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Manganese in PDB 7xit: 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: 7xit 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) 29.88 / 2.18
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.551, 61.551, 82.196, 90, 90, 90
R / Rfree (%) 22.5 / 27.4

Other elements in 7xit:

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
Bromine (Br) 1 atom

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 7xit). 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: 7xit:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7xit

Go back to Manganese Binding Sites List in 7xit
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:35.9
occ:1.00
 OAA A:E6I205 1.7 57.4 1.0
OE2 A:GLU58 1.8 34.6 1.0
OD1 A:ASP23 1.9 38.4 1.0
OD1 A:ASP78 2.0 39.8 1.0
CG A:ASP78 2.7 41.9 1.0
OD2 A:ASP78 2.7 43.5 1.0
CAE A:E6I205 2.8 64.3 1.0
CD A:GLU58 2.8 41.0 1.0
CAB A:E6I205 2.8 68.2 1.0
CG A:ASP23 2.9 41.9 1.0
MN A:MN202 3.1 60.9 1.0
OAK A:E6I205 3.1 65.1 1.0
OAG A:E6I205 3.2 69.9 1.0
OE1 A:GLU58 3.2 40.1 1.0
OD2 A:ASP23 3.3 44.1 1.0
CAJ A:E6I205 3.3 64.2 1.0
NAF A:E6I205 3.4 69.5 1.0
O A:GLY24 3.6 47.4 1.0
CAC A:E6I205 3.8 70.6 1.0
CAD A:E6I205 3.8 71.5 1.0
CG A:GLU58 4.2 33.4 1.0
CB A:ASP78 4.2 44.9 1.0
CB A:ASP23 4.3 38.6 1.0
N A:GLY24 4.3 42.5 1.0
CA A:ASP23 4.6 35.9 1.0
OAL A:E6I205 4.7 61.5 1.0
OAH A:E6I205 4.7 66.2 1.0
C A:GLY24 4.7 49.1 1.0
C A:ASP78 4.7 36.9 1.0
CA A:ASP78 4.9 36.0 1.0
O A:ASP78 5.0 34.9 1.0
N A:SER79 5.0 38.1 1.0

Manganese binding site 2 out of 2 in 7xit

Go back to Manganese Binding Sites List in 7xit
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:60.9
occ:1.00
 OD2 A:ASP23 2.0 44.1 1.0
CAJ A:E6I205 2.2 64.2 1.0
OAK A:E6I205 2.2 65.1 1.0
OD2 A:ASP139 2.3 52.5 1.0
OD2 A:ASP78 2.6 43.5 1.0
CAE A:E6I205 2.7 64.3 1.0
OAL A:E6I205 2.9 61.5 1.0
CG A:ASP23 2.9 41.9 1.0
MN A:MN201 3.1 35.9 1.0
OAA A:E6I205 3.2 57.4 1.0
CG A:ASP139 3.2 43.1 1.0
OD1 A:ASP23 3.2 38.4 1.0
CAD A:E6I205 3.6 71.5 1.0
CG A:ASP78 3.6 41.9 1.0
CB A:ASP139 3.6 43.0 1.0
OD1 A:ASP78 4.0 39.8 1.0
OD1 A:ASP139 4.2 53.6 1.0
CA A:ASP139 4.2 44.7 1.0
CB A:ASP23 4.2 38.6 1.0
CAM A:E6I205 4.3 73.0 1.0
ND2 A:ASN135 4.3 38.6 1.0
CAB A:E6I205 4.4 68.2 1.0
CAC A:E6I205 4.4 70.6 1.0
CB A:ALA128 4.5 41.2 1.0
OD1 A:ASN135 4.8 41.7 1.0
OE2 A:GLU58 4.8 34.6 1.0
CB A:ASP78 4.9 44.9 1.0
CG A:ASN135 4.9 41.4 1.0
CAN A:E6I205 5.0 64.5 1.0
O A:GLY24 5.0 47.4 1.0
O A:ASN135 5.0 47.1 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 11:05:47 2024

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