Magnesium 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
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Intasome Core Bound with Dtg (pdb code 9c9m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hiv-1 Intasome Core Bound with Dtg, PDB code: 9c9m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9c9m

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Magnesium binding site 1 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:7.2
occ:1.00
 O A:HOH408 2.0 8.4 1.0
O A:HOH405 2.0 9.1 1.0
OD2 A:ASP116 2.1 5.0 1.0
OD1 A:ASP64 2.1 5.5 1.0
OAC F:DLU101 2.1 9.9 1.0
OAE F:DLU101 2.1 8.1 1.0
CG A:ASP64 3.0 5.3 1.0
CAS F:DLU101 3.1 6.7 1.0
CG A:ASP116 3.2 8.2 1.0
CAW F:DLU101 3.2 4.9 1.0
OD2 A:ASP64 3.3 6.1 1.0
MG A:MG302 3.4 6.4 1.0
CAY F:DLU101 3.6 8.3 1.0
OD1 A:ASP116 3.6 12.9 1.0
O A:HOH403 3.7 8.6 1.0
O A:HOH409 3.8 8.5 1.0
O A:CYS65 4.0 12.4 1.0
NBC F:DLU101 4.2 10.3 1.0
O F:HOH201 4.2 7.0 1.0
N7 F:DA21 4.2 9.1 0.4
N A:CYS65 4.3 6.5 1.0
CB A:ASP64 4.4 5.9 1.0
CB A:ASP116 4.4 5.2 1.0
CAZ F:DLU101 4.4 6.7 1.0
OE2 A:GLU152 4.5 7.0 1.0
CBA F:DLU101 4.6 8.6 1.0
OAD F:DLU101 4.7 10.0 1.0
N6 F:DA21 4.7 10.6 0.4
CA A:ASP64 4.8 5.6 1.0
O A:HOH401 4.8 21.4 1.0
C A:CYS65 4.9 7.9 1.0
NBD F:DLU101 4.9 7.8 1.0

Magnesium binding site 2 out of 4 in 9c9m

Go back to Magnesium Binding Sites List in 9c9m
Magnesium binding site 2 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:6.4
occ:1.00
 OD2 A:ASP64 2.0 6.1 1.0
OAE F:DLU101 2.0 8.1 1.0
O F:HOH201 2.1 7.0 1.0
OAD F:DLU101 2.2 10.0 1.0
OE2 A:GLU152 2.4 7.0 1.0
OE1 A:GLU152 2.5 9.6 1.0
CD A:GLU152 2.8 5.9 1.0
CAW F:DLU101 2.9 4.9 1.0
CAZ F:DLU101 2.9 6.7 1.0
CG A:ASP64 3.1 5.3 1.0
MG A:MG301 3.4 7.2 1.0
OD1 A:ASP64 3.5 5.5 1.0
O A:HOH403 3.6 8.6 1.0
O A:HOH405 3.8 9.1 1.0
ND2 A:ASN155 3.8 6.2 1.0
O A:CYS65 4.0 12.4 1.0
C5' F:DA21 4.2 11.3 0.6
C8 F:DA21 4.2 10.1 0.4
CAY F:DLU101 4.2 8.3 1.0
CG A:GLU152 4.3 2.9 1.0
CAX F:DLU101 4.3 7.2 1.0
N7 F:DA21 4.3 9.1 0.4
CB A:ASP64 4.4 5.9 1.0
OP1 F:DA21 4.4 14.3 0.4
OP1 F:DA21 4.4 14.2 0.6
OAC F:DLU101 4.5 9.9 1.0
OD2 A:ASP116 4.5 5.0 1.0
O3' F:DC20 4.7 11.1 1.0
NAP F:DLU101 4.8 8.5 1.0
FAG F:DLU101 4.8 8.7 1.0
CAS F:DLU101 4.9 6.7 1.0

Magnesium binding site 3 out of 4 in 9c9m

Go back to Magnesium Binding Sites List in 9c9m
Magnesium binding site 3 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:6.8
occ:1.00
 O I:HOH407 2.0 8.1 1.0
O I:HOH405 2.0 8.9 1.0
OD2 I:ASP116 2.1 5.5 1.0
OD1 I:ASP64 2.1 5.3 1.0
OAC O:DLU101 2.1 9.7 1.0
OAE O:DLU101 2.1 7.8 1.0
CG I:ASP64 3.0 5.3 1.0
CAS O:DLU101 3.1 6.4 1.0
CG I:ASP116 3.2 7.6 1.0
CAW O:DLU101 3.2 4.9 1.0
OD2 I:ASP64 3.3 5.9 1.0
MG I:MG302 3.4 6.3 1.0
CAY O:DLU101 3.6 7.8 1.0
OD1 I:ASP116 3.6 12.1 1.0
O I:HOH403 3.7 8.5 1.0
O I:HOH409 3.8 8.2 1.0
O I:CYS65 4.0 11.7 1.0
O O:HOH201 4.2 6.4 1.0
NBC O:DLU101 4.2 9.5 1.0
N7 O:DA21 4.2 8.8 0.4
N I:CYS65 4.3 6.4 1.0
OE2 I:GLU152 4.4 6.2 1.0
CB I:ASP64 4.4 6.0 1.0
CAZ O:DLU101 4.4 6.7 1.0
CB I:ASP116 4.4 5.0 1.0
CBA O:DLU101 4.6 8.1 1.0
OAD O:DLU101 4.6 9.7 1.0
N6 O:DA21 4.7 10.4 0.4
CA I:ASP64 4.8 5.5 1.0
O I:HOH401 4.8 21.0 1.0
C I:CYS65 4.9 7.0 1.0
NBD O:DLU101 4.9 8.1 1.0

Magnesium binding site 4 out of 4 in 9c9m

Go back to Magnesium Binding Sites List in 9c9m
Magnesium binding site 4 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1 Intasome Core Bound with Dtg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:6.3
occ:1.00
 OD2 I:ASP64 2.0 5.9 1.0
OAE O:DLU101 2.0 7.8 1.0
O O:HOH201 2.1 6.4 1.0
OAD O:DLU101 2.2 9.7 1.0
OE2 I:GLU152 2.2 6.2 1.0
OE1 I:GLU152 2.4 8.9 1.0
CD I:GLU152 2.7 5.2 1.0
CAW O:DLU101 2.9 4.9 1.0
CAZ O:DLU101 2.9 6.7 1.0
CG I:ASP64 3.1 5.3 1.0
MG I:MG301 3.4 6.8 1.0
OD1 I:ASP64 3.5 5.3 1.0
O I:HOH403 3.6 8.5 1.0
ND2 I:ASN155 3.7 6.0 1.0
O I:HOH405 3.8 8.9 1.0
O I:CYS65 4.0 11.7 1.0
CG I:GLU152 4.2 3.3 1.0
CAY O:DLU101 4.2 7.8 1.0
C5' O:DA21 4.2 10.7 0.6
C8 O:DA21 4.3 10.2 0.4
CAX O:DLU101 4.3 6.9 1.0
N7 O:DA21 4.3 8.8 0.4
CB I:ASP64 4.4 6.0 1.0
OP1 O:DA21 4.4 13.4 0.4
OP1 O:DA21 4.5 13.7 0.6
OD2 I:ASP116 4.5 5.5 1.0
OAC O:DLU101 4.5 9.7 1.0
O3' O:DC20 4.7 11.3 1.0
NAP O:DLU101 4.8 8.2 1.0
FAG O:DLU101 4.8 8.9 1.0
CAS O:DLU101 4.9 6.4 1.0
CG I:ASN155 5.0 6.0 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: Sat Oct 5 08:53:03 2024

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