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Zinc in PDB 7xj4: Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester

Enzymatic activity of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester

All present enzymatic activity of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester:
3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester, PDB code: 7xj4 was solved by H.Lu, Y.Komukai, K.Usami, Y.Guo, X.Qiao, M.Nukaga, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.74 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.447, 60.447, 82.426, 90, 90, 90
R / Rfree (%) 21.7 / 24

Other elements in 7xj4:

The structure of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester (pdb code 7xj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester, PDB code: 7xj4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7xj4

Go back to Zinc Binding Sites List in 7xj4
Zinc binding site 1 out of 3 in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:34.2
occ:1.00
 OD1 A:ASP51 2.1 35.2 1.0
O A:HOH313 2.2 21.0 1.0
OD2 A:ASP51 2.5 38.0 1.0
CG A:ASP51 2.6 33.5 1.0
OG1 A:THR50 4.0 34.1 1.0
CB A:ASP51 4.1 35.9 1.0
CB A:THR50 4.2 29.6 1.0
O A:HOH311 4.2 36.2 1.0
N A:ASP51 4.5 28.9 1.0
CA A:ASP51 4.7 30.6 1.0

Zinc binding site 2 out of 3 in 7xj4

Go back to Zinc Binding Sites List in 7xj4
Zinc binding site 2 out of 3 in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:41.0
occ:1.00
 OE2 A:GLU72 1.8 38.5 1.0
OE2 A:GLU119 1.9 42.5 1.0
O A:HOH316 2.3 34.3 1.0
CD A:GLU72 2.8 33.8 1.0
CD A:GLU119 2.9 39.5 1.0
CG A:GLU72 3.1 33.0 1.0
OE1 A:GLU119 3.2 45.8 1.0
OE1 A:GLU72 3.9 33.7 1.0
CG A:GLU119 4.2 38.0 1.0
CB A:GLU119 4.5 36.0 1.0
CE A:LYS120 4.5 46.7 1.0
CB A:GLU72 4.6 30.5 1.0
CD A:LYS120 4.9 40.7 1.0

Zinc binding site 3 out of 3 in 7xj4

Go back to Zinc Binding Sites List in 7xj4
Zinc binding site 3 out of 3 in the Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Engineered Hiv-1 Reverse Transcriptase Rnase H Domain Complexed with Nitrofuran Methoxy(Methoxycarbonyl)Phenyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:48.1
occ:1.00
 OE1 A:GLU113 2.1 51.3 1.0
OE1 A:GLN110 2.5 45.3 1.0
CD A:GLU113 3.0 53.4 1.0
OE2 A:GLU113 3.3 55.4 1.0
CD A:GLN110 3.5 51.8 1.0
NE2 A:GLN110 4.1 52.5 1.0
CG A:GLU113 4.3 41.5 1.0
CB A:GLU113 4.6 40.7 1.0
CG A:GLN110 4.8 43.7 1.0
CA A:GLN110 4.9 35.9 1.0
CB A:GLN110 4.9 36.9 1.0

Reference:

H.Lu, Y.Komukai, K.Usami, Y.Guo, X.Qiao, M.Nukaga, T.Hoshino. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds For Hiv-1 Rnase H Activity. J.Chem.Inf.Model. 2022.
ISSN: ESSN 1549-960X
PubMed: 36184946
DOI: 10.1021/ACS.JCIM.2C00537
Page generated: Wed Oct 30 15:06:14 2024

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