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Manganese 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
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 7xj5). 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: 7xj5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7xj5

Go back to Manganese Binding Sites List in 7xj5
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:Mn202

b:33.9
occ:1.00
 OD1 A:ASP23 1.8 19.6 1.0
OAH A:ECW201 2.2 99.0 1.0
OE2 A:GLU58 2.3 32.0 1.0
OD1 A:ASP78 2.4 21.8 1.0
CG A:ASP23 2.9 22.3 1.0
CD A:GLU58 2.9 24.8 1.0
OE1 A:GLU58 2.9 20.2 1.0
OAA A:ECW201 3.0 72.3 1.0
OD2 A:ASP78 3.1 19.1 1.0
CG A:ASP78 3.1 24.4 1.0
MN A:MN203 3.2 36.8 1.0
OD2 A:ASP23 3.3 24.0 1.0
O A:HOH309 3.3 22.7 1.0
NAF A:ECW201 3.4 87.6 1.0
O A:GLY24 3.6 22.5 1.0
CAB A:ECW201 3.6 72.9 1.0
OAK A:ECW201 3.9 74.9 1.0
N A:GLY24 4.1 17.8 1.0
CAE A:ECW201 4.1 79.5 1.0
CB A:ASP23 4.2 15.6 1.0
NH2 A:ARG147 4.3 38.3 1.0
CG A:GLU58 4.4 17.8 1.0
CA A:ASP23 4.4 17.6 1.0
CAJ A:ECW201 4.4 79.7 1.0
CB A:ASP78 4.5 16.7 1.0
C A:GLY24 4.6 23.6 1.0
OAG A:ECW201 4.7 59.5 1.0
C A:ASP23 4.8 22.2 1.0
CAC A:ECW201 4.9 74.0 1.0
C A:ASP78 4.9 19.8 1.0
CA A:GLY24 4.9 20.5 1.0
OD1 A:ASP139 5.0 34.3 1.0

Manganese binding site 2 out of 2 in 7xj5

Go back to Manganese Binding Sites List in 7xj5
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:Mn203

b:36.8
occ:1.00
 OD2 A:ASP23 1.9 24.0 1.0
OAK A:ECW201 1.9 74.9 1.0
OD2 A:ASP78 2.3 19.1 1.0
OD1 A:ASP139 2.7 34.3 1.0
CG A:ASP23 2.8 22.3 1.0
CAJ A:ECW201 3.1 79.7 1.0
OD1 A:ASP23 3.1 19.6 1.0
MN A:MN202 3.2 33.9 1.0
CG A:ASP139 3.3 34.4 1.0
CB A:ASP139 3.4 28.9 1.0
CG A:ASP78 3.4 24.4 1.0
OAA A:ECW201 3.5 72.3 1.0
CAE A:ECW201 3.7 79.5 1.0
OAO A:ECW201 3.8 65.4 1.0
OD1 A:ASP78 3.9 21.8 1.0
NH2 A:ARG147 3.9 38.3 1.0
ND2 A:ASN135 4.0 19.0 1.0
CB A:ALA128 4.1 42.7 1.0
CB A:ASP23 4.1 15.6 1.0
CA A:ASP139 4.2 22.9 1.0
OAL A:ECW201 4.2 81.4 1.0
OD1 A:ASN135 4.2 19.7 1.0
CAM A:ECW201 4.3 70.3 1.0
OD2 A:ASP139 4.4 41.8 1.0
CAN A:ECW201 4.5 70.4 1.0
CG A:ASN135 4.5 19.1 1.0
O A:ASN135 4.6 19.0 1.0
CB A:ASP78 4.7 16.7 1.0
OAH A:ECW201 4.7 99.0 1.0
CAB A:ECW201 4.7 72.9 1.0
O A:HOH309 4.7 22.7 1.0
N A:ASP139 4.9 21.1 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 11:06:19 2024

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