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Magnesium in PDB 3klf: Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa

Enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa

All present enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa, PDB code: 3klf was solved by X.Tu, K.Das, S.G.Sarafianos, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.83 / 3.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.529, 274.806, 152.371, 90.00, 90.11, 90.00
R / Rfree (%) 26.4 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa (pdb code 3klf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa, PDB code: 3klf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3klf

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Magnesium binding site 1 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:4.8
occ:1.00
 OD2 A:ASP185 2.2 35.1 1.0
O A:VAL111 2.2 36.6 1.0
OD1 A:ASP110 2.3 41.7 1.0
O1G A:ZP4823 2.3 64.6 1.0
O1A A:ZP4823 2.4 46.0 1.0
O2B A:ZP4823 2.4 51.5 1.0
CG A:ASP110 3.0 42.8 1.0
OD2 A:ASP110 3.1 45.3 1.0
PB A:ZP4823 3.2 51.9 1.0
C A:VAL111 3.3 37.8 1.0
O3B A:ZP4823 3.3 58.1 1.0
CG A:ASP185 3.4 33.5 1.0
PG A:ZP4823 3.4 62.8 1.0
PA A:ZP4823 3.5 47.1 1.0
O3A A:ZP4823 3.5 48.3 1.0
CA A:GLY112 3.9 37.2 1.0
N A:GLY112 4.0 37.5 1.0
OD1 A:ASP185 4.0 30.6 1.0
N A:VAL111 4.1 40.0 1.0
N A:ASP113 4.2 38.2 1.0
C5' A:ZP4823 4.3 46.3 1.0
O5' A:ZP4823 4.3 47.5 1.0
CA A:VAL111 4.4 38.4 1.0
O3G A:ZP4823 4.4 67.2 1.0
C A:GLY112 4.4 36.9 1.0
O2G A:ZP4823 4.4 62.9 1.0
C A:ASP110 4.4 40.6 1.0
CB A:ASP110 4.4 42.0 1.0
CB A:ASP185 4.5 32.1 1.0
O1B A:ZP4823 4.6 54.1 1.0
O31 A:ZP4823 4.7 91.3 1.0
O2A A:ZP4823 4.7 47.5 1.0
CA A:ASP110 4.9 40.7 1.0
O A:ASP110 4.9 40.8 1.0
CB A:ALA114 4.9 40.9 1.0
N A:ALA114 5.0 39.2 1.0

Magnesium binding site 2 out of 8 in 3klf

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Magnesium binding site 2 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:38.1
occ:1.00
 OD2 A:ASP443 2.3 48.8 1.0
OD1 A:ASP443 2.6 47.8 1.0
CG A:ASP443 2.8 48.2 1.0
O A:HOH567 2.9 60.6 1.0
OD2 A:ASP498 2.9 58.2 1.0
OD1 A:ASP498 3.3 57.4 1.0
CG A:ASP498 3.5 57.0 1.0
O A:GLY444 3.6 46.4 1.0
OD1 A:ASP549 3.6 64.1 1.0
OP1 C:DC723 4.3 72.5 1.0
CB A:ASP443 4.3 45.8 1.0
CE1 A:HIS539 4.7 74.7 1.0
CG A:ASP549 4.7 64.7 1.0
N A:GLY444 4.7 43.8 1.0
C A:GLY444 4.8 45.8 1.0
OE1 A:GLU478 5.0 69.1 1.0

Magnesium binding site 3 out of 8 in 3klf

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Magnesium binding site 3 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg600

b:5.6
occ:1.00
 OD2 E:ASP185 2.2 37.9 1.0
OD2 E:ASP110 2.3 54.2 1.0
O1G E:ZP4823 2.3 60.0 1.0
O1A E:ZP4823 2.4 46.1 1.0
O2B E:ZP4823 2.4 51.3 1.0
O E:VAL111 2.6 53.2 1.0
PB E:ZP4823 3.1 50.4 1.0
O3B E:ZP4823 3.3 55.8 1.0
CG E:ASP110 3.3 53.2 1.0
PG E:ZP4823 3.3 60.6 1.0
CG E:ASP185 3.4 38.9 1.0
C E:VAL111 3.4 52.7 1.0
O3A E:ZP4823 3.4 48.7 1.0
PA E:ZP4823 3.4 45.7 1.0
OD1 E:ASP110 3.6 54.1 1.0
OD1 E:ASP185 4.0 37.1 1.0
N E:GLY112 4.0 52.1 1.0
CA E:GLY112 4.0 50.5 1.0
N E:VAL111 4.1 51.3 1.0
C5' E:ZP4823 4.3 45.7 1.0
N E:ASP113 4.3 48.7 1.0
CA E:VAL111 4.3 52.1 1.0
O5' E:ZP4823 4.3 45.7 1.0
O2G E:ZP4823 4.3 62.0 1.0
O3G E:ZP4823 4.4 67.9 1.0
CB E:ASP185 4.5 39.4 1.0
C E:ASP110 4.5 50.9 1.0
O1B E:ZP4823 4.6 51.5 1.0
C E:GLY112 4.6 49.1 1.0
CB E:ASP110 4.6 52.7 1.0
O2A E:ZP4823 4.7 46.2 1.0
CB E:ALA114 5.0 43.7 1.0

Magnesium binding site 4 out of 8 in 3klf

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Magnesium binding site 4 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:64.9
occ:1.00
 OD2 E:ASP443 2.3 61.9 1.0
OD1 E:ASP443 2.3 58.0 1.0
CG E:ASP443 2.6 59.2 1.0
OD2 E:ASP498 3.1 59.9 1.0
OD1 E:ASP498 3.2 59.6 1.0
O E:GLY444 3.2 55.6 1.0
CG E:ASP498 3.5 59.3 1.0
OE1 E:GLU478 3.9 73.0 1.0
OD1 E:ASP549 3.9 76.7 1.0
CB E:ASP443 4.2 57.1 1.0
N E:GLY444 4.3 54.4 1.0
OP1 G:DC723 4.3 72.6 1.0
C E:GLY444 4.4 55.2 1.0
CD E:GLU478 4.9 70.8 1.0
OD1 E:ASN474 4.9 62.3 1.0
CA E:ASP443 5.0 55.1 1.0

Magnesium binding site 5 out of 8 in 3klf

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Magnesium binding site 5 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg600

b:32.0
occ:1.00
 O1A I:ZP4823 2.1 83.1 1.0
OD2 I:ASP185 2.2 75.0 1.0
OD2 I:ASP110 2.5 88.0 1.0
O1G I:ZP4823 2.5 94.1 1.0
O2B I:ZP4823 2.5 87.3 1.0
O I:VAL111 2.6 83.7 1.0
PB I:ZP4823 3.2 88.0 1.0
PA I:ZP4823 3.2 83.0 1.0
O3B I:ZP4823 3.3 91.6 1.0
CG I:ASP110 3.3 86.1 1.0
O3A I:ZP4823 3.3 85.4 1.0
C I:VAL111 3.3 83.9 1.0
PG I:ZP4823 3.4 93.7 1.0
CG I:ASP185 3.4 74.0 1.0
OD1 I:ASP110 3.5 86.9 1.0
N I:GLY112 3.9 85.0 1.0
CA I:GLY112 4.0 86.0 1.0
N I:ASP113 4.0 87.0 1.0
C5' I:ZP4823 4.0 77.4 1.0
O5' I:ZP4823 4.1 81.6 1.0
N I:VAL111 4.1 82.7 1.0
OD1 I:ASP185 4.2 73.8 1.0
C I:GLY112 4.3 86.7 1.0
CA I:VAL111 4.3 83.3 1.0
O2G I:ZP4823 4.4 92.7 1.0
O2A I:ZP4823 4.4 81.8 1.0
CB I:ASP185 4.4 73.9 1.0
O3G I:ZP4823 4.5 96.6 1.0
C I:ASP110 4.6 82.3 1.0
O1B I:ZP4823 4.7 87.2 1.0
CB I:ASP110 4.7 84.2 1.0
CB I:ALA114 4.8 88.1 1.0
N I:ALA114 4.8 88.8 1.0
O I:ASP110 5.0 82.7 1.0

Magnesium binding site 6 out of 8 in 3klf

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Magnesium binding site 6 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg602

b:56.1
occ:1.00
 OD1 I:ASP443 2.4 79.8 1.0
O I:HOH565 2.9 70.4 1.0
OD2 I:ASP443 3.0 78.5 1.0
CG I:ASP443 3.1 78.7 1.0
OD1 I:ASP498 3.1 71.1 1.0
O I:GLY444 3.2 80.2 1.0
OD2 I:ASP498 3.4 73.5 1.0
OE1 I:GLU478 3.5 79.4 1.0
CG I:ASP498 3.6 72.7 1.0
OP1 K:DC723 4.2 0.3 1.0
CD I:GLU478 4.4 78.9 1.0
OD1 I:ASN474 4.4 93.8 1.0
C I:GLY444 4.4 80.1 1.0
N I:GLY444 4.5 76.3 1.0
CG I:GLU478 4.5 76.9 1.0
OD1 I:ASP549 4.6 98.9 1.0
CB I:ASP443 4.6 76.5 1.0

Magnesium binding site 7 out of 8 in 3klf

Go back to Magnesium Binding Sites List in 3klf
Magnesium binding site 7 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg600

b:43.5
occ:1.00
 OD2 M:ASP185 2.4 0.2 1.0
O1A M:ZP4823 2.4 0.1 1.0
O M:VAL111 2.5 0.0 1.0
O2B M:ZP4823 2.5 0.8 1.0
OD1 M:ASP110 2.5 0.9 1.0
O1G M:ZP4823 2.6 0.6 1.0
C M:VAL111 3.1 0.2 1.0
CG M:ASP110 3.2 0.3 1.0
OD2 M:ASP110 3.2 0.6 1.0
PB M:ZP4823 3.3 0.8 1.0
O3B M:ZP4823 3.4 0.7 1.0
PG M:ZP4823 3.5 0.0 1.0
N M:GLY112 3.5 0.4 1.0
PA M:ZP4823 3.6 0.9 1.0
CA M:GLY112 3.6 0.7 1.0
O3A M:ZP4823 3.6 0.3 1.0
CG M:ASP185 3.6 0.7 1.0
N M:ASP113 3.9 0.2 1.0
N M:VAL111 3.9 0.8 1.0
C M:GLY112 4.0 0.9 1.0
CA M:VAL111 4.1 0.2 1.0
C5' M:ZP4823 4.2 0.5 1.0
O5' M:ZP4823 4.3 0.1 1.0
OD1 M:ASP185 4.4 0.7 1.0
C M:ASP110 4.4 0.7 1.0
O2G M:ZP4823 4.4 0.3 1.0
CB M:ASP110 4.6 0.6 1.0
CB M:ASP185 4.7 0.9 1.0
O3G M:ZP4823 4.7 0.2 1.0
O31 M:ZP4823 4.7 0.9 1.0
O1B M:ZP4823 4.8 0.0 1.0
O M:ASP110 4.8 0.2 1.0
O2A M:ZP4823 4.8 0.4 1.0
N M:ALA114 4.9 0.1 1.0
CB M:VAL111 5.0 0.2 1.0
CB M:ALA114 5.0 0.5 1.0

Magnesium binding site 8 out of 8 in 3klf

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Magnesium binding site 8 out of 8 in the Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg602

b:65.8
occ:1.00
 OD1 M:ASP498 2.5 73.9 1.0
OE1 M:GLU478 2.7 74.7 1.0
O M:HOH558 2.7 62.2 1.0
OD1 M:ASP443 2.8 85.7 1.0
CG M:ASP498 3.2 74.7 1.0
OD2 M:ASP498 3.4 75.0 1.0
CG M:ASP443 3.7 84.8 1.0
OD2 M:ASP443 3.8 85.0 1.0
CD M:GLU478 3.8 75.0 1.0
O M:GLY444 4.0 87.9 1.0
OP1 O:DC723 4.2 0.0 1.0
CG M:GLU478 4.3 75.1 1.0
OD1 M:ASN474 4.4 70.6 1.0
CB M:ASP498 4.6 73.8 1.0
OE2 M:GLU478 4.9 73.7 1.0
O M:ASP498 4.9 74.8 1.0
C M:ASP498 5.0 74.4 1.0

Reference:

X.Tu, K.Das, Q.Han, J.D.Bauman, A.D.Clark, X.Hou, Y.V.Frenkel, B.L.Gaffney, R.A.Jones, P.L.Boyer, S.H.Hughes, S.G.Sarafianos, E.Arnold. Structural Basis of Hiv-1 Resistance to Azt By Excision. Nat.Struct.Mol.Biol. V. 17 1202 2010.
ISSN: ISSN 1545-9993
PubMed: 20852643
DOI: 10.1038/NSMB.1908
Page generated: Mon Dec 14 08:22:49 2020

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