Zinc in PDB 7t7i: Ebv Nuclear Egress Complex

The structure of Ebv Nuclear Egress Complex, PDB code: 7t7i was solved by M.K.Thorsen, E.E.Heldwein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	106.52 / 3.97
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	238.153, 238.153, 137.532, 90, 90, 90
R / Rfree (%)	27 / 30.8

The binding sites of Zinc atom in the Ebv Nuclear Egress Complex (pdb code 7t7i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Ebv Nuclear Egress Complex, PDB code: 7t7i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Ebv Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ebv Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:125.2 occ:1.00 NE2 B:HIS239 2.2 147.8 1.0 SG B:CYS145 2.3 141.0 1.0 SG B:CYS148 2.3 154.5 1.0 SG B:CYS129 2.3 243.2 1.0 HB3 B:CYS129 2.7 219.2 1.0 CB B:CYS129 2.9 182.7 1.0 HB2 B:CYS148 3.0 201.5 1.0 CE1 B:HIS239 3.0 187.9 1.0 HE1 B:HIS239 3.1 225.5 1.0 HB2 B:CYS129 3.2 219.2 1.0 CB B:CYS148 3.2 167.9 1.0 CD2 B:HIS239 3.3 143.7 1.0 HA B:PRO241 3.3 192.3 1.0 HB3 B:CYS145 3.3 273.3 1.0 CB B:CYS145 3.4 227.8 1.0 HB2 B:CYS145 3.5 273.3 1.0 HD2 B:HIS239 3.5 172.4 1.0 H B:CYS148 3.7 220.9 1.0 HB3 B:CYS148 3.9 201.5 1.0 H B:GLU242 4.1 196.6 1.0 ND1 B:HIS239 4.2 220.1 1.0 N B:CYS148 4.2 184.1 1.0 CA B:PRO241 4.2 160.3 1.0 CA B:CYS148 4.3 218.3 1.0 CG B:HIS239 4.3 169.3 1.0 HB3 B:PRO241 4.4 214.3 1.0 CA B:CYS129 4.4 183.1 1.0 HA2 B:GLY142 4.4 212.7 1.0 HB B:ILE147 4.4 240.0 1.0 HA B:CYS129 4.5 219.7 1.0 HA B:CYS148 4.6 261.9 1.0 N B:GLU242 4.6 163.8 1.0 HB2 B:GLU242 4.6 223.2 1.0 O B:ILE240 4.7 200.3 1.0 CA B:CYS145 4.8 230.4 1.0 C B:PRO241 4.9 182.5 1.0 CB B:PRO241 4.9 178.6 1.0 HD1 B:HIS239 4.9 264.1 1.0

Zinc binding site 2 out of 5 in the Ebv Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ebv Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:140.1 occ:1.00 NE2 D:HIS239 2.0 182.2 1.0 SG D:CYS148 2.3 225.3 1.0 SG D:CYS145 2.3 173.5 1.0 SG D:CYS129 2.3 212.8 1.0 HB3 D:CYS129 2.8 185.5 1.0 HB2 D:CYS148 2.8 216.7 1.0 CE1 D:HIS239 2.8 200.3 1.0 HB3 D:CYS145 2.8 251.1 1.0 HE1 D:HIS239 2.8 240.3 1.0 CB D:CYS129 3.0 154.6 1.0 CB D:CYS145 3.1 209.2 1.0 HB2 D:CYS129 3.1 185.5 1.0 CB D:CYS148 3.1 180.6 1.0 CD2 D:HIS239 3.2 189.3 1.0 HB2 D:CYS145 3.3 251.1 1.0 HA D:PRO241 3.4 222.3 1.0 HD2 D:HIS239 3.5 227.1 1.0 HB3 D:CYS148 3.6 216.7 1.0 H D:CYS148 3.9 261.1 1.0 ND1 D:HIS239 4.0 239.5 1.0 HA2 D:GLY142 4.1 222.2 1.0 H D:GLU242 4.1 190.9 1.0 CG D:HIS239 4.2 205.6 1.0 HB3 D:PRO241 4.2 199.8 1.0 HG1 D:THR140 4.3 251.5 1.0 HG23 D:ILE147 4.3 258.7 1.0 CA D:PRO241 4.3 185.2 1.0 HG22 D:ILE147 4.3 258.7 1.0 CA D:CYS148 4.3 213.2 1.0 N D:CYS148 4.4 217.6 1.0 CA D:CYS129 4.5 155.7 1.0 CA D:CYS145 4.5 204.8 1.0 OG1 D:THR140 4.7 209.6 1.0 N D:GLU242 4.7 159.1 1.0 HA D:CYS148 4.7 255.9 1.0 HA D:CYS129 4.7 186.8 1.0 O D:CYS145 4.7 211.2 1.0 HD1 D:HIS239 4.7 287.4 1.0 CG2 D:ILE147 4.7 215.6 1.0 HB2 D:GLU242 4.7 190.1 1.0 CB D:PRO241 4.8 166.5 1.0 HH22 D:ARG131 4.9 211.9 1.0 HA D:CYS145 4.9 245.7 1.0 C D:CYS145 4.9 218.6 1.0 C D:PRO241 4.9 160.6 1.0 H D:CYS129 5.0 246.9 1.0 O D:ILE240 5.0 195.9 1.0

Zinc binding site 3 out of 5 in the Ebv Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ebv Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:166.4 occ:1.00 NE2 F:HIS239 2.0 242.7 1.0 SG F:CYS129 2.3 238.5 1.0 SG F:CYS145 2.3 251.2 1.0 SG F:CYS148 2.3 192.8 1.0 CE1 F:HIS239 2.9 236.7 1.0 HB2 F:CYS129 2.9 233.3 1.0 HE1 F:HIS239 2.9 284.0 1.0 CB F:CYS129 3.0 194.4 1.0 HB3 F:CYS129 3.0 233.3 1.0 HB2 F:CYS148 3.0 288.7 1.0 CD2 F:HIS239 3.2 233.5 1.0 HB3 F:CYS145 3.3 298.6 1.0 CB F:CYS145 3.3 248.8 1.0 CB F:CYS148 3.3 240.6 1.0 HB2 F:CYS145 3.4 298.6 1.0 H F:CYS148 3.4 324.0 1.0 HD2 F:HIS239 3.5 280.2 1.0 HB F:ILE147 3.9 279.6 1.0 HA F:PRO241 3.9 281.7 1.0 N F:CYS148 3.9 270.0 1.0 HB3 F:CYS148 4.0 288.7 1.0 ND1 F:HIS239 4.0 236.9 1.0 CA F:CYS148 4.1 266.6 1.0 CG F:HIS239 4.2 234.9 1.0 OE1 F:GLU242 4.3 274.4 1.0 HA F:CYS148 4.4 319.9 1.0 CA F:CYS129 4.5 192.1 1.0 HG1 F:THR140 4.5 276.8 1.0 OG1 F:THR140 4.6 230.7 1.0 H F:CYS129 4.6 243.4 1.0 HA2 F:GLY142 4.7 260.2 1.0 CA F:CYS145 4.7 248.8 1.0 HB3 F:PRO241 4.7 244.4 1.0 HD1 F:HIS239 4.8 284.3 1.0 CB F:ILE147 4.8 233.0 1.0 CA F:PRO241 4.9 234.7 1.0 H F:GLU242 4.9 307.6 1.0 C F:ILE147 4.9 223.7 1.0

Zinc binding site 4 out of 5 in the Ebv Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ebv Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn401 b:145.6 occ:1.00 NE2 H:HIS239 2.0 227.3 1.0 SG H:CYS148 2.3 147.5 1.0 SG H:CYS129 2.3 151.9 1.0 SG H:CYS145 2.3 214.1 1.0 HE1 H:HIS239 2.5 217.3 1.0 CE1 H:HIS239 2.6 181.1 1.0 HB2 H:CYS148 2.6 225.9 1.0 HB2 H:CYS129 2.9 177.4 1.0 CB H:CYS129 2.9 147.8 1.0 HB3 H:CYS129 2.9 177.4 1.0 CB H:CYS148 3.0 188.2 1.0 HB3 H:CYS145 3.1 193.6 1.0 CB H:CYS145 3.2 161.3 1.0 CD2 H:HIS239 3.3 202.8 1.0 HB2 H:CYS145 3.3 193.6 1.0 H H:CYS148 3.5 254.2 1.0 HB3 H:CYS148 3.7 225.9 1.0 HD2 H:HIS239 3.7 243.4 1.0 HA H:PRO241 3.8 192.1 1.0 ND1 H:HIS239 3.8 176.7 1.0 CA H:CYS148 3.9 231.4 1.0 N H:CYS148 3.9 211.8 1.0 HA H:CYS148 4.0 277.7 1.0 CG H:HIS239 4.2 173.0 1.0 HG1 H:THR140 4.3 292.9 1.0 HH22 H:ARG131 4.4 219.5 1.0 CA H:CYS129 4.4 185.8 1.0 OG1 H:THR140 4.5 244.1 1.0 HD1 H:HIS239 4.5 212.0 1.0 HB H:ILE147 4.5 188.3 1.0 H H:GLU242 4.6 215.5 1.0 H H:CYS129 4.6 238.7 1.0 HH21 H:ARG131 4.6 219.5 1.0 NH2 H:ARG131 4.6 182.9 1.0 CA H:CYS145 4.6 161.7 1.0 HA2 H:GLY142 4.7 261.4 1.0 CA H:PRO241 4.7 160.1 1.0 HB3 H:PRO241 4.9 228.1 1.0 HA H:CYS129 4.9 223.0 1.0 O H:CYS145 4.9 210.4 1.0 N H:CYS129 5.0 198.9 1.0 C H:CYS129 5.0 161.1 1.0

Zinc binding site 5 out of 5 in the Ebv Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ebv Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn401 b:205.4 occ:1.00 NE2 J:HIS239 2.1 265.2 1.0 SG J:CYS148 2.3 230.2 1.0 SG J:CYS129 2.3 295.0 1.0 SG J:CYS145 2.3 289.0 1.0 HB2 J:CYS129 2.9 355.9 1.0 CE1 J:HIS239 3.0 267.5 1.0 CB J:CYS129 3.0 296.6 1.0 HB2 J:CYS148 3.0 307.5 1.0 CD2 J:HIS239 3.1 275.2 1.0 HE1 J:HIS239 3.1 321.1 1.0 HB3 J:CYS129 3.1 355.9 1.0 CB J:CYS148 3.2 256.2 1.0 HB3 J:CYS145 3.3 345.8 1.0 HD2 J:HIS239 3.3 330.2 1.0 CB J:CYS145 3.3 288.1 1.0 H J:CYS148 3.4 378.1 1.0 HB2 J:CYS145 3.5 345.8 1.0 N J:CYS148 3.8 315.0 1.0 HA J:PRO241 3.9 313.9 1.0 CA J:CYS148 4.0 286.8 1.0 HB J:ILE147 4.0 357.0 1.0 HA J:CYS148 4.0 344.1 1.0 HB3 J:CYS148 4.0 307.5 1.0 ND1 J:HIS239 4.1 283.8 1.0 CG J:HIS239 4.1 279.3 1.0 HE J:ARG131 4.3 271.3 1.0 HG1 J:THR140 4.3 271.7 1.0 CA J:CYS129 4.5 298.4 1.0 HH21 J:ARG131 4.5 288.4 1.0 H J:GLU242 4.7 303.1 1.0 CA J:CYS145 4.8 286.1 1.0 HD1 J:HIS239 4.8 340.6 1.0 C J:ILE147 4.8 297.0 1.0 OG1 J:THR140 4.9 226.4 1.0 CA J:PRO241 4.9 261.5 1.0 C J:CYS129 4.9 298.7 1.0 HA J:CYS129 4.9 358.1 1.0 CB J:ILE147 4.9 297.5 1.0 HA2 J:GLY142 4.9 273.1 1.0 H J:LEU130 5.0 330.7 1.0 O J:ILE240 5.0 295.2 1.0 H J:ILE147 5.0 353.7 1.0 HG22 J:ILE147 5.0 358.7 1.0

M.K.Thorsen, E.B.Draganova, E.E.Heldwein. The Nuclear Egress Complex of Epstein-Barr Virus Buds Membranes Through An Oligomerization-Driven Mechanism. Plos Pathog. V. 18 10623 2022.
ISSN: ESSN 1553-7374
PubMed: 35802751
DOI: 10.1371/JOURNAL.PPAT.1010623