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Manganese 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:

Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7xj7

Go back to Manganese Binding Sites List in 7xj7
Manganese 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 Manganese with other atoms in the Mn 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:Mn201

b:20.6
occ:1.00
 OE2 A:GLU58 1.8 24.1 1.0
SAA A:EGI205 1.9 43.5 1.0
OD1 A:ASP23 1.9 24.4 1.0
OD1 A:ASP78 2.0 23.0 1.0
CG A:ASP78 2.8 26.8 1.0
CD A:GLU58 2.8 24.2 1.0
OD2 A:ASP78 3.0 25.5 1.0
CG A:ASP23 3.0 26.1 1.0
OE1 A:GLU58 3.1 24.4 1.0
MN A:MN202 3.2 31.6 1.0
CAB A:EGI205 3.3 39.8 1.0
CAE A:EGI205 3.4 44.2 1.0
OD2 A:ASP23 3.4 26.9 1.0
OAJ A:EGI205 3.4 45.5 1.0
O A:HOH315 3.4 23.9 1.0
OAH A:EGI205 3.7 37.7 1.0
O A:GLY24 3.7 28.6 1.0
O A:HOH307 3.8 35.9 1.0
NAF A:EGI205 3.8 42.5 1.0
CAI A:EGI205 3.8 44.8 1.0
CG A:GLU58 4.2 24.9 1.0
CB A:ASP78 4.2 22.6 1.0
N A:GLY24 4.3 26.2 1.0
CB A:ASP23 4.3 22.5 1.0
CAC A:EGI205 4.3 43.8 1.0
CAD A:EGI205 4.4 44.8 1.0
CA A:ASP23 4.6 22.7 1.0
C A:ASP78 4.6 25.5 1.0
CA A:ASP78 4.8 22.8 1.0
C A:GLY24 4.8 27.5 1.0
O A:ASP78 4.8 23.5 1.0
O A:HOH322 4.8 33.3 1.0
N A:SER79 4.9 22.1 1.0
N A:ASP78 4.9 21.7 1.0

Manganese binding site 2 out of 2 in 7xj7

Go back to Manganese Binding Sites List in 7xj7
Manganese 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 Manganese with other atoms in the Mn 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:Mn202

b:31.6
occ:1.00
 O A:HOH322 1.9 33.3 1.0
OD2 A:ASP23 2.0 26.9 1.0
OD1 A:ASP139 2.3 34.5 1.0
OD2 A:ASP78 2.4 25.5 1.0
OAJ A:EGI205 2.5 45.5 1.0
SAA A:EGI205 2.7 43.5 1.0
CAE A:EGI205 2.9 44.2 1.0
CG A:ASP23 2.9 26.1 1.0
CAI A:EGI205 2.9 44.8 1.0
MN A:MN201 3.2 20.6 1.0
OD1 A:ASP23 3.2 24.4 1.0
CG A:ASP139 3.2 33.4 1.0
CG A:ASP78 3.4 26.8 1.0
CB A:ASP139 3.5 27.2 1.0
OD1 A:ASP78 3.7 23.0 1.0
CAD A:EGI205 3.8 44.8 1.0
CAB A:EGI205 3.9 39.8 1.0
OAK A:EGI205 4.0 46.4 1.0
ND2 A:ASN135 4.2 23.8 1.0
CA A:ASP139 4.2 26.2 1.0
CAC A:EGI205 4.2 43.8 1.0
CB A:ASP23 4.3 22.5 1.0
CB A:ALA128 4.3 32.7 1.0
OD2 A:ASP139 4.4 37.6 1.0
OD1 A:ASN135 4.4 27.9 1.0
CB A:ASP78 4.6 22.6 1.0
CG A:ASN135 4.7 24.4 1.0
NAF A:EGI205 4.9 42.5 1.0
OE2 A:GLU58 5.0 24.1 1.0
O A:ASN135 5.0 27.0 1.0
O A:HOH315 5.0 23.9 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: Sun Oct 6 11:06:21 2024

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