Zinc in PDB 6xf9: Crystal Structure of Kshv ORF68

The structure of Crystal Structure of Kshv ORF68, PDB code: 6xf9 was solved by A.L.Didychuk, S.N.Gates, A.Martin, B.Glaunsinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 2.22
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	134.987, 224.042, 192.27, 90, 90, 90
R / Rfree (%)	22.2 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Kshv ORF68 (pdb code 6xf9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of Kshv ORF68, PDB code: 6xf9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Crystal Structure of Kshv ORF68


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 Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:49.4 occ:1.00 ND1 A:HIS130 2.0 47.4 1.0 SG A:CYS55 2.3 42.0 1.0 SG A:CYS52 2.3 47.7 1.0 SG A:CYS136 2.3 46.8 1.0 CE1 A:HIS130 2.7 48.2 1.0 CB A:CYS136 3.0 47.3 1.0 CB A:CYS52 3.2 50.7 1.0 CG A:HIS130 3.2 45.5 1.0 CB A:CYS55 3.3 46.6 1.0 N A:CYS55 3.6 42.2 1.0 CB A:HIS130 3.8 44.1 1.0 CA A:CYS55 3.9 46.4 1.0 NE2 A:HIS130 4.0 46.9 1.0 CD2 A:HIS130 4.2 45.3 1.0 CA A:HIS130 4.2 42.7 1.0 CA A:CYS136 4.5 46.0 1.0 CA A:CYS52 4.6 50.7 1.0 C A:VAL54 4.6 45.2 1.0 CB A:VAL54 4.7 36.5 1.0 C A:CYS52 4.9 50.5 1.0

Zinc binding site 2 out of 15 in the Crystal Structure of Kshv ORF68


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 Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:42.5 occ:1.00 ND1 A:HIS366 2.2 42.8 1.0 SG A:CYS296 2.3 46.1 1.0 SG A:CYS299 2.3 41.4 1.0 SG A:CYS373 2.3 45.0 1.0 CE1 A:HIS366 3.1 42.8 1.0 CB A:CYS296 3.2 45.4 1.0 CB A:CYS373 3.2 44.9 1.0 CG A:HIS366 3.3 44.1 1.0 CB A:CYS299 3.4 41.8 1.0 N A:CYS299 3.5 43.7 1.0 CB A:HIS366 3.7 45.2 1.0 CA A:CYS299 3.9 42.7 1.0 CA A:CYS373 3.9 44.5 1.0 CA A:HIS366 4.2 44.7 1.0 NE2 A:HIS366 4.2 43.6 1.0 CD2 A:HIS366 4.4 44.6 1.0 C A:LEU298 4.4 43.0 1.0 CA A:CYS296 4.6 46.6 1.0 CB A:LEU298 4.7 44.8 1.0 N A:CYS373 4.7 44.9 1.0 C A:CYS296 4.9 47.6 1.0 CA A:LEU298 4.9 44.8 1.0 N A:LEU298 5.0 45.8 1.0

Zinc binding site 3 out of 15 in the Crystal Structure of Kshv ORF68


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 Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:45.9 occ:1.00 NE2 A:HIS452 2.0 37.1 1.0 SG A:CYS191 2.3 58.7 1.0 SG A:CYS415 2.3 47.1 1.0 SG A:CYS192 2.4 51.1 1.0 CE1 A:HIS452 2.9 35.9 1.0 CD2 A:HIS452 3.1 42.0 1.0 CB A:CYS191 3.3 57.5 1.0 CB A:CYS192 3.3 51.3 1.0 CB A:CYS415 3.4 44.5 1.0 N A:CYS192 3.7 52.2 1.0 C A:CYS191 3.9 59.5 1.0 ND1 A:HIS452 4.1 39.3 1.0 CA A:CYS192 4.1 52.5 1.0 CA A:CYS191 4.1 58.9 1.0 CG A:HIS452 4.2 43.3 1.0 OG1 A:THR195 4.2 51.4 1.0 O A:CYS191 4.6 58.7 1.0 CG2 A:THR195 4.6 52.2 1.0 CA A:CYS415 4.6 45.6 1.0 CG2 A:VAL418 4.7 41.4 1.0 N A:CYS191 4.8 59.9 1.0

Zinc binding site 4 out of 15 in the Crystal Structure of Kshv ORF68


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 Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:48.8 occ:1.00 ND1 B:HIS130 2.0 53.0 1.0 SG B:CYS52 2.3 50.3 1.0 SG B:CYS136 2.3 48.6 1.0 SG B:CYS55 2.3 54.6 1.0 CE1 B:HIS130 2.9 52.3 1.0 CB B:CYS136 3.1 47.1 1.0 CG B:HIS130 3.2 51.7 1.0 CB B:CYS52 3.2 53.6 1.0 CB B:CYS55 3.3 55.5 1.0 N B:CYS55 3.6 50.6 1.0 CB B:HIS130 3.6 52.0 1.0 CA B:CYS55 3.9 53.7 1.0 NE2 B:HIS130 4.0 50.6 1.0 CA B:HIS130 4.1 49.8 1.0 CD2 B:HIS130 4.2 50.2 1.0 CA B:CYS136 4.6 44.7 1.0 C B:VAL54 4.6 52.4 1.0 CA B:CYS52 4.7 53.6 1.0 CB B:VAL54 4.8 47.6 1.0

Zinc binding site 5 out of 15 in the Crystal Structure of Kshv ORF68


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 Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:46.0 occ:1.00 ND1 B:HIS366 2.2 46.4 1.0 SG B:CYS296 2.2 48.5 1.0 SG B:CYS299 2.3 45.0 1.0 SG B:CYS373 2.3 49.4 1.0 CE1 B:HIS366 3.0 45.1 1.0 CB B:CYS296 3.1 48.4 1.0 CB B:CYS373 3.2 47.3 1.0 CG B:HIS366 3.3 47.8 1.0 CB B:CYS299 3.6 45.5 1.0 N B:CYS299 3.7 47.7 1.0 CB B:HIS366 3.7 49.7 1.0 CA B:CYS373 3.8 45.4 1.0 CA B:CYS299 4.1 46.1 1.0 NE2 B:HIS366 4.2 45.5 1.0 CA B:HIS366 4.2 48.8 1.0 CD2 B:HIS366 4.3 47.1 1.0 C B:LEU298 4.5 43.7 1.0 CA B:CYS296 4.5 49.9 1.0 CB B:LEU298 4.6 45.6 1.0 N B:CYS373 4.7 44.6 1.0 C B:CYS296 4.8 49.5 1.0 O B:CYS296 4.9 48.4 1.0 C B:CYS373 4.9 44.4 1.0 CA B:LEU298 4.9 45.1 1.0 N B:LEU298 5.0 46.0 1.0

Zinc binding site 6 out of 15 in the Crystal Structure of Kshv ORF68


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:47.2 occ:1.00 NE2 B:HIS452 2.0 43.8 1.0 SG B:CYS415 2.3 45.5 1.0 SG B:CYS192 2.3 45.2 1.0 SG B:CYS191 2.3 51.6 1.0 CE1 B:HIS452 3.0 43.6 1.0 CD2 B:HIS452 3.0 44.0 1.0 CB B:CYS191 3.3 52.8 1.0 CB B:CYS415 3.4 44.5 1.0 CB B:CYS192 3.4 46.0 1.0 N B:CYS192 3.8 49.7 1.0 C B:CYS191 4.0 55.1 1.0 ND1 B:HIS452 4.1 43.8 1.0 CA B:CYS191 4.2 55.4 1.0 CG B:HIS452 4.2 44.1 1.0 CG2 B:THR195 4.2 38.5 1.0 CA B:CYS192 4.2 48.5 1.0 CG2 B:VAL418 4.4 38.1 1.0 OG1 B:THR195 4.5 41.5 1.0 CA B:CYS415 4.6 44.9 1.0 O B:CYS191 4.6 55.0 1.0 N B:CYS191 4.7 57.0 1.0 CB B:THR195 5.0 41.3 1.0

Zinc binding site 7 out of 15 in the Crystal Structure of Kshv ORF68


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:46.6 occ:1.00 ND1 C:HIS130 2.1 49.9 1.0 SG C:CYS136 2.3 42.5 1.0 SG C:CYS52 2.3 40.9 1.0 SG C:CYS55 2.3 47.3 1.0 CE1 C:HIS130 3.1 53.1 1.0 CB C:CYS136 3.1 45.5 1.0 CG C:HIS130 3.2 47.2 1.0 CB C:CYS52 3.2 45.1 1.0 CB C:CYS55 3.3 52.6 1.0 CB C:HIS130 3.5 43.5 1.0 N C:CYS55 3.5 51.4 1.0 CA C:CYS55 3.9 54.9 1.0 CA C:HIS130 4.0 38.0 1.0 NE2 C:HIS130 4.2 51.9 1.0 CD2 C:HIS130 4.3 48.1 1.0 C C:VAL54 4.6 44.5 1.0 CA C:CYS52 4.6 48.2 1.0 CA C:CYS136 4.6 43.4 1.0 CB C:VAL54 4.6 33.9 1.0 N C:HIS130 5.0 35.6 1.0 C C:CYS52 5.0 51.4 1.0 CA C:VAL54 5.0 39.4 1.0 O C:CYS52 5.0 55.2 1.0

Zinc binding site 8 out of 15 in the Crystal Structure of Kshv ORF68


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:46.8 occ:1.00 ND1 C:HIS366 2.2 40.1 1.0 SG C:CYS296 2.3 49.8 1.0 SG C:CYS299 2.3 43.6 1.0 SG C:CYS373 2.3 45.4 1.0 CE1 C:HIS366 3.1 40.8 1.0 CB C:CYS296 3.2 47.8 1.0 CB C:CYS373 3.3 46.0 1.0 CG C:HIS366 3.3 40.5 1.0 CB C:CYS299 3.5 44.1 1.0 CB C:HIS366 3.7 40.1 1.0 N C:CYS299 3.8 44.1 1.0 CA C:CYS373 3.9 45.9 1.0 CA C:CYS299 4.1 44.4 1.0 CA C:HIS366 4.2 40.2 1.0 NE2 C:HIS366 4.3 41.5 1.0 CD2 C:HIS366 4.4 41.5 1.0 C C:LEU298 4.6 49.1 1.0 CA C:CYS296 4.6 47.8 1.0 N C:CYS373 4.8 45.3 1.0 CB C:LEU298 4.8 48.6 1.0 C C:CYS296 5.0 47.1 1.0

Zinc binding site 9 out of 15 in the Crystal Structure of Kshv ORF68


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:49.4 occ:1.00 NE2 C:HIS452 2.1 43.0 1.0 SG C:CYS415 2.3 43.4 1.0 SG C:CYS192 2.3 50.1 1.0 SG C:CYS191 2.3 54.2 1.0 CE1 C:HIS452 3.1 40.7 1.0 CD2 C:HIS452 3.1 45.7 1.0 CB C:CYS192 3.2 50.4 1.0 CB C:CYS191 3.2 53.3 1.0 CB C:CYS415 3.2 43.2 1.0 N C:CYS192 3.5 49.5 1.0 C C:CYS191 3.8 60.1 1.0 CA C:CYS192 3.9 50.9 1.0 CA C:CYS191 4.0 57.3 1.0 OG1 C:THR195 4.1 63.8 1.0 ND1 C:HIS452 4.2 41.4 1.0 CG C:HIS452 4.2 44.9 1.0 CG2 C:THR195 4.3 60.3 1.0 O C:CYS191 4.4 59.1 1.0 CA C:CYS415 4.4 42.1 1.0 N C:CYS191 4.6 59.6 1.0 CG2 C:VAL418 4.6 42.9 1.0 C C:CYS192 4.8 53.8 1.0 CB C:THR195 4.9 63.7 1.0

Zinc binding site 10 out of 15 in the Crystal Structure of Kshv ORF68


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Kshv ORF68 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:50.9 occ:1.00 ND1 D:HIS130 2.1 46.0 1.0 SG D:CYS55 2.3 51.9 1.0 SG D:CYS136 2.3 48.1 1.0 SG D:CYS52 2.3 52.1 1.0 CE1 D:HIS130 2.9 46.3 1.0 CB D:CYS136 3.1 48.3 1.0 CG D:HIS130 3.2 45.9 1.0 CB D:CYS52 3.2 53.2 1.0 CB D:CYS55 3.4 53.2 1.0 CB D:HIS130 3.6 46.0 1.0 N D:CYS55 3.7 53.0 1.0 CA D:CYS55 4.0 53.3 1.0 CA D:HIS130 4.0 44.9 1.0 NE2 D:HIS130 4.1 46.0 1.0 CD2 D:HIS130 4.2 45.8 1.0 CA D:CYS52 4.6 54.8 1.0 CA D:CYS136 4.6 48.5 1.0 C D:VAL54 4.7 47.5 1.0 CB D:VAL54 4.8 46.2 1.0 C D:CYS52 4.9 55.6 1.0 O D:HIS130 4.9 44.3 1.0 O D:CYS52 4.9 56.0 1.0 C D:HIS130 5.0 44.3 1.0 OD2 E:ASP331 5.0 54.2 1.0

A.L.Didychuk, S.N.Gates, M.R.Gardner, L.M.Strong, A.Martin, B.A.Glaunsinger. A Pentameric Protein Ring with Novel Architecture Is Required For Herpesviral Packaging. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 33554858
DOI: 10.7554/ELIFE.62261