Zinc in PDB 7xj7: 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: 7xj7 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) 29.77 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.812, 60.812, 82.506, 90, 90, 90
R / Rfree (%) 22.5 / 26.1

Other elements in 7xj7:

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 7xj7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 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: 7xj7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7xj7

Go back to Zinc Binding Sites List in 7xj7
Zinc binding site 1 out of 2 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:33.9
occ:1.00
OE2 A:GLU72 1.8 33.8 1.0
OE1 A:GLU119 2.0 39.5 1.0
O A:HOH339 2.2 31.0 1.0
CD A:GLU72 2.8 32.0 1.0
CD A:GLU119 2.9 38.8 1.0
CG A:GLU72 3.1 31.6 1.0
OE2 A:GLU119 3.2 40.6 1.0
OE1 A:GLU72 3.9 29.1 1.0
CG A:GLU119 4.3 33.4 1.0
CB A:GLU72 4.6 27.2 1.0
CB A:GLU119 4.6 32.4 1.0
NZ A:LYS120 4.9 46.8 1.0

Zinc binding site 2 out of 2 in 7xj7

Go back to Zinc Binding Sites List in 7xj7
Zinc binding site 2 out of 2 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:27.1
occ:1.00
OD1 A:ASP51 2.1 33.1 1.0
O A:HOH342 2.2 15.8 1.0
OD2 A:ASP51 2.5 30.1 1.0
CG A:ASP51 2.6 26.5 1.0
OG1 A:THR50 4.1 26.3 1.0
CB A:ASP51 4.1 29.1 1.0
O A:HOH327 4.1 28.2 1.0
CB A:THR50 4.2 24.5 1.0
N A:ASP51 4.5 25.1 1.0
O A:HOH312 4.7 36.2 1.0
CA A:ASP51 4.8 26.6 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: Sat Apr 8 05:54:31 2023

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