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Magnesium in PDB 4r5p: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor, PDB code: 4r5p was solved by K.Das, S.E.Martinez, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.54 / 2.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.905, 133.529, 139.218, 90.00, 97.81, 90.00
R / Rfree (%) 19.5 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor (pdb code 4r5p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor, PDB code: 4r5p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4r5p

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Magnesium binding site 1 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.2
occ:1.00
 O18 A:3JY602 2.3 0.3 1.0
O14 A:3JY602 2.5 0.8 1.0
OD2 A:ASP185 2.5 0.9 1.0
OD1 A:ASP110 2.5 93.3 1.0
O17 A:3JY602 2.6 0.8 1.0
O A:VAL111 2.6 96.2 1.0
P16 A:3JY602 2.9 0.8 1.0
C13 A:3JY602 3.3 0.8 1.0
C12 A:3JY602 3.5 0.9 1.0
CG A:ASP110 3.5 98.5 1.0
O11 A:3JY602 3.7 0.3 1.0
CG A:ASP185 3.7 91.5 1.0
OD2 A:ASP110 3.8 0.0 1.0
C A:VAL111 3.9 98.0 1.0
OD1 A:ASP185 4.3 87.1 1.0
O19 A:3JY602 4.4 96.6 1.0
O15 A:3JY602 4.5 97.7 1.0
N A:ASP113 4.7 98.5 1.0
N A:GLY112 4.7 0.9 1.0
N A:VAL111 4.7 93.4 1.0
CA A:GLY112 4.8 0.8 1.0
CB A:ASP185 4.8 87.8 1.0
CA A:VAL111 4.9 91.6 1.0
CB A:ASP110 4.9 95.1 1.0
C10 A:3JY602 4.9 99.1 1.0

Magnesium binding site 2 out of 6 in 4r5p

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Magnesium binding site 2 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:72.4
occ:1.00
 OD1 A:ASP549 2.4 74.3 1.0
OD2 A:ASP443 2.5 61.9 1.0
O A:HOH701 2.5 61.8 1.0
CG A:ASP443 3.3 57.9 1.0
OD1 A:ASP443 3.3 55.6 1.0
CG A:ASP549 3.7 74.8 1.0
ND2 A:ASN498 4.1 53.0 1.0
OD1 A:ASN498 4.1 51.4 1.0
OP1 T:DC723 4.4 96.3 1.0
NE2 A:HIS539 4.4 67.6 1.0
CG A:ASN498 4.5 48.9 1.0
O A:GLY444 4.5 58.0 1.0
CB A:ASP549 4.5 65.0 1.0
OD2 A:ASP549 4.6 72.6 1.0
CB A:ASP443 4.7 43.7 1.0
CB A:ALA538 4.8 50.2 1.0
CA A:ASP549 4.9 66.0 1.0
CE1 A:HIS539 5.0 70.6 1.0

Magnesium binding site 3 out of 6 in 4r5p

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Magnesium binding site 3 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:63.8
occ:1.00
 OD1 C:ASP549 2.3 64.0 1.0
OD2 C:ASP443 2.4 60.3 1.0
O C:HOH701 2.4 56.1 1.0
OD1 C:ASP443 2.9 49.0 1.0
CG C:ASP443 3.0 52.6 1.0
ND2 C:ASN498 3.4 45.0 1.0
CG C:ASP549 3.6 62.4 1.0
O C:GLY444 4.2 58.4 1.0
OD1 C:ASN498 4.3 48.1 1.0
CG C:ASN498 4.3 42.5 1.0
OD2 C:ASP549 4.4 60.9 1.0
CB C:ASP549 4.5 51.0 1.0
CB C:ASP443 4.5 41.7 1.0
NE2 C:HIS539 4.8 67.5 1.0
CB C:ALA538 4.8 47.7 1.0
OP1 E:DC723 4.9 0.4 1.0
CA C:ASP549 5.0 54.4 1.0

Magnesium binding site 4 out of 6 in 4r5p

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Magnesium binding site 4 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:0.0
occ:1.00
 O14 C:3JY602 2.2 95.7 1.0
O17 C:3JY602 2.3 0.3 1.0
O18 C:3JY602 2.4 0.8 1.0
OD2 C:ASP110 2.5 0.5 1.0
OD2 C:ASP185 2.5 0.1 1.0
O C:VAL111 2.6 0.6 1.0
P16 C:3JY602 2.6 0.5 1.0
C13 C:3JY602 2.9 0.0 1.0
C12 C:3JY602 3.0 0.5 1.0
O11 C:3JY602 3.0 0.5 1.0
CG C:ASP185 3.6 92.5 1.0
CG C:ASP110 3.8 0.1 1.0
C C:VAL111 3.8 0.2 1.0
O15 C:3JY602 4.0 0.2 1.0
OD1 C:ASP185 4.0 88.7 1.0
O19 C:3JY602 4.1 0.5 1.0
N C:VAL111 4.3 0.0 1.0
C10 C:3JY602 4.3 0.3 1.0
OD1 C:ASP110 4.4 0.6 1.0
CA C:VAL111 4.6 0.5 1.0
CB C:ASP185 4.7 92.6 1.0
CB C:ALA114 4.7 0.6 1.0
N C:GLY112 4.8 0.2 1.0
N C:ASP113 4.8 0.5 1.0
N C:ALA114 4.8 0.6 1.0
CB C:ASP110 4.8 0.7 1.0
CA C:GLY112 4.9 0.1 1.0

Magnesium binding site 5 out of 6 in 4r5p

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Magnesium binding site 5 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:51.7
occ:1.00
 OE1 B:GLN23 2.7 50.6 1.0
O B:THR58 2.9 51.0 1.0
N B:THR131 2.9 55.6 1.0
ND2 B:ASN57 3.0 58.6 1.0
O B:THR131 3.0 59.3 1.0
CB B:GLN23 3.1 45.1 1.0
CA B:THR131 3.6 50.8 1.0
CD B:GLN23 3.6 47.7 1.0
OD1 B:ASN57 3.6 62.0 1.0
CB B:THR131 3.6 58.3 1.0
CG B:ASN57 3.7 63.8 1.0
C B:THR131 3.7 51.7 1.0
CG B:GLN23 3.7 41.8 1.0
C B:THR58 3.8 50.6 1.0
CA B:PRO59 3.8 47.2 1.0
CA B:GLN23 3.9 43.1 1.0
C B:PHE130 3.9 57.7 1.0
OG1 B:THR131 4.0 61.2 1.0
CA B:PHE130 4.1 57.8 1.0
N B:VAL60 4.1 45.5 1.0
N B:PRO59 4.2 56.9 1.0
N B:GLN23 4.3 46.8 1.0
C B:PRO59 4.3 44.1 1.0
CG1 B:VAL60 4.3 43.7 1.0
CB B:PHE130 4.4 50.6 1.0
N B:THR58 4.8 60.6 1.0
NE2 B:GLN23 4.8 46.8 1.0
CB B:VAL60 4.9 45.0 1.0
CA B:THR58 4.9 53.0 1.0
O B:PHE130 5.0 62.2 1.0
CG2 B:THR131 5.0 55.1 1.0
O B:VAL21 5.0 60.4 1.0

Magnesium binding site 6 out of 6 in 4r5p

Go back to Magnesium Binding Sites List in 4r5p
Magnesium binding site 6 out of 6 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor


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 Hiv-1 Reverse Transcriptase (Rt) with Dna and A Nucleoside Triphosphate Mimic Alpha-Carboxy Nucleoside Phosphonate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:57.5
occ:1.00
 O D:THR58 2.4 59.0 1.0
OE1 D:GLN23 2.7 60.7 1.0
N D:THR131 2.8 63.0 1.0
ND2 D:ASN57 2.8 63.4 1.0
O D:THR131 3.1 69.1 1.0
OD1 D:ASN57 3.2 67.5 1.0
CG D:ASN57 3.4 67.4 1.0
C D:THR58 3.5 61.9 1.0
CA D:THR131 3.6 61.8 1.0
C D:PHE130 3.6 65.2 1.0
CA D:PHE130 3.6 66.6 1.0
CB D:GLN23 3.6 52.0 1.0
CD D:GLN23 3.7 60.1 1.0
C D:THR131 3.8 63.2 1.0
CA D:PRO59 3.8 56.3 1.0
CB D:PHE130 3.8 68.5 1.0
CB D:THR131 3.9 63.1 1.0
N D:VAL60 4.1 55.3 1.0
N D:PRO59 4.1 65.8 1.0
CG D:GLN23 4.1 57.9 1.0
C D:PRO59 4.2 56.5 1.0
CG1 D:VAL60 4.3 55.1 1.0
OG1 D:THR131 4.3 64.0 1.0
CA D:GLN23 4.3 56.5 1.0
N D:THR58 4.4 71.6 1.0
CA D:THR58 4.6 63.6 1.0
N D:GLN23 4.6 59.1 1.0
O D:PHE130 4.7 68.8 1.0
CB D:VAL60 4.8 55.2 1.0
CB D:ASN57 4.8 67.0 1.0
O D:VAL21 4.9 62.9 1.0
NE2 D:GLN23 4.9 58.4 1.0
N D:PHE130 4.9 69.8 1.0

Reference:

J.Balzarini, K.Das, J.A.Bernatchez, S.E.Martinez, M.Ngure, S.Keane, A.Ford, N.Maguire, N.Mullins, J.John, Y.Kim, W.Dehaen, J.Vande Voorde, S.Liekens, L.Naesens, M.Gotte, A.R.Maguire, E.Arnold. Alpha-Carboxy Nucleoside Phosphonates As Universal Nucleoside Triphosphate Mimics. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25733891
DOI: 10.1073/PNAS.1420233112
Page generated: Mon Dec 14 19:29:44 2020

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