Zinc in PDB 7xj5: 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: 7xj5 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) 34.40 / 1.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.289, 61.289, 83.116, 90, 90, 90
R / Rfree (%) 27 / 29.8

Other elements in 7xj5:

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:

Bromine (Br) 1 atom
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 7xj5). 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: 7xj5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7xj5

Go back to Zinc Binding Sites List in 7xj5
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:Zn204

b:20.9
occ:1.00
OD1 A:ASP51 2.1 21.1 1.0
O A:HOH326 2.1 12.2 1.0
OD2 A:ASP51 2.6 24.3 1.0
CG A:ASP51 2.6 22.7 1.0
CB A:ASP51 4.1 23.6 1.0
O A:HOH317 4.2 24.1 1.0
OG1 A:THR50 4.2 21.3 1.0
CB A:THR50 4.3 21.3 1.0
N A:ASP51 4.6 23.0 1.0
CA A:ASP51 4.8 24.9 1.0

Zinc binding site 2 out of 2 in 7xj5

Go back to Zinc Binding Sites List in 7xj5
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:Zn205

b:76.2
occ:1.00
OE2 A:GLU72 1.8 34.4 1.0
OE1 A:GLU119 1.8 33.2 1.0
CD A:GLU72 2.7 23.4 1.0
CD A:GLU119 2.8 28.1 1.0
CG A:GLU72 3.0 21.6 1.0
OE2 A:GLU119 3.2 31.9 1.0
OE1 A:GLU72 3.9 19.3 1.0
CG A:GLU119 4.2 27.7 1.0
CB A:GLU119 4.5 21.2 1.0
CB A:GLU72 4.6 22.4 1.0
CB A:LEU71 4.9 23.3 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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