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Magnesium in PDB 3oyl: Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048

Protein crystallography data

The structure of Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048, PDB code: 3oyl was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.09 / 2.54
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.700, 159.700, 123.510, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 22.7

Other elements in 3oyl:

The structure of Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048 (pdb code 3oyl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048, PDB code: 3oyl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3oyl

Go back to Magnesium Binding Sites List in 3oyl
Magnesium binding site 1 out of 3 in the Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048


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 the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:42.5
occ:1.00
O D:HOH325 2.0 46.1 1.0
OAG A:ZZX398 2.0 52.3 1.0
OD1 A:ASP128 2.1 45.3 1.0
OD1 A:ASP185 2.2 48.4 1.0
OAE A:ZZX398 2.2 49.4 1.0
O A:HOH399 2.3 40.5 1.0
CAW A:ZZX398 2.9 54.1 1.0
CAS A:ZZX398 3.0 53.7 1.0
CG A:ASP128 3.0 44.1 1.0
CAY A:ZZX398 3.2 54.3 1.0
OD2 A:ASP128 3.3 44.9 1.0
CG A:ASP185 3.3 47.7 1.0
MG A:MG397 3.7 48.8 1.0
O A:HOH533 3.7 65.2 1.0
OD2 A:ASP185 3.8 48.1 1.0
N6 D:DA17 3.9 95.1 1.0
O D:HOH26 4.1 41.5 1.0
O A:HOH431 4.1 40.1 1.0
O A:TYR129 4.2 43.5 1.0
CBA A:ZZX398 4.3 53.9 1.0
N A:TYR129 4.3 44.0 1.0
NBD A:ZZX398 4.3 55.2 1.0
CB A:ASP128 4.4 42.6 1.0
OE2 A:GLU221 4.4 44.5 1.0
O D:HOH322 4.5 42.7 1.0
CB A:ASP185 4.6 47.7 1.0
NBF A:ZZX398 4.6 54.8 1.0
N7 D:DA17 4.7 93.5 1.0
CA A:ASP128 4.8 43.4 1.0
C6 D:DA17 4.8 95.2 1.0
O D:HOH289 4.8 48.5 1.0
CAM A:ZZX398 4.9 54.6 1.0
OAF A:ZZX398 5.0 51.0 1.0

Magnesium binding site 2 out of 3 in 3oyl

Go back to Magnesium Binding Sites List in 3oyl
Magnesium binding site 2 out of 3 in the Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048


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 the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg397

b:48.8
occ:1.00
OAF A:ZZX398 2.0 51.0 1.0
OE2 A:GLU221 2.1 44.5 1.0
OE1 A:GLU221 2.1 45.2 1.0
OD2 A:ASP128 2.1 44.9 1.0
OAG A:ZZX398 2.2 52.3 1.0
O D:HOH26 2.3 41.5 1.0
CD A:GLU221 2.4 43.4 1.0
CAZ A:ZZX398 2.9 52.6 1.0
CAW A:ZZX398 3.1 54.1 1.0
CBA A:ZZX398 3.2 53.9 1.0
CG A:ASP128 3.3 44.1 1.0
MG A:MG396 3.7 42.5 1.0
ND2 A:ASN224 3.8 41.6 1.0
OD1 A:ASP128 3.8 45.3 1.0
O A:HOH533 3.9 65.2 1.0
CG A:GLU221 3.9 41.5 1.0
NBE A:ZZX398 4.2 52.1 1.0
OP1 D:DA17 4.3 55.8 1.0
O D:HOH325 4.4 46.1 1.0
O A:TYR129 4.4 43.5 1.0
CAY A:ZZX398 4.4 54.3 1.0
N7 D:DA17 4.5 93.5 1.0
CB A:ASP128 4.5 42.6 1.0
CBB A:ZZX398 4.6 54.6 1.0
CAN A:ZZX398 4.7 47.1 1.0
O3' D:DC16 4.7 49.4 1.0
CB A:GLU221 4.8 41.0 1.0
C8 D:DA17 4.8 93.2 1.0
OD1 A:ASP185 4.9 48.4 1.0
CB A:PRO214 4.9 42.8 1.0
C2' D:DC16 4.9 43.1 1.0
CA A:GLU221 5.0 41.0 1.0

Magnesium binding site 3 out of 3 in 3oyl

Go back to Magnesium Binding Sites List in 3oyl
Magnesium binding site 3 out of 3 in the Crystal Structure of the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048


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 the Pfv S217H Mutant Intasome Bound to Magnesium and the Insti MK2048 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg394

b:88.2
occ:1.00
O B:HOH429 2.1 63.5 1.0
O B:HOH395 2.2 54.3 1.0
OD1 B:ASP185 2.2 53.4 1.0
OD1 B:ASP128 2.3 60.0 1.0
CG B:ASP185 3.3 52.1 1.0
CG B:ASP128 3.3 58.2 1.0
OD2 B:ASP128 3.6 61.5 1.0
OD2 B:ASP185 3.6 53.7 1.0
O B:HOH406 3.9 42.8 1.0
O B:TYR129 4.5 57.9 1.0
N B:TYR129 4.5 55.7 1.0
CB B:ASP185 4.6 50.7 1.0
CB B:ASP128 4.7 56.0 1.0
CA B:ASP128 5.0 55.1 1.0

Reference:

S.Hare, A.M.Vos, R.F.Clayton, J.W.Thuring, M.D.Cummings, P.Cherepanov. Molecular Mechanisms of Retroviral Integrase Inhibition and the Evolution of Viral Resistance. Proc.Natl.Acad.Sci.Usa V. 107 20057 2010.
ISSN: ISSN 0027-8424
PubMed: 21030679
DOI: 10.1073/PNAS.1010246107
Page generated: Mon Dec 14 08:38:13 2020

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