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Magnesium in PDB 4dg1: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A:
2.7.7.49; 2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A, PDB code: 4dg1 was solved by X.Tu, K.A.Kirby, B.Marchand, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.08 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.230, 72.150, 109.240, 90.00, 97.52, 90.00
R / Rfree (%) 23.2 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A (pdb code 4dg1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A, PDB code: 4dg1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4dg1

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Magnesium binding site 1 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A


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 Polymorphism Mutation K172A and K173A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:52.4
occ:1.00
 O A:HOH817 2.4 42.6 1.0
O A:THR351 2.5 38.6 1.0
NZ A:LYS350 2.6 37.1 1.0
O3 A:GOL607 3.0 45.0 1.0
O A:GLN269 3.2 42.0 1.0
CG A:LYS350 3.3 38.6 1.0
CE A:LYS350 3.4 41.6 1.0
C A:THR351 3.4 40.5 1.0
O A:ILE270 3.9 43.4 1.0
C A:GLN269 3.9 45.9 1.0
CD A:LYS350 3.9 39.3 1.0
CA A:GLY352 3.9 43.2 1.0
OH A:TYR339 4.0 42.6 1.0
N A:THR351 4.1 33.4 1.0
N A:GLY352 4.1 39.0 1.0
C A:ILE270 4.3 45.2 1.0
C3 A:GOL607 4.3 52.0 1.0
O2 A:GOL607 4.4 57.2 1.0
O A:HOH760 4.4 48.4 1.0
CA A:THR351 4.5 38.5 1.0
C2 A:GOL607 4.6 44.8 1.0
N A:ILE270 4.6 35.6 1.0
CA A:ILE270 4.7 34.9 1.0
CB A:LYS350 4.7 35.2 1.0
CA A:GLN269 4.7 48.0 1.0
O A:TYR271 4.8 49.4 1.0
CZ A:TYR339 4.8 39.6 1.0
C A:LYS350 4.8 36.1 1.0
O A:SER268 4.8 43.7 1.0
C A:TYR271 4.9 44.2 1.0
N A:TYR271 5.0 32.6 1.0
CA A:LYS350 5.0 32.6 1.0

Magnesium binding site 2 out of 4 in 4dg1

Go back to Magnesium Binding Sites List in 4dg1
Magnesium binding site 2 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A


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 Polymorphism Mutation K172A and K173A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:67.7
occ:1.00
 OD1 A:ASP443 2.7 66.1 1.0
OD1 A:ASP498 3.1 44.1 1.0
N A:GLY444 3.2 54.9 1.0
O A:GLY444 3.3 54.7 1.0
CG A:GLU478 3.4 48.9 1.0
O A:HOH840 3.4 55.0 1.0
CG A:ASP443 3.8 70.6 1.0
CA A:ASP443 3.9 39.3 1.0
CG A:ASP498 4.0 46.2 1.0
O A:HOH756 4.0 38.6 1.0
CA A:GLY444 4.0 48.2 1.0
C A:ASP443 4.0 44.0 1.0
C A:GLY444 4.1 56.6 1.0
OD2 A:ASP498 4.1 47.5 1.0
CD A:GLU478 4.3 61.4 1.0
CB A:GLU478 4.3 42.0 1.0
CB A:ASP443 4.4 56.1 1.0
CA A:GLU478 4.5 39.3 1.0
OD2 A:ASP443 4.6 75.5 1.0
OE2 A:GLU478 4.7 65.4 1.0
CB A:SER499 4.8 31.4 1.0
N A:SER499 4.9 27.5 1.0
OE1 A:GLU478 5.0 53.8 1.0

Magnesium binding site 3 out of 4 in 4dg1

Go back to Magnesium Binding Sites List in 4dg1
Magnesium binding site 3 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A


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 Polymorphism Mutation K172A and K173A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:67.0
occ:1.00
 OE1 A:GLU233 2.3 50.9 1.0
CE1 A:HIS235 2.7 49.6 1.0
O A:HOH812 2.9 54.0 1.0
NE2 A:HIS235 2.9 52.5 1.0
CD A:GLU233 3.1 53.9 1.0
CB A:GLU233 3.4 43.3 1.0
CB A:PRO226 3.5 60.1 1.0
CG A:PRO226 3.6 63.4 1.0
OE2 A:GLU233 3.8 66.3 1.0
CG A:GLU233 3.8 37.8 1.0
ND1 A:HIS235 4.0 51.0 1.0
CD2 A:HIS235 4.2 53.5 1.0
NE2 A:GLN242 4.2 62.8 1.0
CB A:THR240 4.3 45.1 1.0
CD A:PRO226 4.3 59.3 1.0
CG2 A:THR240 4.7 51.5 1.0
OG1 A:THR240 4.7 45.1 1.0
CA A:GLU233 4.8 41.1 1.0
CG A:HIS235 4.8 44.6 1.0
O A:GLU233 4.8 42.5 1.0
CA A:PRO226 4.9 58.3 1.0

Magnesium binding site 4 out of 4 in 4dg1

Go back to Magnesium Binding Sites List in 4dg1
Magnesium binding site 4 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) with Polymorphism Mutation K172A and K173A


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 Polymorphism Mutation K172A and K173A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:29.2
occ:0.82
 OE1 B:GLN23 2.6 24.9 1.0
N B:THR131 2.8 25.9 1.0
O B:THR58 3.0 28.0 1.0
O B:THR131 3.0 32.0 1.0
ND2 B:ASN57 3.0 24.1 1.0
OD1 B:ASN57 3.3 31.7 1.0
CA B:THR131 3.5 28.1 1.0
CB B:THR131 3.5 32.2 1.0
CD B:GLN23 3.6 29.1 1.0
CG B:ASN57 3.6 31.0 1.0
CB B:GLN23 3.6 28.9 1.0
C B:THR131 3.7 27.1 1.0
CA B:PRO59 3.8 26.8 1.0
OG1 B:THR131 3.8 32.7 1.0
C B:THR58 3.8 28.9 1.0
C B:PHE130 3.8 26.8 1.0
CG B:GLN23 3.9 22.6 1.0
CA B:PHE130 3.9 22.8 1.0
N B:VAL60 4.0 26.1 1.0
N B:PRO59 4.1 20.3 1.0
CB B:PHE130 4.1 24.5 1.0
C B:PRO59 4.2 30.0 1.0
CA B:GLN23 4.3 28.1 1.0
CG2 B:VAL60 4.4 23.9 1.0
CG1 B:VAL60 4.5 40.0 1.0
N B:THR58 4.7 26.9 1.0
NE2 B:GLN23 4.8 25.6 1.0
CB B:VAL60 4.9 23.8 1.0
N B:GLN23 4.9 34.1 1.0
CG2 B:THR131 4.9 37.2 1.0
O B:PHE130 4.9 29.0 1.0
CA B:THR58 5.0 30.1 1.0

Reference:

A.Hachiya, B.Marchand, K.A.Kirby, E.Michailidis, X.Tu, K.Palczewski, Y.T.Ong, Z.Li, D.T.Griffin, M.M.Schuckmann, J.Tanuma, S.Oka, K.Singh, E.N.Kodama, S.G.Sarafianos. Hiv-1 Reverse Transcriptase (Rt) Polymorphism 172K Suppresses the Effect of Clinically Relevant Drug Resistance Mutations to Both Nucleoside and Non-Nucleoside Rt Inhibitors. J.Biol.Chem. V. 287 29988 2012.
ISSN: ISSN 0021-9258
PubMed: 22761416
DOI: 10.1074/JBC.M112.351551
Page generated: Thu Aug 15 17:07:43 2024

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