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Cadmium in PDB 3vq5: Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine

Protein crystallography data

The structure of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine, PDB code: 3vq5 was solved by J.Wielens, D.K.Chalmers, M.W.Parker, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.55 / 1.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 49.130, 49.130, 103.050, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.3

Other elements in 3vq5:

The structure of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine (pdb code 3vq5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine, PDB code: 3vq5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3vq5

Go back to Cadmium Binding Sites List in 3vq5
Cadmium binding site 1 out of 4 in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:20.3
occ:1.00
OE1 A:GLU92 1.7 20.9 1.0
NE2 A:HIS67 2.3 17.8 1.0
SG A:CYS65 2.5 19.6 1.0
CD A:GLU92 2.8 20.3 1.0
CE1 A:HIS67 3.0 23.2 1.0
OE2 A:GLU92 3.0 23.2 1.0
CB A:CYS65 3.3 18.6 1.0
CD2 A:HIS67 3.4 23.0 1.0
O A:HOH1103 3.6 17.1 1.0
CD A:CD1002 3.7 19.2 1.0
ND1 A:HIS67 4.2 26.0 1.0
CG A:GLU92 4.3 18.0 1.0
CG A:HIS67 4.5 24.1 1.0
CA A:CYS65 4.6 17.5 1.0
C A:CYS65 4.7 20.6 1.0
O A:HOH1118 5.0 36.5 1.0

Cadmium binding site 2 out of 4 in 3vq5

Go back to Cadmium Binding Sites List in 3vq5
Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:19.2
occ:1.00
O A:HOH1106 2.3 16.9 1.0
O A:HOH1103 2.4 17.1 1.0
OD2 A:ASP116 2.4 23.6 1.0
CL A:CL1003 2.5 18.7 1.0
OE2 A:GLU92 2.5 23.2 1.0
SG A:CYS65 2.6 19.6 1.0
CG A:ASP116 3.4 21.1 1.0
CD A:GLU92 3.4 20.3 1.0
CB A:CYS65 3.6 18.6 1.0
OD1 A:ASP116 3.6 21.3 1.0
CD A:CD1001 3.7 20.3 1.0
OE1 A:GLU92 3.8 20.9 1.0
O A:HOH1112 3.9 23.7 1.0
OD1 A:ASN120 4.2 19.5 1.0
O A:HOH1111 4.2 19.9 1.0
O A:HOH1105 4.4 21.5 1.0
CG A:GLU92 4.4 18.0 1.0
N A:CYS65 4.5 18.1 1.0
CA A:CYS65 4.6 17.5 1.0
ND2 A:ASN120 4.7 16.0 1.0
CB A:ASP116 4.7 21.5 1.0
CG A:ASN120 4.9 18.5 1.0

Cadmium binding site 3 out of 4 in 3vq5

Go back to Cadmium Binding Sites List in 3vq5
Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:20.3
occ:1.00
OE1 B:GLU92 1.8 22.6 1.0
NE2 B:HIS67 2.3 18.8 1.0
SG B:CYS65 2.5 19.6 1.0
CD B:GLU92 2.9 17.7 1.0
CE1 B:HIS67 3.0 21.8 1.0
OE2 B:GLU92 3.0 22.5 1.0
CD2 B:HIS67 3.4 22.6 1.0
CB B:CYS65 3.4 20.8 1.0
O B:HOH403 3.6 17.3 1.0
CD B:CD302 3.7 19.2 1.0
ND1 B:HIS67 4.2 25.1 1.0
CG B:GLU92 4.3 19.0 1.0
CG B:HIS67 4.4 20.7 1.0
CA B:CYS65 4.6 17.9 1.0
C B:CYS65 4.7 19.4 1.0
O B:HOH428 4.8 36.1 1.0
O B:CYS65 5.0 19.0 1.0

Cadmium binding site 4 out of 4 in 3vq5

Go back to Cadmium Binding Sites List in 3vq5
Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv-1 in Core Domain in Complex with N-Methyl-1-(4-Methyl-2-Phenyl-1, 3-Thiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:19.2
occ:1.00
O B:HOH404 2.3 18.3 1.0
O B:HOH403 2.3 17.3 1.0
OE2 B:GLU92 2.5 22.5 1.0
OD2 B:ASP116 2.5 22.2 1.0
CL B:CL303 2.5 19.2 1.0
SG B:CYS65 2.5 19.6 1.0
CD B:GLU92 3.4 17.7 1.0
CG B:ASP116 3.4 20.2 1.0
OD1 B:ASP116 3.6 19.9 1.0
CB B:CYS65 3.6 20.8 1.0
CD B:CD301 3.7 20.3 1.0
OE1 B:GLU92 3.8 22.6 1.0
O B:HOH411 3.9 26.3 1.0
OD1 B:ASN120 4.2 19.8 1.0
O B:HOH412 4.2 20.0 1.0
O B:HOH407 4.4 21.8 1.0
CG B:GLU92 4.5 19.0 1.0
N B:CYS65 4.5 18.4 1.0
CA B:CYS65 4.6 17.9 1.0
ND2 B:ASN120 4.7 16.5 1.0
CB B:ASP116 4.8 21.6 1.0
CG B:ASN120 4.9 19.1 1.0

Reference:

J.Wielens, S.J.Headey, D.I.Rhodes, R.J.Mulder, O.Dolezal, J.J.Deadman, J.Newman, D.K.Chalmers, M.W.Parker, T.S.Peat, M.J.Scanlon. Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification? J Biomol Screen V. 18 147 2013.
ISSN: ISSN 1087-0571
PubMed: 23139382
DOI: 10.1177/1087057112465979
Page generated: Sat Dec 12 08:23:26 2020

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