Zinc in PDB 5m1q: Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc

The structure of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc, PDB code: 5m1q was solved by R.G.Xu, H.T.Jenkins, M.Chechik, E.V.Blagova, S.J.Greive, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 1.45
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	60.983, 60.983, 90.396, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 21.1

The binding sites of Zinc atom in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc (pdb code 5m1q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc, PDB code: 5m1q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc


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 the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.4 occ:1.00 OD1 A:ASP300 2.0 23.9 1.0 OD2 A:ASP429 2.1 19.2 1.0 ND1 A:HIS427 2.2 29.4 1.0 O A:HOH694 2.2 16.5 1.0 CG A:ASP429 2.8 17.9 1.0 OD1 A:ASP429 2.9 19.8 1.0 CG A:ASP300 3.0 26.6 1.0 CE1 A:HIS427 3.1 30.1 1.0 CG A:HIS427 3.1 28.2 1.0 OD2 A:ASP300 3.3 27.4 1.0 CB A:HIS427 3.4 26.4 1.0 O A:HOH617 3.8 26.5 1.0 CA A:HIS427 3.9 26.1 1.0 NE2 A:HIS427 4.2 30.1 1.0 CD2 A:HIS427 4.2 29.2 1.0 N A:TYR301 4.2 25.1 1.0 CB A:ASP429 4.2 16.9 1.0 CB A:ASP300 4.4 27.1 1.0 N A:ASP428 4.4 21.6 1.0 N A:ASP429 4.5 17.2 1.0 ZN A:ZN503 4.6 25.1 0.6 O A:HOH603 4.6 22.4 1.0 C A:HIS427 4.7 23.3 1.0 CA A:ASP300 4.7 27.8 1.0 CD1 A:TYR301 4.8 29.5 1.0 CB A:TYR301 4.9 25.6 1.0 CA A:ASP429 4.9 16.3 1.0 O A:TYR301 5.0 22.7 1.0 C A:ASP300 5.0 26.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc


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 the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.8 occ:0.60 OE2 A:GLU337 1.9 26.8 1.0 NE2 A:HIS341 2.1 27.9 1.0 O A:HOH624 2.2 29.3 1.0 CE1 A:HIS341 2.9 26.9 1.0 CD A:GLU337 2.9 23.7 1.0 CD2 A:HIS341 3.3 25.8 1.0 CG A:GLU337 3.3 23.6 1.0 CB A:GLU337 4.0 22.0 1.0 OE1 A:GLU337 4.1 24.6 1.0 ND1 A:HIS341 4.1 26.7 1.0 NZ A:LYS333 4.1 40.9 1.0 CG A:HIS341 4.3 24.3 1.0 O A:HOH674 4.6 35.1 1.0 CA A:GLU337 4.9 20.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc


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 the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:25.1 occ:0.60 O A:HOH649 2.0 34.8 1.0 O A:HOH602 2.0 39.3 1.0 OD1 A:ASP429 2.0 19.8 1.0 O A:HOH646 2.1 28.8 1.0 OD2 A:ASP294 2.2 22.2 0.6 O A:HOH617 2.3 26.5 1.0 CG A:ASP294 3.1 21.3 0.6 CG A:ASP429 3.1 17.9 1.0 OD1 A:ASP294 3.4 23.4 0.6 CB A:ASP429 3.6 16.9 1.0 CA A:ASP429 3.9 16.3 1.0 OD2 A:ASP300 4.1 27.4 1.0 O A:PHE295 4.1 28.2 1.0 CG A:ASP294 4.1 19.3 0.4 O A:TYR301 4.2 22.7 1.0 OD1 A:ASP294 4.2 19.6 0.4 OD2 A:ASP429 4.2 19.2 1.0 OD2 A:ASP294 4.3 20.9 0.4 OD1 A:ASP428 4.5 26.1 1.0 O A:HOH694 4.5 16.5 1.0 CB A:ASP294 4.5 20.5 0.6 N A:ASP429 4.5 17.2 1.0 CB A:ASP294 4.5 19.1 0.4 ZN A:ZN501 4.6 22.4 1.0 CG A:ASP300 4.8 26.6 1.0 C A:PHE295 4.8 26.8 1.0 OD1 A:ASP300 5.0 23.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc


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 the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:27.3 occ:0.60 ZN A:ZN504 0.0 27.3 0.6 ZN A:ZN504 1.8 31.4 0.4 OD1 A:ASP264 2.0 24.9 1.0 O A:HOH691 2.4 44.9 1.0 CG A:ASP264 2.8 24.4 1.0 O A:HOH686 2.8 50.7 1.0 OD2 A:ASP264 2.9 26.3 1.0 CB A:ASP264 4.2 21.7 1.0 CA A:ASP264 4.7 19.0 1.0 N A:ASP264 4.9 19.4 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Large Terminase Nuclease From Thermophilic Phage G20C with Bound Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:31.4 occ:0.40 ZN A:ZN504 0.0 31.4 0.4 ZN A:ZN504 1.8 27.3 0.6 OD2 A:ASP264 2.3 26.3 1.0 OD1 A:ASP264 2.9 24.9 1.0 CG A:ASP264 2.9 24.4 1.0 O A:HOH691 3.1 44.9 1.0 O A:HOH667 4.2 37.5 1.0 CB A:ASP264 4.3 21.7 1.0 O A:HOH686 4.6 50.7 1.0

R.G.Xu, H.T.Jenkins, M.Chechik, E.V.Blagova, A.Lopatina, E.Klimuk, L.Minakhin, K.Severinov, S.J.Greive, A.A.Antson. Viral Genome Packaging Terminase Cleaves Dna Using the Canonical Ruvc-Like Two-Metal Catalysis Mechanism. Nucleic Acids Res. V. 45 3580 2017.
ISSN: ESSN 1362-4962
PubMed: 28100693
DOI: 10.1093/NAR/GKW1354