1.0 C A:ASN555 4.5 30.0 1.0 CD A:PRO580 4.5 39.7 1.0 HA A:GLN586 4.6 44.6 1.0 HD3 A:PRO580 4.6 47.8 1.0 HA A:HIS556 4.6 52.3 1.0 HB3 A:PHE589 4.7 38.3 1.0 CA A:ASN555 4.7 29.3 1.0 HA A:CYS587 4.8 35.0 1.0 CD1 A:LEU581 4.9 47.0 1.0 C A:GLN586 4.9 36.1 1.0 C A:CYS579 4.9 37.1 1.0 H A:LYS558 4.9 45.8 1.0 C A:CYS587 4.9 40.6 1.0 HB2 A:LEU581 5.0 53.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains


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 Human NEIL3 Tandem Zinc Finger Grf Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:32.0 occ:1.00 SG B:CYS541 2.3 31.2 1.0 ND1 B:HIS510 2.3 33.3 1.0 SG B:CYS533 2.4 32.1 1.0 SG B:CYS507 2.6 37.9 1.0 HB3 B:CYS541 2.8 42.1 1.0 CB B:CYS507 2.9 31.7 1.0 H B:HIS510 3.0 44.6 1.0 CB B:CYS541 3.1 35.0 1.0 CE1 B:HIS510 3.1 34.1 1.0 HE1 B:HIS510 3.2 40.2 1.0 HB2 B:HIS510 3.3 66.1 1.0 H B:CYS541 3.3 39.0 1.0 CG B:HIS510 3.4 62.2 1.0 CB B:CYS533 3.4 30.5 1.0 CB B:HIS510 3.7 54.9 1.0 HB2 B:CYS541 3.8 42.1 1.0 N B:HIS510 3.8 37.1 1.0 HD2 B:PRO534 3.9 42.5 1.0 N B:CYS541 3.9 32.4 1.0 CA B:CYS541 4.1 35.3 1.0 CA B:HIS510 4.3 54.1 1.0 HD12 B:LEU535 4.3 43.7 1.0 NE2 B:HIS510 4.3 67.5 1.0 CA B:CYS533 4.4 33.3 1.0 CA B:CYS507 4.4 30.8 1.0 HG B:LEU535 4.4 51.9 1.0 O B:HIS510 4.4 73.0 1.0 H B:LYS509 4.4 47.4 1.0 CD2 B:HIS510 4.5 68.0 1.0 HA B:GLN540 4.6 40.0 1.0 HB3 B:HIS510 4.6 66.1 1.0 C B:HIS510 4.7 62.9 1.0 HD11 B:LEU535 4.7 43.7 1.0 CB B:LYS509 4.7 36.7 1.0 H B:SER508 4.8 49.9 1.0 HB3 B:PHE543 4.8 47.8 1.0 HA B:CYS541 4.8 42.5 1.0 CD B:PRO534 4.8 35.3 1.0 HB2 B:PHE543 4.8 47.8 1.0 CD1 B:LEU535 4.9 37.1 1.0 N B:LYS509 4.9 39.3 1.0 C B:CYS507 4.9 36.1 1.0 C B:LYS509 4.9 36.4 1.0 H B:PHE543 4.9 46.9 1.0 H B:ARG512 4.9 37.6 1.0 C B:GLN540 5.0 33.1 1.0 N B:SER508 5.0 41.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human NEIL3 Tandem Zinc Finger Grf Domains


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 Human NEIL3 Tandem Zinc Finger Grf Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:32.7 occ:1.00 ND1 B:HIS556 2.2 40.9 1.0 SG B:CYS579 2.3 24.8 1.0 SG B:CYS587 2.3 35.5 1.0 SG B:CYS554 2.4 38.5 1.0 H B:HIS556 2.7 51.0 1.0 HB2 B:CYS579 2.9 31.3 1.0 HB2 B:CYS554 2.9 43.4 1.0 HB2 B:HIS556 2.9 48.3 1.0 CE1 B:HIS556 3.1 41.1 1.0 CB B:CYS579 3.1 25.9 1.0 CG B:HIS556 3.2 40.4 1.0 CB B:CYS587 3.2 38.1 1.0 CB B:CYS554 3.2 36.0 1.0 HE1 B:HIS556 3.3 49.5 1.0 CB B:HIS556 3.5 40.1 1.0 N B:HIS556 3.5 42.3 1.0 HA B:CYS579 3.6 32.5 1.0 H B:ASN555 3.7 48.3 1.0 N B:CYS587 3.7 40.0 1.0 HD2 B:PRO580 3.8 28.6 1.0 HB3 B:CYS554 3.8 43.4 1.0 HB3 B:CYS579 3.9 31.3 1.0 CA B:CYS579 3.9 26.9 1.0 N B:ASN555 4.0 40.1 1.0 CA B:CYS587 4.0 39.3 1.0 CA B:HIS556 4.1 43.2 1.0 HD12 B:LEU581 4.1 52.7 1.0 HG B:LEU581 4.2 51.8 1.0 NE2 B:HIS556 4.2 43.8 1.0 CD2 B:HIS556 4.3 41.8 1.0 HB2 B:ASN555 4.3 54.1 1.0 HB3 B:HIS556 4.3 48.3 1.0 C B:CYS554 4.4 38.7 1.0 CA B:CYS554 4.4 35.1 1.0 HD3 B:PRO580 4.5 28.6 1.0 CD B:PRO580 4.5 23.7 1.0 HA B:GLN586 4.5 53.6 1.0 C B:ASN555 4.5 39.4 1.0 HA B:HIS556 4.7 52.0 1.0 HB2 B:PHE589 4.7 51.4 1.0 CA B:ASN555 4.7 39.3 1.0 HB3 B:PHE589 4.7 51.4 1.0 H B:PHE589 4.8 51.7 1.0 CD1 B:LEU581 4.8 43.8 1.0 C B:CYS587 4.8 44.7 1.0 C B:GLN586 4.9 42.1 1.0 HD11 B:LEU581 4.9 52.7 1.0 H B:GLY557 4.9 40.2 1.0 C B:CYS579 4.9 27.4 1.0 N B:CYS579 4.9 26.0 1.0 H B:CYS579 5.0 31.4 1.0 HA B:CYS554 5.0 42.3 1.0 CG B:LEU581 5.0 43.1 1.0 CB B:ASN555 5.0 44.9 1.0

A.A.Rodriguez, J.L.Wojtaszek, B.H.Greer, T.Haldar, K.S.Gates, R.S.Williams, B.F.Eichman. An Autoinhibitory Role For the Grf Zinc Finger Domain of Dna Glycosylase NEIL3. J.Biol.Chem. V. 295 15566 2020.
ISSN: ESSN 1083-351X
PubMed: 32878989
DOI: 10.1074/JBC.RA120.015541