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Iodine in PDB 6vlh: Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand

Enzymatic activity of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand

All present enzymatic activity of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand:
2.7.7.49;

Protein crystallography data

The structure of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand, PDB code: 6vlh was solved by M.A.Gorman, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.31 / 2.04
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 46.306, 46.306, 139.148, 90, 90, 90
R / Rfree (%) 21 / 29.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand (pdb code 6vlh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand, PDB code: 6vlh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 6vlh

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Iodine binding site 1 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:58.0
occ:1.00
 HE2 A:LYS173 2.4 59.6 1.0
HZ2 A:LYS71 2.5 62.6 1.0
HG11 A:VAL88 3.0 54.1 1.0
HZ1 A:LYS71 3.1 62.6 1.0
NZ A:LYS71 3.1 52.2 1.0
CE A:LYS173 3.3 49.7 1.0
HB3 A:HIS171 3.4 52.1 1.0
HE3 A:LYS71 3.4 52.0 1.0
HE3 A:LYS173 3.5 59.6 1.0
H A:LYS173 3.5 44.3 1.0
HB3 A:LYS173 3.5 49.4 1.0
HB3 A:LEU172 3.6 42.5 1.0
HZ1 A:LYS173 3.6 44.3 1.0
HD3 A:LYS71 3.6 50.8 1.0
CE A:LYS71 3.7 43.3 1.0
CG1 A:VAL88 3.8 45.1 1.0
HG12 A:VAL88 3.8 54.1 1.0
HZ3 A:LYS71 3.9 62.6 1.0
NZ A:LYS173 3.9 37.0 1.0
H A:LEU172 3.9 50.3 1.0
HG2 A:LYS173 3.9 31.4 1.0
HG21 A:VAL88 4.1 44.6 1.0
HB A:VAL88 4.1 41.3 1.0
N A:LYS173 4.2 36.9 1.0
CD A:LYS71 4.2 42.4 1.0
HZ3 A:LYS173 4.2 44.3 1.0
CB A:LYS173 4.3 41.1 1.0
HD2 A:HIS171 4.3 71.6 1.0
CB A:HIS171 4.3 43.4 1.0
CD A:LYS173 4.4 38.0 1.0
CG A:LYS173 4.4 26.2 1.0
CB A:VAL88 4.4 34.4 1.0
N A:LEU172 4.5 41.9 1.0
CB A:LEU172 4.5 35.4 1.0
HG13 A:VAL88 4.5 54.1 1.0
HB2 A:HIS171 4.6 52.1 1.0
HE2 A:LYS71 4.6 52.0 1.0
HG2 A:LYS71 4.7 43.0 1.0
HZ2 A:LYS173 4.7 44.3 1.0
HD23 A:LEU172 4.7 43.1 1.0
HD2 A:LYS173 4.7 45.5 1.0
CG2 A:VAL88 4.8 37.2 1.0
CA A:LYS173 4.8 38.7 1.0
CD2 A:HIS171 4.8 59.7 1.0
HD2 A:LYS71 4.9 50.8 1.0
CA A:LEU172 4.9 37.4 1.0
CG A:HIS171 4.9 55.4 1.0
C A:LEU172 4.9 38.1 1.0

Iodine binding site 2 out of 6 in 6vlh

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Iodine binding site 2 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:46.1
occ:0.99
 H A:GLY70 3.0 51.1 1.0
HA2 A:GLY70 3.0 44.3 1.0
HB3 A:HIS67 3.1 49.5 1.0
HB2 A:HIS67 3.2 49.5 1.0
CB A:HIS67 3.6 41.3 1.0
N A:GLY70 3.7 42.5 1.0
H A:LYS71 3.8 57.4 1.0
CA A:GLY70 3.8 36.9 1.0
N A:LEU68 4.1 31.3 1.0
HA A:LEU68 4.2 37.6 1.0
H A:LEU68 4.2 37.6 1.0
C A:HIS67 4.3 39.8 1.0
C A:LEU68 4.4 37.0 1.0
HA3 A:GLY70 4.4 44.3 1.0
N A:LYS71 4.4 47.9 1.0
CA A:LEU68 4.5 31.4 1.0
CA A:HIS67 4.5 46.3 1.0
N A:GLU69 4.6 44.7 1.0
H A:GLU69 4.6 53.6 1.0
CG A:HIS67 4.7 40.5 1.0
C A:GLY70 4.7 30.8 1.0
O A:LYS71 4.7 30.5 1.0
O A:LEU68 4.8 39.5 1.0
HA A:HIS67 4.8 55.6 1.0
O A:HIS67 4.8 43.4 1.0
C A:GLU69 4.9 35.5 1.0

Iodine binding site 3 out of 6 in 6vlh

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Iodine binding site 3 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:56.2
occ:1.00
 HD3 A:ARG187 2.6 69.8 1.0
H A:ARG187 3.0 49.1 1.0
HA A:LYS186 3.0 41.5 1.0
CD A:ARG187 3.4 58.2 1.0
HD2 A:ARG187 3.4 69.8 1.0
HG2 A:ARG187 3.5 60.9 1.0
N A:ARG187 3.8 40.9 1.0
CA A:LYS186 3.9 34.6 1.0
CG A:ARG187 4.0 50.8 1.0
HE2 A:LYS186 4.0 57.0 1.0
HD2 A:LYS186 4.0 49.3 1.0
O A:LYS185 4.2 24.2 1.0
HB2 A:LYS186 4.2 48.7 1.0
C A:LYS186 4.4 42.0 1.0
NE A:ARG187 4.6 50.6 1.0
CB A:LYS186 4.6 40.6 1.0
HH22 A:ARG187 4.6 66.3 1.0
CE A:LYS186 4.7 47.5 1.0
HE3 A:LYS186 4.7 57.0 1.0
CD A:LYS186 4.7 41.1 1.0
HG3 A:ARG187 4.7 60.9 1.0
HB3 A:ARG187 4.7 56.7 1.0
CB A:ARG187 4.8 47.2 1.0
CA A:ARG187 4.8 42.2 1.0
N A:LYS186 4.9 24.4 1.0
C A:LYS185 5.0 22.7 1.0

Iodine binding site 4 out of 6 in 6vlh

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Iodine binding site 4 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:78.3
occ:1.00
 HA3 A:GLY82 3.0 20.3 1.0
HE1 A:HIS183 3.1 33.2 1.0
HE1 A:MET154 3.4 41.3 1.0
HH21 A:ARG199 3.6 44.0 1.0
HB2 A:ALA196 3.7 22.2 1.0
O A:HOH402 3.7 35.0 1.0
CE1 A:HIS183 3.7 27.6 1.0
CA A:GLY82 3.9 16.9 1.0
HE2 A:HIS183 3.9 31.1 1.0
HA2 A:GLY82 4.1 20.3 1.0
O A:GLY82 4.1 20.1 1.0
NE2 A:HIS183 4.1 25.9 1.0
CE A:MET154 4.3 34.4 1.0
NH2 A:ARG199 4.4 36.7 1.0
C A:GLY82 4.4 13.7 1.0
O A:SER81 4.4 28.3 1.0
O A:HOH408 4.4 30.0 1.0
HE3 A:MET154 4.5 41.3 1.0
CB A:ALA196 4.6 18.5 1.0
HB1 A:ALA196 4.6 22.2 1.0
HH22 A:ARG199 4.6 44.0 1.0
ND1 A:HIS183 4.8 28.7 1.0
N A:GLY82 4.9 22.7 1.0
HE2 A:MET154 4.9 41.3 1.0
SD A:MET154 5.0 65.1 1.0

Iodine binding site 5 out of 6 in 6vlh

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Iodine binding site 5 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:52.8
occ:0.95
 H B:LYS173 2.8 39.0 1.0
HD3 B:LYS173 2.9 51.4 1.0
HE2 B:LYS71 3.0 42.3 1.0
HB3 B:LEU172 3.4 43.8 1.0
H B:LEU172 3.4 46.3 1.0
HB2 B:LYS173 3.5 35.3 1.0
HB3 B:HIS171 3.5 52.1 1.0
N B:LYS173 3.6 32.5 1.0
HD3 B:LYS71 3.7 49.2 1.0
CD B:LYS173 3.7 42.9 1.0
HG3 B:LYS173 3.8 44.7 1.0
CE B:LYS71 3.8 35.3 1.0
HD2 B:LYS71 3.8 49.2 1.0
N B:LEU172 3.8 38.5 1.0
HD2 B:LYS173 4.0 51.4 1.0
CD B:LYS71 4.0 41.0 1.0
HA B:HIS171 4.0 51.3 1.0
CG B:LYS173 4.1 37.3 1.0
CB B:LYS173 4.1 29.4 1.0
CB B:LEU172 4.2 36.5 1.0
CB B:HIS171 4.3 43.4 1.0
CA B:LEU172 4.4 35.5 1.0
HG11 B:VAL88 4.4 38.0 1.0
HD2 B:HIS171 4.4 62.1 1.0
HE3 B:LYS71 4.4 42.3 1.0
CA B:LYS173 4.4 33.8 1.0
C B:LEU172 4.4 31.6 1.0
CA B:HIS171 4.5 42.8 1.0
C B:HIS171 4.5 38.2 1.0
HZ3 B:LYS71 4.6 43.6 1.0
HB2 B:LEU172 4.6 43.8 1.0
NZ B:LYS71 4.7 36.3 1.0
HA B:LYS173 4.7 40.6 1.0
HE2 B:LYS173 4.8 50.8 1.0
CD2 B:HIS171 4.8 51.7 1.0
CG B:HIS171 4.8 46.5 1.0
CE B:LYS173 4.9 42.4 1.0
HZ1 B:LYS71 4.9 43.6 1.0
HB3 B:LYS173 5.0 35.3 1.0

Iodine binding site 6 out of 6 in 6vlh

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Iodine binding site 6 out of 6 in the Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hiv Integrase Core Domain (in) in Complex with Dimer-Spanning Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:58.8
occ:1.00
 H B:GLY70 2.7 40.8 1.0
HA B:LEU68 3.5 36.4 1.0
N B:GLY70 3.5 34.0 1.0
HA2 B:GLY70 3.5 35.3 1.0
HB3 B:HIS67 3.7 47.1 1.0
H B:GLU69 3.7 50.0 1.0
N B:LEU68 3.9 40.6 1.0
N B:GLU69 4.0 41.7 1.0
CA B:LEU68 4.0 30.3 1.0
H B:LEU68 4.0 48.7 1.0
CA B:GLY70 4.1 29.4 1.0
C B:LEU68 4.1 44.1 1.0
HB2 B:HIS67 4.2 47.1 1.0
C B:HIS67 4.3 37.8 1.0
CB B:HIS67 4.4 39.3 1.0
O B:HIS67 4.6 33.0 1.0
C B:GLU69 4.6 28.3 1.0
HA3 B:GLY70 4.7 35.3 1.0
CA B:GLU69 4.8 27.4 1.0
HD12 B:LEU68 4.8 55.5 1.0
H B:LYS71 4.8 56.9 1.0
O B:LEU68 4.9 42.5 1.0
HA B:GLU69 4.9 32.8 1.0
CA B:HIS67 4.9 47.1 1.0

Reference:

M.Scanlon, M.A.Gorman. Hiv Integrase Core Domain (in) in Complex with Dimeric Spanning Inhibitor To Be Published.
Page generated: Mon Aug 12 00:25:03 2024

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