Zinc in PDB 9rmu: Siv Integrase in Complex with Rna Stem-Loop

The binding sites of Zinc atom in the Siv Integrase in Complex with Rna Stem-Loop (pdb code 9rmu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Siv Integrase in Complex with Rna Stem-Loop, PDB code: 9rmu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:100.1 occ:1.00 CE1 A:HIS12 2.1 74.8 1.0 ND1 A:HIS16 2.3 74.8 1.0 SG A:CYS43 2.4 93.7 1.0 NE2 A:HIS12 2.4 68.9 1.0 SG A:CYS40 2.4 95.7 1.0 CE1 A:HIS16 3.0 79.4 1.0 ND1 A:HIS12 3.3 69.5 1.0 CB A:CYS40 3.4 87.7 1.0 CG A:HIS16 3.5 63.2 1.0 CB A:CYS43 3.6 97.4 1.0 CD2 A:HIS12 3.7 57.0 1.0 N A:CYS43 4.0 100.3 1.0 CB A:HIS16 4.0 50.9 1.0 CG A:HIS12 4.1 57.8 1.0 NE2 A:HIS16 4.2 77.4 1.0 CA A:CYS43 4.3 99.0 1.0 CA A:HIS16 4.4 49.2 1.0 CD2 A:HIS16 4.5 66.7 1.0 O A:HIS12 4.6 65.7 1.0 CB A:LYS42 4.7 87.2 1.0 CA A:CYS40 4.9 92.3 1.0 C A:LYS42 4.9 98.8 1.0

Zinc binding site 2 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:133.8 occ:1.00 ND1 B:HIS16 2.3 97.9 1.0 NE2 B:HIS12 2.3 99.8 1.0 SG B:CYS43 2.4 120.1 1.0 SG B:CYS40 2.4 122.8 1.0 CD2 B:HIS12 3.2 94.5 1.0 CE1 B:HIS12 3.2 93.7 1.0 CE1 B:HIS16 3.3 100.0 1.0 CG B:HIS16 3.3 90.9 1.0 CB B:CYS43 3.3 121.7 1.0 CB B:CYS40 3.5 118.4 1.0 CB B:HIS16 3.5 87.3 1.0 ND1 B:HIS12 4.3 88.6 1.0 CG B:HIS12 4.3 88.7 1.0 CA B:HIS16 4.4 87.0 1.0 NE2 B:HIS16 4.4 96.8 1.0 CD2 B:HIS16 4.4 92.8 1.0 CA B:CYS43 4.4 120.9 1.0 O B:LYS42 4.5 116.1 1.0 N B:CYS43 4.6 119.9 1.0 C B:LYS42 4.6 118.5 1.0 CA B:CYS40 4.9 120.3 1.0 O B:HIS12 4.9 95.4 1.0

Zinc binding site 3 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:125.5 occ:1.00 NE2 C:HIS12 2.3 97.0 1.0 ND1 C:HIS16 2.3 102.8 1.0 SG C:CYS40 2.4 115.5 1.0 SG C:CYS43 2.4 119.2 1.0 CD2 C:HIS12 3.0 97.5 1.0 CE1 C:HIS16 3.1 99.2 1.0 CB C:CYS40 3.2 111.9 1.0 CE1 C:HIS12 3.3 92.7 1.0 CB C:CYS43 3.4 112.6 1.0 CG C:HIS16 3.4 93.9 1.0 O C:LYS42 3.7 108.4 1.0 CB C:HIS16 3.9 88.8 1.0 CG C:HIS12 4.2 93.6 1.0 C C:LYS42 4.2 107.0 1.0 NE2 C:HIS16 4.3 96.3 1.0 ND1 C:HIS12 4.3 92.3 1.0 CA C:HIS16 4.4 83.1 1.0 CA C:CYS43 4.5 109.5 1.0 CD2 C:HIS16 4.5 91.7 1.0 N C:CYS43 4.6 108.3 1.0 CA C:CYS40 4.6 111.8 1.0 O C:HIS12 4.7 97.1 1.0 OE1 C:GLN164 5.0 92.1 1.0

Zinc binding site 4 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:128.2 occ:1.00 ND1 D:HIS16 2.3 109.8 1.0 NE2 D:HIS12 2.3 109.8 1.0 SG D:CYS40 2.4 122.4 1.0 SG D:CYS43 2.4 127.6 1.0 CE1 D:HIS16 2.7 109.1 1.0 CD2 D:HIS12 2.8 105.3 1.0 CB D:CYS40 3.3 121.5 1.0 CE1 D:HIS12 3.4 107.6 1.0 CG D:HIS16 3.5 103.1 1.0 CB D:CYS43 3.8 125.8 1.0 CG D:HIS12 4.0 99.6 1.0 NE2 D:HIS16 4.0 104.8 1.0 O D:HIS12 4.0 102.8 1.0 N D:CYS43 4.0 126.3 1.0 CB D:LYS42 4.1 119.8 1.0 ND1 D:HIS12 4.2 103.5 1.0 CB D:HIS16 4.2 98.4 1.0 CD2 D:HIS16 4.4 101.5 1.0 CA D:CYS43 4.5 127.8 1.0 CG D:LYS42 4.6 119.6 1.0 CA D:HIS16 4.6 97.2 1.0 CA D:CYS40 4.7 122.6 1.0 C D:LYS42 4.8 125.4 1.0 CA D:LYS42 4.9 123.0 1.0 N D:LYS42 4.9 126.0 1.0

Zinc binding site 5 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn301 b:150.1 occ:1.00 ND1 b:HIS16 2.3 121.7 1.0 NE2 b:HIS12 2.3 119.5 1.0 SG b:CYS40 2.4 123.0 1.0 SG b:CYS43 2.4 138.1 1.0 CD2 b:HIS12 3.1 117.8 1.0 CE1 b:HIS16 3.2 123.6 1.0 CE1 b:HIS12 3.3 113.4 1.0 CG b:HIS16 3.3 114.5 1.0 CB b:CYS43 3.3 129.0 1.0 CB b:CYS40 3.4 119.4 1.0 CB b:HIS16 3.6 109.9 1.0 O b:LYS42 4.3 129.5 1.0 CG b:HIS12 4.3 115.4 1.0 NE2 b:HIS16 4.3 120.2 1.0 ND1 b:HIS12 4.3 110.5 1.0 CA b:CYS43 4.4 131.3 1.0 CD2 b:HIS16 4.4 114.8 1.0 CA b:HIS16 4.5 107.8 1.0 C b:LYS42 4.5 131.6 1.0 N b:CYS43 4.5 132.7 1.0 CG b:LYS42 4.6 128.4 1.0 CA b:CYS40 4.9 119.8 1.0 O b:HIS12 5.0 114.2 1.0

Zinc binding site 6 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:100.9 occ:1.00 CE1 E:HIS12 2.1 78.0 1.0 ND1 E:HIS16 2.3 76.8 1.0 SG E:CYS43 2.4 98.9 1.0 NE2 E:HIS12 2.4 70.8 1.0 SG E:CYS40 2.4 98.9 1.0 CE1 E:HIS16 3.0 82.1 1.0 ND1 E:HIS12 3.3 72.9 1.0 CB E:CYS40 3.4 90.5 1.0 CG E:HIS16 3.5 65.7 1.0 CB E:CYS43 3.6 103.0 1.0 CD2 E:HIS12 3.7 58.1 1.0 N E:CYS43 4.0 105.0 1.0 CB E:HIS16 4.0 52.2 1.0 CG E:HIS12 4.1 59.9 1.0 NE2 E:HIS16 4.2 79.3 1.0 CA E:CYS43 4.3 103.7 1.0 CA E:HIS16 4.3 51.4 1.0 CD2 E:HIS16 4.5 69.8 1.0 O E:HIS12 4.6 67.5 1.0 CB E:LYS42 4.7 91.0 1.0 CA E:CYS40 4.9 96.0 1.0 C E:LYS42 4.9 103.3 1.0

Zinc binding site 7 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:133.8 occ:1.00 ND1 F:HIS16 2.3 95.9 1.0 NE2 F:HIS12 2.3 97.8 1.0 SG F:CYS43 2.4 117.8 1.0 SG F:CYS40 2.4 120.9 1.0 CD2 F:HIS12 3.2 91.6 1.0 CE1 F:HIS12 3.2 91.4 1.0 CE1 F:HIS16 3.2 98.0 1.0 CG F:HIS16 3.3 88.5 1.0 CB F:CYS43 3.3 119.8 1.0 CB F:CYS40 3.5 116.4 1.0 CB F:HIS16 3.5 84.4 1.0 ND1 F:HIS12 4.3 85.6 1.0 CG F:HIS12 4.3 85.8 1.0 CA F:HIS16 4.4 84.1 1.0 NE2 F:HIS16 4.4 94.0 1.0 CD2 F:HIS16 4.4 89.9 1.0 CA F:CYS43 4.5 119.3 1.0 O F:LYS42 4.5 114.4 1.0 N F:CYS43 4.6 118.7 1.0 C F:LYS42 4.7 116.8 1.0 CA F:CYS40 4.9 118.2 1.0 O F:HIS12 4.9 93.0 1.0

Zinc binding site 8 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:123.5 occ:1.00 NE2 G:HIS12 2.3 98.1 1.0 ND1 G:HIS16 2.3 102.4 1.0 SG G:CYS40 2.4 113.9 1.0 SG G:CYS43 2.4 117.8 1.0 CD2 G:HIS12 3.0 98.1 1.0 CE1 G:HIS16 3.1 99.4 1.0 CB G:CYS40 3.1 110.5 1.0 CE1 G:HIS12 3.3 92.1 1.0 CB G:CYS43 3.4 110.8 1.0 CG G:HIS16 3.4 93.7 1.0 O G:LYS42 3.7 107.7 1.0 CB G:HIS16 3.9 87.0 1.0 CG G:HIS12 4.1 92.5 1.0 C G:LYS42 4.2 105.7 1.0 NE2 G:HIS16 4.3 96.6 1.0 ND1 G:HIS12 4.3 89.9 1.0 CA G:CYS43 4.4 108.0 1.0 CA G:HIS16 4.5 80.4 1.0 CD2 G:HIS16 4.5 92.2 1.0 N G:CYS43 4.6 107.3 1.0 CA G:CYS40 4.6 110.2 1.0 O G:HIS12 4.6 96.9 1.0

Zinc binding site 9 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:133.9 occ:1.00 ND1 H:HIS16 2.3 115.3 1.0 NE2 H:HIS12 2.3 111.5 1.0 SG H:CYS40 2.4 128.0 1.0 SG H:CYS43 2.4 128.6 1.0 CE1 H:HIS16 2.7 113.9 1.0 CD2 H:HIS12 2.8 107.0 1.0 CB H:CYS40 3.2 125.1 1.0 CE1 H:HIS12 3.4 110.3 1.0 CG H:HIS16 3.5 108.0 1.0 CB H:CYS43 3.9 128.7 1.0 NE2 H:HIS16 4.0 110.0 1.0 CG H:HIS12 4.0 100.8 1.0 N H:CYS43 4.0 128.6 1.0 O H:HIS12 4.0 108.3 1.0 CB H:LYS42 4.1 125.5 1.0 ND1 H:HIS12 4.2 106.1 1.0 CB H:HIS16 4.2 102.2 1.0 CD2 H:HIS16 4.4 107.2 1.0 CA H:CYS43 4.6 130.8 1.0 CG H:LYS42 4.6 126.3 1.0 CA H:HIS16 4.6 101.3 1.0 CA H:CYS40 4.7 125.5 1.0 C H:LYS42 4.8 128.5 1.0 CA H:LYS42 4.8 128.1 1.0 N H:LYS42 4.9 131.2 1.0

Zinc binding site 10 out of 10 in the Siv Integrase in Complex with Rna Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Siv Integrase in Complex with Rna Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn301 b:125.5 occ:1.00 ND1 f:HIS16 2.3 102.8 1.0 NE2 f:HIS12 2.3 103.8 1.0 SG f:CYS43 2.3 113.9 1.0 SG f:CYS40 2.4 114.1 1.0 CD2 f:HIS12 3.1 102.8 1.0 CE1 f:HIS16 3.1 105.5 1.0 CE1 f:HIS12 3.3 97.7 1.0 CG f:HIS16 3.3 98.5 1.0 CB f:CYS40 3.4 103.8 1.0 CB f:CYS43 3.5 109.0 1.0 CB f:HIS16 3.7 93.0 1.0 O f:LYS42 4.2 116.4 1.0 CG f:HIS12 4.2 101.8 1.0 NE2 f:HIS16 4.3 104.6 1.0 ND1 f:HIS12 4.3 95.4 1.0 CD2 f:HIS16 4.4 101.3 1.0 C f:LYS42 4.5 114.3 1.0 CA f:HIS16 4.5 93.2 1.0 CA f:CYS43 4.5 112.2 1.0 N f:CYS43 4.6 113.2 1.0 CA f:CYS40 4.9 102.2 1.0 O f:HIS12 4.9 101.6 1.0

M.R.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 Basis For Integrase-Rna Binding and Retention of Viral Rna Within Hiv-1 Capsid Cores To Be Published.