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Magnesium in PDB 3kle: Crystal Structure of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa

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

All present enzymatic activity of Crystal Structure of Azt-Resistant 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 Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa, PDB code: 3kle 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 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.738, 283.330, 155.233, 90.00, 89.73, 90.00
R / Rfree (%) 28 / 30.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa (pdb code 3kle). 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 Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked to A Dsdna with A Bound Excision Product, Aztppppa, PDB code: 3kle:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3kle

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Magnesium binding site 1 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:27.2
occ:1.00
 OD2 A:ASP110 1.9 49.1 1.0
O2B A:ZP4823 2.0 62.8 1.0
O2G A:ZP4823 2.1 84.7 1.0
O1A A:ZP4823 2.1 47.8 1.0
O A:VAL111 2.2 50.3 1.0
OD2 A:ASP185 2.4 51.5 1.0
CG A:ASP110 3.0 51.2 1.0
PB A:ZP4823 3.1 64.4 1.0
PG A:ZP4823 3.1 87.9 1.0
C A:VAL111 3.1 48.3 1.0
PA A:ZP4823 3.4 51.2 1.0
O3B A:ZP4823 3.4 75.2 1.0
OD1 A:ASP110 3.5 52.7 1.0
O3A A:ZP4823 3.6 54.5 1.0
N A:VAL111 3.6 45.5 1.0
CG A:ASP185 3.7 49.5 1.0
O1G A:ZP4823 3.8 86.8 1.0
CA A:VAL111 3.9 46.3 1.0
N A:GLY112 4.0 48.8 1.0
C5' A:ZP4823 4.1 50.8 1.0
O5' A:ZP4823 4.2 50.8 1.0
CA A:GLY112 4.2 50.9 1.0
OD1 A:ASP185 4.3 51.5 1.0
CB A:ASP110 4.3 49.2 1.0
N A:ASP113 4.4 52.5 1.0
C A:ASP110 4.4 45.0 1.0
O1B A:ZP4823 4.5 63.5 1.0
CB A:ALA114 4.5 54.6 1.0
O3G A:ZP4823 4.5 92.1 1.0
O2A A:ZP4823 4.6 45.5 1.0
C A:GLY112 4.6 52.4 1.0
CB A:VAL111 4.6 46.4 1.0
N A:ALA114 4.6 53.4 1.0
CB A:ASP185 4.8 45.0 1.0
CA A:ASP110 4.8 46.6 1.0

Magnesium binding site 2 out of 8 in 3kle

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Magnesium binding site 2 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:24.6
occ:1.00
 OD1 A:ASP443 2.7 59.1 1.0
OD2 A:ASP443 2.8 59.0 1.0
OE2 A:GLU478 2.8 79.2 1.0
OD1 A:ASP498 3.1 55.0 1.0
O A:HOH561 3.1 42.0 1.0
CG A:ASP443 3.1 59.2 1.0
OD2 A:ASP498 3.1 53.9 1.0
CG A:ASP498 3.5 54.8 1.0
O A:GLY444 3.6 52.3 1.0
CD A:GLU478 3.7 77.8 1.0
OP1 C:DC723 3.7 95.0 1.0
CG A:GLU478 4.0 71.9 1.0
OD1 A:ASN474 4.6 66.0 1.0
CB A:ASP443 4.6 56.5 1.0
N A:GLY444 4.8 52.2 1.0
OE1 A:GLU478 4.8 78.9 1.0
C A:GLY444 4.8 51.7 1.0
CB A:ASP498 5.0 53.4 1.0

Magnesium binding site 3 out of 8 in 3kle

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Magnesium binding site 3 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:28.2
occ:1.00
 O2B E:ZP4823 1.9 71.8 1.0
OD2 E:ASP110 2.1 67.3 1.0
O2G E:ZP4823 2.3 83.7 1.0
O E:VAL111 2.3 59.3 1.0
O1A E:ZP4823 2.3 60.7 1.0
OD2 E:ASP185 2.5 44.1 1.0
PB E:ZP4823 3.1 73.9 1.0
CG E:ASP110 3.1 64.4 1.0
C E:VAL111 3.1 58.3 1.0
PG E:ZP4823 3.2 86.9 1.0
PA E:ZP4823 3.4 62.5 1.0
O3B E:ZP4823 3.5 79.8 1.0
OD1 E:ASP110 3.5 66.9 1.0
N E:VAL111 3.5 57.0 1.0
O3A E:ZP4823 3.6 66.7 1.0
CG E:ASP185 3.7 45.1 1.0
CA E:VAL111 3.8 57.0 1.0
O1G E:ZP4823 3.9 86.5 1.0
C5' E:ZP4823 3.9 59.2 1.0
N E:GLY112 4.0 60.2 1.0
O5' E:ZP4823 4.2 60.9 1.0
CA E:GLY112 4.2 62.7 1.0
OD1 E:ASP185 4.2 45.2 1.0
N E:ASP113 4.3 65.0 1.0
CB E:ASP110 4.4 61.4 1.0
C E:ASP110 4.4 57.4 1.0
O1B E:ZP4823 4.4 74.6 1.0
CB E:ALA114 4.4 57.0 1.0
C E:GLY112 4.5 64.4 1.0
N E:ALA114 4.6 59.8 1.0
CB E:VAL111 4.6 56.9 1.0
O3G E:ZP4823 4.6 89.2 1.0
O2A E:ZP4823 4.7 59.6 1.0
CB E:ASP185 4.8 44.9 1.0
CA E:ASP110 4.8 58.0 1.0

Magnesium binding site 4 out of 8 in 3kle

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Magnesium binding site 4 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:13.0
occ:1.00
 OD1 E:ASP443 2.5 61.6 1.0
OE2 E:GLU478 2.7 80.8 1.0
OD1 E:ASP498 2.8 66.3 1.0
OD2 E:ASP498 2.8 66.0 1.0
OD2 E:ASP443 3.1 60.1 1.0
CG E:ASP498 3.1 66.1 1.0
CG E:ASP443 3.2 62.0 1.0
CD E:GLU478 3.6 79.5 1.0
OP1 G:DC723 3.7 88.4 1.0
O E:GLY444 3.9 62.1 1.0
CG E:GLU478 3.9 74.0 1.0
CB E:ASP498 4.6 62.8 1.0
OE1 E:GLU478 4.7 81.7 1.0
CB E:ASP443 4.7 61.7 1.0
OD1 E:ASN474 4.8 84.7 1.0
CB E:ALA538 4.9 66.5 1.0
N E:GLY444 4.9 60.8 1.0

Magnesium binding site 5 out of 8 in 3kle

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Magnesium binding site 5 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:96.8
occ:1.00
 O2B I:ZP4823 2.2 0.2 1.0
OD2 I:ASP110 2.2 0.5 1.0
O1A I:ZP4823 2.3 0.1 1.0
O2G I:ZP4823 2.4 0.9 1.0
O I:VAL111 2.4 0.3 1.0
OD2 I:ASP185 2.6 0.5 1.0
CG I:ASP110 3.2 0.1 1.0
PB I:ZP4823 3.4 0.1 1.0
C I:VAL111 3.4 0.2 1.0
PG I:ZP4823 3.5 0.2 1.0
OD1 I:ASP110 3.5 0.5 1.0
PA I:ZP4823 3.5 0.2 1.0
O3B I:ZP4823 3.7 0.0 1.0
O3A I:ZP4823 3.8 0.8 1.0
CG I:ASP185 3.8 0.2 1.0
N I:VAL111 3.9 0.9 1.0
CA I:VAL111 4.1 0.9 1.0
O1G I:ZP4823 4.2 0.2 1.0
N I:GLY112 4.2 0.9 1.0
C5' I:ZP4823 4.3 0.8 1.0
N I:ASP113 4.3 0.6 1.0
N I:ALA114 4.4 0.4 1.0
CA I:GLY112 4.4 0.8 1.0
O5' I:ZP4823 4.4 0.6 1.0
CB I:ALA114 4.5 0.1 1.0
OD1 I:ASP185 4.5 0.2 1.0
CB I:ASP110 4.6 0.8 1.0
C I:GLY112 4.6 0.1 1.0
C I:ASP110 4.6 0.0 1.0
O1B I:ZP4823 4.7 0.2 1.0
O2A I:ZP4823 4.7 0.6 1.0
CB I:VAL111 4.8 0.5 1.0
O3G I:ZP4823 4.8 0.9 1.0
CB I:ASP185 4.9 0.8 1.0

Magnesium binding site 6 out of 8 in 3kle

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Magnesium binding site 6 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:64.9
occ:1.00
 O I:HOH561 2.4 71.2 1.0
OD1 I:ASP443 2.5 0.5 1.0
OD2 I:ASP443 2.6 0.2 1.0
OD2 I:ASP498 2.8 0.2 1.0
CG I:ASP443 2.9 0.6 1.0
OD1 I:ASP498 3.0 0.3 1.0
OE2 I:GLU478 3.1 0.5 1.0
CG I:ASP498 3.3 0.8 1.0
O I:GLY444 3.7 0.4 1.0
CD I:GLU478 4.0 0.1 1.0
OP1 K:DC723 4.1 0.9 1.0
CG I:GLU478 4.2 0.1 1.0
CB I:ASP443 4.5 0.2 1.0
CB I:ASP498 4.7 0.8 1.0
N I:GLY444 4.8 0.1 1.0
C I:GLY444 4.9 0.1 1.0
OD1 I:ASP549 4.9 0.3 1.0

Magnesium binding site 7 out of 8 in 3kle

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Magnesium binding site 7 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:0.4
occ:1.00
 O M:VAL111 1.9 0.2 1.0
O1A M:ZP4823 2.1 0.6 1.0
OD2 M:ASP110 2.2 0.4 1.0
O2B M:ZP4823 2.3 0.1 1.0
O2G M:ZP4823 2.3 0.5 1.0
OD2 M:ASP185 2.4 0.4 1.0
C M:VAL111 2.8 0.7 1.0
CG M:ASP110 3.1 0.8 1.0
N M:VAL111 3.3 0.0 1.0
PB M:ZP4823 3.4 0.0 1.0
PA M:ZP4823 3.4 0.3 1.0
PG M:ZP4823 3.4 0.9 1.0
OD1 M:ASP110 3.5 0.4 1.0
CA M:VAL111 3.6 0.7 1.0
CG M:ASP185 3.6 0.5 1.0
O3A M:ZP4823 3.7 0.8 1.0
O3B M:ZP4823 3.8 0.1 1.0
N M:GLY112 3.8 0.8 1.0
C5' M:ZP4823 4.0 0.3 1.0
O1G M:ZP4823 4.0 0.5 1.0
CB M:ALA114 4.1 0.5 1.0
CA M:GLY112 4.2 0.9 1.0
CB M:VAL111 4.2 0.7 1.0
O5' M:ZP4823 4.2 0.7 1.0
N M:ASP113 4.3 0.6 1.0
C M:ASP110 4.3 0.9 1.0
OD1 M:ASP185 4.3 0.1 1.0
N M:ALA114 4.4 0.1 1.0
CB M:ASP110 4.4 0.9 1.0
C M:GLY112 4.4 0.1 1.0
CB M:ASP185 4.6 0.7 1.0
O2A M:ZP4823 4.6 0.7 1.0
CA M:ASP110 4.7 0.1 1.0
O3G M:ZP4823 4.8 0.4 1.0
O1B M:ZP4823 4.8 0.6 1.0
CA M:ALA114 4.8 0.9 1.0

Magnesium binding site 8 out of 8 in 3kle

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Magnesium binding site 8 out of 8 in the Crystal Structure of Azt-Resistant 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 Azt-Resistant 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:94.0
occ:1.00
 OD1 M:ASP443 2.5 0.9 1.0
OD2 M:ASP443 2.7 0.1 1.0
OD2 M:ASP498 2.8 0.8 1.0
CG M:ASP443 3.0 0.1 1.0
OD1 M:ASP498 3.0 0.9 1.0
OE2 M:GLU478 3.1 0.7 1.0
CG M:ASP498 3.3 0.6 1.0
O M:GLY444 3.7 0.1 1.0
OP1 O:DC723 3.8 0.6 1.0
CD M:GLU478 3.9 0.6 1.0
CG M:GLU478 4.2 0.1 1.0
CB M:ASP443 4.5 0.3 1.0
CB M:ASP498 4.7 0.4 1.0
N M:GLY444 4.8 0.5 1.0
C M:GLY444 4.9 0.6 1.0
OD1 M:ASN474 4.9 0.6 1.0
CB M:ALA538 5.0 0.5 1.0
OD1 M:ASP549 5.0 0.5 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: Wed Aug 14 18:10:48 2024

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