Zinc in PDB 5w3v: Crystal Structure of Macaque APOBEC3H in Complex with Rna

The structure of Crystal Structure of Macaque APOBEC3H in Complex with Rna, PDB code: 5w3v was solved by J.A.Bohn, K.Thummar, A.York, A.Raymond, W.C.Brown, P.D.Bieniasz, T.Hatziioannou, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.66 / 2.24
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.960, 89.310, 134.370, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Macaque APOBEC3H in Complex with Rna (pdb code 5w3v). 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 Macaque APOBEC3H in Complex with Rna, PDB code: 5w3v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Macaque APOBEC3H in Complex with Rna


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 Macaque APOBEC3H in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:72.0 occ:1.00 ND1 A:HIS54 2.0 0.8 1.0 O A:HOH442 2.1 66.8 1.0 SG A:CYS88 2.3 61.0 1.0 SG A:CYS85 2.3 60.5 1.0 CE1 A:HIS54 2.8 91.3 1.0 O A:HOH419 3.2 80.0 1.0 CG A:HIS54 3.2 94.5 1.0 CB A:CYS85 3.3 41.6 1.0 CB A:CYS88 3.3 50.1 1.0 OE1 A:GLU56 3.7 75.9 1.0 CB A:HIS54 3.8 87.1 1.0 NE2 A:HIS54 4.0 86.4 1.0 CA A:HIS54 4.1 70.4 1.0 N A:CYS85 4.1 55.3 1.0 CD2 A:HIS54 4.2 85.2 1.0 O A:ASP53 4.2 80.6 1.0 N A:CYS88 4.2 47.3 1.0 CA A:CYS85 4.3 55.1 1.0 OG A:SER87 4.3 80.3 1.0 CA A:CYS88 4.4 56.2 1.0 O A:HOH431 4.5 0.2 1.0 CD A:GLU56 4.6 66.4 1.0 O A:HOH405 4.8 0.7 1.0 C A:CYS85 4.9 56.3 1.0 O A:CYS85 4.9 61.0 1.0 C A:ASP53 5.0 93.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Macaque APOBEC3H in Complex with Rna


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 Macaque APOBEC3H in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:81.1 occ:1.00 ND1 B:HIS54 2.0 0.2 1.0 O B:HOH409 2.1 77.6 1.0 SG B:CYS88 2.3 93.7 1.0 SG B:CYS85 2.3 68.7 1.0 CE1 B:HIS54 2.9 0.3 1.0 CG B:HIS54 3.1 0.8 1.0 CB B:CYS88 3.2 80.1 1.0 CB B:CYS85 3.2 67.0 1.0 CB B:HIS54 3.5 89.8 1.0 N B:CYS85 3.8 71.8 1.0 NE2 B:HIS54 4.1 1.0 1.0 CA B:CYS85 4.1 68.8 1.0 N B:CYS88 4.1 83.8 1.0 OE1 B:GLU56 4.1 0.3 1.0 CD2 B:HIS54 4.2 0.8 1.0 O B:HOH411 4.3 76.5 1.0 CA B:CYS88 4.3 81.0 1.0 OE2 B:GLU56 4.4 86.5 1.0 CD B:GLU56 4.4 91.8 1.0 C B:CYS85 4.7 71.1 1.0 O B:CYS85 4.8 80.3 1.0 C B:PRO84 5.0 72.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Macaque APOBEC3H in Complex with Rna


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 Macaque APOBEC3H in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:91.7 occ:1.00 ND1 C:HIS54 2.0 0.2 1.0 O C:HOH411 2.1 0.5 1.0 SG C:CYS88 2.3 91.5 1.0 SG C:CYS85 2.3 81.0 1.0 CE1 C:HIS54 2.7 0.3 1.0 CB C:CYS85 3.2 71.3 1.0 CB C:CYS88 3.2 78.9 1.0 CG C:HIS54 3.2 0.1 1.0 N C:CYS85 3.8 82.8 1.0 OE2 C:GLU56 3.8 99.0 1.0 CB C:HIS54 3.9 0.8 1.0 NE2 C:HIS54 3.9 0.5 1.0 CA C:CYS85 4.0 79.0 1.0 CA C:HIS54 4.1 0.2 1.0 CD2 C:HIS54 4.2 0.3 1.0 N C:CYS88 4.2 74.3 1.0 CA C:CYS88 4.3 84.7 1.0 CD C:GLU56 4.4 0.1 1.0 O C:HOH421 4.4 71.0 1.0 OG C:SER87 4.5 0.7 1.0 OE1 C:GLU56 4.5 0.3 1.0 O C:HOH418 4.6 74.0 1.0 C C:CYS85 4.7 80.5 1.0 O C:CYS85 4.7 76.9 1.0 C C:PRO84 4.9 77.1 1.0 N C:HIS54 5.0 0.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Macaque APOBEC3H in Complex with Rna


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 Macaque APOBEC3H in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:68.1 occ:1.00 ND1 D:HIS54 2.0 0.0 1.0 O D:HOH437 2.1 47.1 1.0 SG D:CYS85 2.3 63.1 1.0 SG D:CYS88 2.3 58.4 1.0 CE1 D:HIS54 3.0 0.5 1.0 CG D:HIS54 3.0 80.3 1.0 O D:HOH465 3.2 73.4 1.0 CB D:CYS85 3.3 47.9 1.0 CB D:HIS54 3.4 62.5 1.0 CB D:CYS88 3.4 56.1 1.0 N D:CYS85 3.9 58.6 1.0 NE2 D:HIS54 4.1 91.5 1.0 N D:CYS88 4.1 60.7 1.0 CA D:CYS85 4.2 54.9 1.0 CD2 D:HIS54 4.2 88.4 1.0 OE1 D:GLU56 4.2 67.3 1.0 CA D:CYS88 4.4 52.0 1.0 O D:HOH446 4.4 78.7 1.0 O D:HOH436 4.4 61.8 1.0 CD D:GLU56 4.5 60.5 1.0 OE2 D:GLU56 4.5 78.5 1.0 C D:CYS85 4.7 59.6 1.0 O D:CYS85 4.8 60.9 1.0 O D:HOH419 4.9 69.2 1.0 CA D:HIS54 4.9 70.8 1.0

J.A.Bohn, K.Thummar, A.York, A.Raymond, W.C.Brown, P.D.Bieniasz, T.Hatziioannou, J.L.Smith. APOBEC3H Structure Reveals An Unusual Mechanism of Interaction with Duplex Rna. Nat Commun V. 8 1021 2017.
ISSN: ESSN 2041-1723
PubMed: 29044109
DOI: 10.1038/S41467-017-01309-6