Zinc in PDB 9c9m: Hiv-1 Intasome Core Bound with Dtg

Other elements in 9c9m:

The structure of Hiv-1 Intasome Core Bound with Dtg also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Hiv-1 Intasome Core Bound with Dtg (pdb code 9c9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hiv-1 Intasome Core Bound with Dtg, PDB code: 9c9m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9c9m

Go back to Zinc Binding Sites List in 9c9m
Zinc binding site 1 out of 2 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:27.1
occ:1.00
ND1 A:HIS16 2.1 9.3 1.0
NE2 A:HIS12 2.1 18.2 1.0
SG A:CYS40 2.2 17.5 1.0
SG A:CYS43 2.2 19.4 1.0
CE1 A:HIS12 2.8 14.4 1.0
CE1 A:HIS16 3.0 10.9 1.0
CD2 A:HIS12 3.1 12.2 1.0
CG A:HIS16 3.1 10.4 1.0
CB A:CYS40 3.2 14.4 1.0
CB A:HIS16 3.5 9.6 1.0
CB A:CYS43 3.5 12.2 1.0
ND1 A:HIS12 3.9 15.5 1.0
CA A:HIS16 4.0 10.5 1.0
N A:CYS43 4.0 12.7 1.0
CG A:HIS12 4.0 17.1 1.0
NE2 A:HIS16 4.2 12.9 1.0
CD2 A:HIS16 4.2 10.1 1.0
CA A:CYS43 4.3 15.3 1.0
CB A:LYS42 4.5 17.3 1.0
C A:LYS42 4.5 10.9 1.0
CA A:CYS40 4.6 16.0 1.0
O A:HIS12 4.7 14.6 1.0
NE2 I:GLN164 4.7 10.4 1.0
C A:HIS16 4.9 10.2 1.0
CA A:LYS42 4.9 12.6 1.0
C A:CYS40 5.0 19.6 1.0
N A:LYS42 5.0 16.0 1.0
O A:CYS40 5.0 21.5 1.0

Zinc binding site 2 out of 2 in 9c9m

Go back to Zinc Binding Sites List in 9c9m
Zinc binding site 2 out of 2 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn303

b:28.1
occ:1.00
ND1 I:HIS16 2.1 8.8 1.0
NE2 I:HIS12 2.1 17.8 1.0
SG I:CYS40 2.2 17.4 1.0
SG I:CYS43 2.2 19.6 1.0
CE1 I:HIS12 2.8 14.7 1.0
CE1 I:HIS16 3.0 10.6 1.0
CD2 I:HIS12 3.1 12.9 1.0
CG I:HIS16 3.1 10.1 1.0
CB I:CYS40 3.2 14.4 1.0
CB I:HIS16 3.5 9.7 1.0
CB I:CYS43 3.5 11.6 1.0
ND1 I:HIS12 3.9 15.3 1.0
CA I:HIS16 4.0 10.9 1.0
N I:CYS43 4.0 13.2 1.0
CG I:HIS12 4.0 18.1 1.0
NE2 I:HIS16 4.2 11.9 1.0
CD2 I:HIS16 4.2 9.8 1.0
CA I:CYS43 4.3 15.8 1.0
CB I:LYS42 4.5 19.1 1.0
C I:LYS42 4.5 11.0 1.0
CA I:CYS40 4.6 15.8 1.0
O I:HIS12 4.7 14.8 1.0
NE2 A:GLN164 4.7 9.8 1.0
C I:HIS16 4.9 10.5 1.0
CA I:LYS42 4.9 13.2 1.0
N I:LYS42 5.0 16.6 1.0
C I:CYS40 5.0 19.6 1.0
O I:CYS40 5.0 21.5 1.0

Reference:

M.Li, X.Chen, Z.Li, Y.Cui, A.Engelman, R.Craigie. Hiv-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies By Cryo-Em and Reveal the Role of the Integrase C-Terminal Tail in Hiv-1 Integration Viruses 2024.
ISSN: ESSN 1999-4915
Page generated: Thu Oct 31 14:50:34 2024

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