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Zinc in PDB 7xiu: 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: 7xiu 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) 43.88 / 2.09
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.061, 62.061, 83.001, 90, 90, 90
R / Rfree (%) 22.1 / 26.7

Other elements in 7xiu:

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 7xiu). 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: 7xiu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7xiu

Go back to Zinc Binding Sites List in 7xiu
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:36.6
occ:1.00
 OD1 A:ASP51 2.1 39.5 1.0
OD2 A:ASP51 2.7 35.8 1.0
CG A:ASP51 2.7 37.8 1.0
OG1 A:THR50 4.1 30.3 1.0
CB A:THR50 4.2 34.8 1.0
CB A:ASP51 4.2 32.5 1.0
N A:ASP51 4.6 31.4 1.0
CA A:ASP51 4.9 33.1 1.0

Zinc binding site 2 out of 2 in 7xiu

Go back to Zinc Binding Sites List in 7xiu
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:38.2
occ:1.00
 OE2 A:GLU72 1.9 40.5 1.0
OE1 A:GLU119 1.9 48.2 1.0
O A:HOH322 2.3 30.3 1.0
CD A:GLU119 2.8 50.5 1.0
CD A:GLU72 2.9 39.4 1.0
OE2 A:GLU119 3.0 50.9 1.0
CG A:GLU72 3.2 39.0 1.0
OE1 A:GLU72 4.0 33.9 1.0
CG A:GLU119 4.1 48.9 1.0
CB A:GLU119 4.6 40.7 1.0
CB A:GLU72 4.7 33.7 1.0
O A:HOH319 4.7 37.5 1.0
CE A:LYS120 5.0 43.5 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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