Manganese 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:

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

Manganese binding site 1 out of 2 in 7xiu

Go back to Manganese Binding Sites List in 7xiu
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:28.0
occ:1.00
SAA A:E81203 1.8 48.1 1.0
OE2 A:GLU58 1.9 33.5 1.0
OD1 A:ASP78 1.9 33.3 1.0
OD1 A:ASP23 2.0 30.0 1.0
CD A:GLU58 2.7 35.9 1.0
CG A:ASP78 2.8 36.7 1.0
OE1 A:GLU58 2.9 32.3 1.0
OD2 A:ASP78 3.0 38.1 1.0
CAB A:E81203 3.0 55.5 1.0
OAH A:E81203 3.1 55.1 1.0
CG A:ASP23 3.1 36.8 1.0
MN A:MN202 3.3 42.7 1.0
O A:HOH302 3.4 32.4 1.0
CAE A:E81203 3.5 56.4 1.0
NAF A:E81203 3.5 61.6 1.0
OD2 A:ASP23 3.5 32.6 1.0
O A:GLY24 3.8 37.8 1.0
OAJ A:E81203 4.0 51.4 1.0
CG A:GLU58 4.1 25.9 1.0
CAC A:E81203 4.2 57.1 1.0
CAI A:E81203 4.2 55.4 1.0
CB A:ASP78 4.2 33.3 1.0
N A:GLY24 4.3 30.2 1.0
CAD A:E81203 4.3 61.6 1.0
CB A:ASP23 4.4 30.4 1.0
C A:ASP78 4.6 36.9 1.0
CA A:ASP23 4.6 30.9 1.0
CA A:ASP78 4.8 32.0 1.0
O A:ASP78 4.8 32.7 1.0
N A:SER79 4.8 28.4 1.0
N A:ASP78 4.9 32.8 1.0
C A:GLY24 4.9 36.2 1.0
OD2 A:ASP139 4.9 52.8 1.0

Manganese binding site 2 out of 2 in 7xiu

Go back to Manganese Binding Sites List in 7xiu
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:42.7
occ:1.00
OD2 A:ASP139 1.8 52.8 1.0
OD2 A:ASP23 2.1 32.6 1.0
SAA A:E81203 2.3 48.1 1.0
OD2 A:ASP78 2.4 38.1 1.0
CAE A:E81203 2.5 56.4 1.0
OAJ A:E81203 2.7 51.4 1.0
CAI A:E81203 2.7 55.4 1.0
CG A:ASP139 2.9 44.8 1.0
CG A:ASP23 3.0 36.8 1.0
MN A:MN201 3.3 28.0 1.0
OD1 A:ASP23 3.3 30.0 1.0
CAD A:E81203 3.4 61.6 1.0
CG A:ASP78 3.4 36.7 1.0
CAB A:E81203 3.6 55.5 1.0
CB A:ASP139 3.6 39.4 1.0
OD1 A:ASP78 3.8 33.3 1.0
OAK A:E81203 3.8 58.6 1.0
OD1 A:ASP139 3.9 40.1 1.0
CAC A:E81203 3.9 57.1 1.0
CA A:ASP139 4.3 40.5 1.0
ND2 A:ASN135 4.3 32.7 1.0
CB A:ASP23 4.4 30.4 1.0
OD1 A:ASN135 4.5 33.6 1.0
CB A:ALA128 4.5 43.4 1.0
NAF A:E81203 4.6 61.6 1.0
CB A:ASP78 4.7 33.3 1.0
CG A:ASN135 4.8 35.4 1.0
CAL A:E81203 4.9 56.8 1.0
O A:ASN135 5.0 37.1 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: Fri Apr 7 13:03:18 2023

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