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Manganese in PDB 3qin: Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor, PDB code: 3qin was solved by E.B.Lansdon, T.A.Kirschberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.12 / 1.70
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.841, 90.370, 111.922, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.3

Other elements in 3qin:

The structure of Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor also contains other interesting chemical elements:

Bromine (Br) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor (pdb code 3qin). 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 Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor, PDB code: 3qin:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3qin

Go back to Manganese Binding Sites List in 3qin
Manganese binding site 1 out of 2 in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor


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 Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:22.1
occ:1.00
O14 A:P1Y700 2.0 22.4 1.0
OE1 A:GLU478 2.0 23.9 1.0
OD1 A:ASP443 2.1 21.8 1.0
OD2 A:ASP498 2.1 20.7 1.0
O18 A:P1Y700 2.2 22.8 1.0
CD A:GLU478 3.0 21.2 1.0
CG A:ASP498 3.1 21.2 1.0
C11 A:P1Y700 3.1 24.0 1.0
C16 A:P1Y700 3.1 23.8 1.0
CG A:ASP443 3.2 19.4 1.0
OE2 A:GLU478 3.3 22.1 1.0
OD1 A:ASP498 3.4 25.7 1.0
C10 A:P1Y700 3.5 26.2 1.0
OD2 A:ASP443 3.7 21.9 1.0
MN A:MN2 3.7 22.3 1.0
O A:HOH8 3.7 27.7 1.0
O A:HOH42 3.9 34.1 1.0
O A:HOH563 4.0 20.8 1.0
O A:GLY444 4.3 23.2 1.0
C12 A:P1Y700 4.3 21.5 1.0
CG A:GLU478 4.4 22.1 1.0
O17 A:P1Y700 4.4 28.0 1.0
CB A:ASP443 4.4 19.8 1.0
O A:HOH562 4.5 23.2 1.0
CB A:ASP498 4.5 20.5 1.0
N A:GLY444 4.5 21.3 1.0
C A:ASP498 4.5 22.2 1.0
N A:SER499 4.5 23.2 1.0
O A:HOH18 4.5 29.4 1.0
CA A:ASP443 4.6 20.2 1.0
O15 A:P1Y700 4.7 22.4 1.0
CB A:SER499 4.8 25.2 1.0
O A:ASP498 4.8 22.9 1.0
CA A:ASP498 4.8 19.9 1.0
CA A:SER499 4.8 25.1 1.0
N09 A:P1Y700 4.9 22.2 1.0
N A:ASP498 5.0 20.0 1.0

Manganese binding site 2 out of 2 in 3qin

Go back to Manganese Binding Sites List in 3qin
Manganese binding site 2 out of 2 in the Crystal Structure of Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor


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 Hiv-1 Rnase H P15 with Engineered E. Coli Loop and Pyrimidinol Carboxylic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:22.3
occ:1.00
OD2 A:ASP549 2.1 21.8 1.0
OD2 A:ASP443 2.1 21.9 1.0
O15 A:P1Y700 2.2 22.4 1.0
O A:HOH563 2.2 20.8 1.0
O A:HOH562 2.2 23.2 1.0
O14 A:P1Y700 2.4 22.4 1.0
C12 A:P1Y700 3.0 21.5 1.0
CG A:ASP443 3.1 19.4 1.0
C11 A:P1Y700 3.1 24.0 1.0
CG A:ASP549 3.2 21.4 1.0
OD1 A:ASP443 3.3 21.8 1.0
CB A:ASP549 3.6 17.8 1.0
MN A:MN1 3.7 22.1 1.0
NH1 A:ARG557 4.0 29.8 1.0
NE2 A:HIS539 4.0 28.3 1.0
OD1 A:ASP498 4.1 25.7 1.0
CA A:ASP549 4.2 23.6 1.0
N13 A:P1Y700 4.3 23.4 1.0
OD1 A:ASP549 4.3 26.3 1.0
O A:GLY444 4.3 23.2 1.0
O A:HOH67 4.3 41.6 1.0
C10 A:P1Y700 4.4 26.2 1.0
CB A:ASP443 4.5 19.8 1.0
O A:HOH9 4.6 25.5 1.0
CE1 A:HIS539 4.7 27.5 1.0
OD2 A:ASP498 4.8 20.7 1.0
CD2 A:HIS539 4.9 27.4 1.0
CG A:ASP498 4.9 21.2 1.0

Reference:

E.B.Lansdon, Q.Liu, S.A.Leavitt, M.Balakrishnan, J.K.Perry, C.Lancaster-Moyer, N.Kutty, X.Liu, N.H.Squires, W.J.Watkins, T.A.Kirschberg. Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione Hiv-1 Rnase H Inhibitors. Antimicrob.Agents Chemother. V. 55 2905 2011.
ISSN: ISSN 0066-4804
PubMed: 21464257
DOI: 10.1128/AAC.01594-10
Page generated: Tue Dec 15 04:14:23 2020

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