Zinc in PDB 9rmx: Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)

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Binding sites:

The binding sites of Zinc atom in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) (pdb code 9rmx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm), PDB code: 9rmx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:285.7 occ:1.00 NE2 A:HIS12 2.3 212.5 1.0 ND1 A:HIS16 2.3 178.8 1.0 SG A:CYS43 2.4 199.0 1.0 SG A:CYS40 2.4 206.8 1.0 CE1 A:HIS12 2.6 212.5 1.0 CB A:CYS40 3.0 206.8 1.0 CE1 A:HIS16 3.2 178.8 1.0 CD2 A:HIS12 3.3 212.5 1.0 CB A:CYS43 3.4 199.0 1.0 CG A:HIS16 3.4 178.8 1.0 ND1 A:HIS12 3.6 212.5 1.0 CB A:HIS16 3.8 178.8 1.0 CD A:LYS42 3.8 200.8 1.0 CG A:HIS12 3.9 212.5 1.0 N A:CYS43 4.0 199.0 1.0 O A:HIS12 4.2 212.5 1.0 CA A:HIS16 4.2 178.8 1.0 CA A:CYS43 4.3 199.0 1.0 NE2 A:HIS16 4.3 178.8 1.0 NZ A:LYS42 4.5 200.8 1.0 CA A:CYS40 4.5 206.8 1.0 CD2 A:HIS16 4.5 178.8 1.0 CB A:LYS42 4.7 200.8 1.0 O A:VAL37 4.8 208.9 1.0 CE A:LYS42 4.8 200.8 1.0 CG A:LYS42 4.9 200.8 1.0 C A:LYS42 5.0 200.8 1.0 C A:HIS16 5.0 178.8 1.0

Zinc binding site 2 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:318.1 occ:1.00 ND1 B:HIS16 2.3 251.1 1.0 NE2 B:HIS12 2.3 255.7 1.0 SG B:CYS40 2.4 248.9 1.0 SG B:CYS43 2.4 212.4 1.0 CB B:CYS40 2.9 248.9 1.0 CE1 B:HIS12 3.0 255.7 1.0 CD2 B:HIS12 3.1 255.7 1.0 CG B:HIS16 3.1 251.1 1.0 CB B:CYS43 3.3 212.4 1.0 CB B:HIS16 3.3 251.1 1.0 CE1 B:HIS16 3.4 251.1 1.0 ND1 B:HIS12 3.9 255.7 1.0 CA B:HIS16 4.0 251.1 1.0 CG B:HIS12 4.0 255.7 1.0 N B:CYS43 4.2 212.4 1.0 CD2 B:HIS16 4.3 251.1 1.0 CA B:CYS43 4.4 212.4 1.0 O B:HIS12 4.4 255.7 1.0 NE2 B:HIS16 4.4 251.1 1.0 CA B:CYS40 4.4 248.9 1.0 OE1 B:GLN164 4.6 224.1 1.0 O B:VAL37 4.7 259.4 1.0 C B:HIS16 4.7 251.1 1.0 C B:LYS42 4.7 232.0 1.0 O B:HIS16 5.0 251.1 1.0 C B:CYS40 5.0 248.9 1.0

Zinc binding site 3 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:381.4 occ:1.00 ND1 C:HIS16 2.3 269.4 1.0 NE2 C:HIS12 2.4 274.3 1.0 SG C:CYS43 2.4 266.2 1.0 SG C:CYS40 2.4 254.7 1.0 CB C:CYS40 2.8 254.7 1.0 CE1 C:HIS12 2.8 274.3 1.0 CG C:HIS16 3.1 269.4 1.0 CB C:HIS16 3.2 269.4 1.0 CB C:CYS43 3.2 266.2 1.0 CD2 C:HIS12 3.2 274.3 1.0 CE1 C:HIS16 3.4 269.4 1.0 CA C:HIS16 3.7 269.4 1.0 ND1 C:HIS12 3.8 274.3 1.0 CG C:HIS12 4.0 274.3 1.0 O C:HIS12 4.2 274.3 1.0 N C:CYS43 4.2 266.2 1.0 CD2 C:HIS16 4.3 269.4 1.0 CA C:CYS40 4.3 254.7 1.0 CA C:CYS43 4.3 266.2 1.0 NE2 C:HIS16 4.4 269.4 1.0 C C:HIS16 4.5 269.4 1.0 O C:VAL37 4.7 235.1 1.0 O C:HIS16 4.8 269.4 1.0 C C:LYS42 4.8 258.9 1.0 N C:HIS16 4.8 269.4 1.0 C C:CYS40 4.9 254.7 1.0

Zinc binding site 4 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:341.2 occ:1.00 ND1 D:HIS16 2.3 263.7 1.0 NE2 D:HIS12 2.4 270.3 1.0 SG D:CYS40 2.4 279.2 1.0 SG D:CYS43 2.4 285.0 1.0 CB D:CYS40 2.8 279.2 1.0 CE1 D:HIS12 2.9 270.3 1.0 CB D:CYS43 3.0 285.0 1.0 CG D:HIS16 3.0 263.7 1.0 CB D:HIS16 3.1 263.7 1.0 CD2 D:HIS12 3.2 270.3 1.0 CE1 D:HIS16 3.4 263.7 1.0 CA D:HIS16 3.7 263.7 1.0 ND1 D:HIS12 3.8 270.3 1.0 CG D:HIS12 4.0 270.3 1.0 CA D:CYS43 4.2 285.0 1.0 O D:HIS12 4.2 270.3 1.0 CD2 D:HIS16 4.2 263.7 1.0 N D:CYS43 4.3 285.0 1.0 CA D:CYS40 4.3 279.2 1.0 NE2 D:HIS16 4.4 263.7 1.0 O D:VAL37 4.5 270.0 1.0 CG D:LYS42 4.6 287.1 1.0 C D:HIS16 4.6 263.7 1.0 O D:HIS16 4.8 263.7 1.0 N D:HIS16 4.9 263.7 1.0 C D:LYS42 4.9 287.1 1.0 C D:CYS40 5.0 279.2 1.0

Zinc binding site 5 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:315.3 occ:1.00 NE2 E:HIS12 2.3 232.2 1.0 ND1 E:HIS16 2.3 201.0 1.0 SG E:CYS43 2.4 215.7 1.0 SG E:CYS40 2.4 229.9 1.0 CE1 E:HIS12 2.5 232.2 1.0 CB E:CYS40 2.7 229.9 1.0 CG E:HIS16 3.3 201.0 1.0 CE1 E:HIS16 3.3 201.0 1.0 CD2 E:HIS12 3.3 232.2 1.0 CB E:CYS43 3.4 215.7 1.0 ND1 E:HIS12 3.5 232.2 1.0 CB E:HIS16 3.5 201.0 1.0 CG E:HIS12 3.9 232.2 1.0 CA E:HIS16 3.9 201.0 1.0 O E:HIS12 4.1 232.2 1.0 N E:CYS43 4.2 215.7 1.0 CA E:CYS40 4.2 229.9 1.0 CA E:CYS43 4.4 215.7 1.0 NE2 E:HIS16 4.4 201.0 1.0 CD2 E:HIS16 4.4 201.0 1.0 NE2 H:GLN164 4.6 215.3 1.0 O E:VAL37 4.6 241.9 1.0 C E:HIS16 4.7 201.0 1.0 C E:LYS42 4.8 207.7 1.0 C E:CYS40 4.9 229.9 1.0 O E:CYS40 5.0 229.9 1.0

Zinc binding site 6 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:270.7 occ:1.00 ND1 F:HIS16 2.3 217.1 1.0 NE2 F:HIS12 2.3 219.7 1.0 SG F:CYS40 2.4 214.7 1.0 SG F:CYS43 2.4 188.0 1.0 CB F:CYS40 2.9 214.7 1.0 CE1 F:HIS12 2.9 219.7 1.0 CG F:HIS16 3.0 217.1 1.0 CB F:HIS16 3.1 217.1 1.0 CD2 F:HIS12 3.2 219.7 1.0 CA F:HIS16 3.4 217.1 1.0 CB F:CYS43 3.4 188.0 1.0 CE1 F:HIS16 3.4 217.1 1.0 ND1 F:HIS12 3.9 219.7 1.0 CG F:HIS12 4.1 219.7 1.0 C F:HIS16 4.1 217.1 1.0 CD2 F:HIS16 4.2 217.1 1.0 N F:CYS43 4.3 188.0 1.0 O F:HIS12 4.3 219.7 1.0 O F:HIS16 4.3 217.1 1.0 CA F:CYS40 4.4 214.7 1.0 NE2 F:HIS16 4.4 217.1 1.0 CA F:CYS43 4.4 188.0 1.0 N F:HIS16 4.6 217.1 1.0 O F:VAL37 4.6 215.5 1.0 C F:LYS42 4.7 201.5 1.0 C F:CYS40 4.9 214.7 1.0 CB F:LYS42 5.0 201.5 1.0

Zinc binding site 7 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:346.1 occ:1.00 ND1 G:HIS16 2.3 254.4 1.0 NE2 G:HIS12 2.3 262.7 1.0 SG G:CYS43 2.4 238.4 1.0 SG G:CYS40 2.4 242.2 1.0 CB G:CYS40 2.7 242.2 1.0 CE1 G:HIS12 2.8 262.7 1.0 CG G:HIS16 3.2 254.4 1.0 CD2 G:HIS12 3.2 262.7 1.0 CE1 G:HIS16 3.3 254.4 1.0 CB G:CYS43 3.3 238.4 1.0 CB G:HIS16 3.5 254.4 1.0 ND1 G:HIS12 3.7 262.7 1.0 CA G:HIS16 3.9 254.4 1.0 CG G:HIS12 4.0 262.7 1.0 N G:CYS43 4.2 238.4 1.0 O G:HIS12 4.2 262.7 1.0 CA G:CYS40 4.3 242.2 1.0 NE2 G:HIS16 4.3 254.4 1.0 CD2 G:HIS16 4.4 254.4 1.0 CA G:CYS43 4.4 238.4 1.0 O G:VAL37 4.6 224.3 1.0 C G:HIS16 4.7 254.4 1.0 C G:LYS42 4.8 249.2 1.0 C G:CYS40 4.8 242.2 1.0 CB G:LYS42 5.0 249.2 1.0

Zinc binding site 8 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:358.8 occ:1.00 ND1 H:HIS16 2.3 259.6 1.0 NE2 H:HIS12 2.3 271.2 1.0 SG H:CYS43 2.4 284.8 1.0 SG H:CYS40 2.4 282.9 1.0 CE1 H:HIS12 2.7 271.2 1.0 CB H:CYS40 2.8 282.9 1.0 CG H:HIS16 3.1 259.6 1.0 CB H:CYS43 3.1 284.8 1.0 CB H:HIS16 3.2 259.6 1.0 CD2 H:HIS12 3.3 271.2 1.0 CE1 H:HIS16 3.3 259.6 1.0 ND1 H:HIS12 3.6 271.2 1.0 CA H:HIS16 3.9 259.6 1.0 CG H:HIS12 4.0 271.2 1.0 N H:CYS43 4.1 284.8 1.0 CA H:CYS43 4.2 284.8 1.0 CD2 H:HIS16 4.2 259.6 1.0 O H:HIS12 4.3 271.2 1.0 CA H:CYS40 4.3 282.9 1.0 NE2 H:HIS16 4.3 259.6 1.0 O H:VAL37 4.6 278.2 1.0 C H:HIS16 4.7 259.6 1.0 C H:LYS42 4.7 260.5 1.0 C H:CYS40 4.9 282.9 1.0 O H:HIS16 5.0 259.6 1.0 CB H:LYS42 5.0 260.5 1.0

Zinc binding site 9 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:283.4 occ:1.00 NE2 I:HIS12 2.3 227.6 1.0 ND1 I:HIS16 2.3 225.7 1.0 SG I:CYS40 2.4 245.4 1.0 SG I:CYS43 2.4 249.7 1.0 CE1 I:HIS12 3.0 227.6 1.0 CD2 I:HIS12 3.1 227.6 1.0 CG I:HIS16 3.1 225.7 1.0 CB I:CYS40 3.2 245.4 1.0 CB I:CYS43 3.2 249.7 1.0 CB I:HIS16 3.3 225.7 1.0 CE1 I:HIS16 3.3 225.7 1.0 N I:CYS43 3.9 249.7 1.0 CA I:HIS16 3.9 225.7 1.0 ND1 I:HIS12 4.0 227.6 1.0 CG I:HIS12 4.0 227.6 1.0 CA I:CYS43 4.2 249.7 1.0 CD2 I:HIS16 4.3 225.7 1.0 O I:HIS12 4.3 227.6 1.0 CE I:LYS42 4.4 249.2 1.0 NE2 I:HIS16 4.4 225.7 1.0 NZ I:LYS42 4.5 249.2 1.0 CA I:CYS40 4.6 245.4 1.0 C I:HIS16 4.7 225.7 1.0 C I:LYS42 4.8 249.2 1.0 CB I:LYS42 4.8 249.2 1.0 O I:HIS16 4.9 225.7 1.0

Zinc binding site 10 out of 12 in the Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryoem Reconstruction of Integrase Filament at the Lumen of Native Hiv-1 Cores (Box Size 34.2 Nm) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:164.7 occ:1.00 ND1 J:HIS16 2.3 135.7 1.0 NE2 J:HIS12 2.3 129.9 1.0 SG J:CYS40 2.4 128.1 1.0 SG J:CYS43 2.4 136.7 1.0 CE1 J:HIS12 3.1 129.9 1.0 CG J:HIS16 3.1 135.7 1.0 CB J:CYS40 3.1 128.1 1.0 CD2 J:HIS12 3.1 129.9 1.0 CB J:HIS16 3.2 135.7 1.0 CB J:CYS43 3.3 136.7 1.0 CE1 J:HIS16 3.3 135.7 1.0 CA J:HIS16 3.8 135.7 1.0 ND1 J:HIS12 4.0 129.9 1.0 CG J:HIS12 4.0 129.9 1.0 N J:CYS43 4.1 136.7 1.0 CD2 J:HIS16 4.2 135.7 1.0 CA J:CYS43 4.3 136.7 1.0 NE2 J:HIS16 4.3 135.7 1.0 O J:HIS12 4.3 129.9 1.0 CA J:CYS40 4.6 128.1 1.0 C J:HIS16 4.6 135.7 1.0 O J:HIS16 4.9 135.7 1.0 N J:HIS16 4.9 135.7 1.0 CB J:LYS42 5.0 136.3 1.0

M.Singer, Z.Li, J.S.Rey, J.Hope, N.J.Cook, E.Punch, J.Smith, Z.Zhou, S.Maslen, L.Masino, A.Nans, M.Skehel, I.A.Taylor, P.Zhang, J.R.Perilla, A.N.Engelman, P.Cherepanov. Structural Bases For Integrase-Rna Binding and Retention of Viral Rna Within Hiv-1 Capsid Cores To Be Published.