Atomistry » Manganese » PDB 7x9j-7yzp » 7xit
Atomistry »
  Manganese »
    PDB 7x9j-7yzp »
      7xit »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy