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Magnesium in PDB 1qs4: Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

Enzymatic activity of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

All present enzymatic activity of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone:
2.7.7.49;

Protein crystallography data

The structure of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone, PDB code: 1qs4 was solved by Y.Goldgur, R.Craigie, T.Fujiwara, T.Yoshinaga, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.07 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.233, 46.735, 141.361, 90.00, 105.55, 90.00
R / Rfree (%) 20.9 / 25.5

Other elements in 1qs4:

The structure of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone (pdb code 1qs4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone, PDB code: 1qs4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1qs4

Go back to Magnesium Binding Sites List in 1qs4
Magnesium binding site 1 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:37.1
occ:1.00
OD1 A:ASP116 2.3 30.4 1.0
O A:HOH1120 2.3 34.4 1.0
OD1 A:ASP64 2.3 31.9 1.0
O A:HOH1076 2.3 32.4 1.0
O A:HOH1073 2.4 29.0 1.0
O A:HOH1013 2.4 37.1 1.0
CG A:ASP64 3.3 29.5 1.0
CG A:ASP116 3.3 31.2 1.0
OD2 A:ASP64 3.5 29.6 1.0
OD2 A:ASP116 3.8 30.7 1.0
O A:HOH1047 4.0 23.5 1.0
O A:HOH1042 4.1 34.3 1.0
O A:CYS65 4.3 30.7 1.0
N A:CYS65 4.4 29.0 1.0
O A:HOH1077 4.5 31.6 1.0
CB A:ASP116 4.6 30.9 1.0
CB A:ASP64 4.6 29.7 1.0
CA A:ASP64 5.0 29.5 1.0
N9 A:1001004 5.0 57.3 1.0

Magnesium binding site 2 out of 3 in 1qs4

Go back to Magnesium Binding Sites List in 1qs4
Magnesium binding site 2 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:44.8
occ:1.00
OD1 B:ASP116 2.3 30.4 1.0
OD1 B:ASP64 2.4 32.4 1.0
O B:HOH1100 2.5 39.8 1.0
O B:HOH1185 2.5 54.2 1.0
O B:HOH1118 2.5 57.3 1.0
O B:HOH1092 2.5 30.7 1.0
CG B:ASP64 3.3 30.7 1.0
CG B:ASP116 3.5 29.5 1.0
OD2 B:ASP64 3.5 31.8 1.0
OD2 B:ASP116 3.9 29.2 1.0
O B:CYS65 4.2 33.4 1.0
O B:HOH1016 4.2 22.9 1.0
O B:HOH1097 4.3 48.0 1.0
N B:CYS65 4.5 30.7 1.0
O B:HOH1108 4.5 48.3 1.0
O B:HOH1179 4.5 54.3 1.0
CB B:ASP64 4.7 29.2 1.0
CB B:ASP116 4.7 28.6 1.0
O B:HOH1173 4.9 50.4 1.0

Magnesium binding site 3 out of 3 in 1qs4

Go back to Magnesium Binding Sites List in 1qs4
Magnesium binding site 3 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:44.8
occ:1.00
O C:HOH1050 2.3 27.8 1.0
O C:HOH1105 2.4 38.0 1.0
OD1 C:ASP116 2.4 24.0 1.0
O C:HOH1023 2.5 22.1 1.0
O C:HOH1103 2.6 47.2 1.0
OD1 C:ASP64 2.6 26.4 1.0
CG C:ASP116 3.5 23.7 1.0
CG C:ASP64 3.5 25.0 1.0
OD2 C:ASP64 3.7 24.7 1.0
OD2 C:ASP116 3.9 22.5 1.0
O C:HOH1138 3.9 44.4 1.0
O C:HOH1104 4.0 43.0 1.0
O C:HOH1024 4.4 21.0 1.0
O C:CYS65 4.4 24.6 1.0
O C:HOH1107 4.5 31.7 1.0
N C:CYS65 4.7 22.4 1.0
O C:HOH1156 4.7 52.9 1.0
CB C:ASP116 4.8 22.4 1.0
O C:HOH1131 4.9 44.5 1.0
CB C:ASP64 4.9 23.4 1.0

Reference:

Y.Goldgur, R.Craigie, G.H.Cohen, T.Fujiwara, T.Yoshinaga, T.Fujishita, H.Sugimoto, T.Endo, H.Murai, D.R.Davies. Structure of the Hiv-1 Integrase Catalytic Domain Complexed with An Inhibitor: A Platform For Antiviral Drug Design. Proc.Natl.Acad.Sci.Usa V. 96 13040 1999.
ISSN: ISSN 0027-8424
PubMed: 10557269
DOI: 10.1073/PNAS.96.23.13040
Page generated: Mon Dec 14 06:39:24 2020

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