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Magnesium in PDB 5cz2: Crystal Structure of A Two-Domain Fragment of Mmtv Integrase

Enzymatic activity of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase

All present enzymatic activity of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase, PDB code: 5cz2 was solved by N.Cook, A.Ballandras-Colas, A.Engelman, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.57 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.370, 83.150, 141.140, 90.00, 90.19, 90.00
R / Rfree (%) 24.1 / 28

Other elements in 5cz2:

The structure of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase (pdb code 5cz2). 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 A Two-Domain Fragment of Mmtv Integrase, PDB code: 5cz2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 1 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:53.0
occ:1.00
 OD1 A:ASP65 2.1 66.7 1.0
OD2 A:ASP122 2.1 92.3 1.0
CG A:ASP65 3.0 67.7 1.0
CG A:ASP122 3.1 91.5 1.0
OD2 A:ASP65 3.3 71.9 1.0
OD1 A:ASP122 3.4 91.1 1.0
N A:VAL66 4.0 59.4 1.0
O A:VAL66 4.2 65.6 1.0
CB A:ASP65 4.3 65.9 1.0
CE1 A:TYR127 4.4 58.6 1.0
CB A:ASP122 4.4 91.2 1.0
CA A:ASP65 4.5 63.1 1.0
CB A:ALA124 4.6 0.9 1.0
CB A:VAL66 4.8 44.4 1.0
C A:ASP65 4.8 58.6 1.0
CA A:VAL66 4.8 50.5 1.0
C A:VAL66 4.9 57.2 1.0

Magnesium binding site 2 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 2 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:52.6
occ:1.00
 OD1 B:ASP65 2.1 85.7 1.0
OD2 B:ASP122 2.1 60.0 1.0
OD2 B:ASP65 2.1 82.8 1.0
CG B:ASP65 2.4 80.8 1.0
CG B:ASP122 3.3 62.1 1.0
CB B:ASP65 3.9 70.6 1.0
O B:VAL66 4.0 45.6 1.0
OD1 B:ASP122 4.1 60.9 1.0
CB B:ASP122 4.3 60.8 1.0
N B:VAL66 4.4 50.1 1.0
CA B:ASP65 4.6 59.0 1.0
C B:ASP65 4.9 56.4 1.0

Magnesium binding site 3 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 3 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:65.6
occ:1.00
 OD1 C:ASP65 2.1 78.1 1.0
OD2 C:ASP122 2.1 75.1 1.0
OD2 C:ASP65 2.1 79.7 1.0
CG C:ASP65 2.4 74.5 1.0
CG C:ASP122 3.3 81.4 1.0
CB C:ASP65 3.9 63.0 1.0
O C:VAL66 3.9 75.3 1.0
OD1 C:ASP122 4.0 90.5 1.0
N C:VAL66 4.3 52.3 1.0
CB C:ASP122 4.4 79.7 1.0
CA C:ASP65 4.6 52.4 1.0
C C:ASP65 4.9 48.6 1.0
C C:VAL66 4.9 65.6 1.0

Magnesium binding site 4 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 4 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:81.2
occ:1.00
 OD1 D:ASP65 2.1 0.9 1.0
OD2 D:ASP122 2.1 0.9 1.0
OD2 D:ASP65 2.1 0.2 1.0
CG D:ASP65 2.4 96.9 1.0
CG D:ASP122 3.3 0.8 1.0
CB D:ASP65 3.9 86.2 1.0
OD1 D:ASP122 4.1 0.9 1.0
O D:VAL66 4.2 70.8 1.0
CB D:ASP122 4.2 0.6 1.0
N D:VAL66 4.6 73.4 1.0
CA D:ASP65 4.7 76.9 1.0
OE2 D:GLU158 4.7 0.7 1.0

Magnesium binding site 5 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 5 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:46.7
occ:1.00
 OD1 E:ASP65 2.0 50.0 1.0
OD2 E:ASP122 2.1 90.5 1.0
OD2 E:ASP65 2.1 57.2 1.0
CG E:ASP65 2.4 50.0 1.0
CG E:ASP122 3.3 89.8 1.0
CB E:ASP65 3.9 48.5 1.0
O E:VAL66 3.9 72.2 1.0
OD1 E:ASP122 4.0 92.1 1.0
N E:VAL66 4.2 61.0 1.0
CB E:ASP122 4.4 85.7 1.0
CA E:ASP65 4.6 52.4 1.0
C E:ASP65 4.8 57.5 1.0
C E:VAL66 4.8 70.1 1.0

Magnesium binding site 6 out of 6 in 5cz2

Go back to Magnesium Binding Sites List in 5cz2
Magnesium binding site 6 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:53.5
occ:1.00
 OD2 F:ASP122 2.1 93.8 1.0
OD1 F:ASP65 2.1 95.1 1.0
CG F:ASP65 2.9 91.4 1.0
OD2 F:ASP65 3.1 94.3 1.0
CG F:ASP122 3.1 95.4 1.0
OD1 F:ASP122 3.6 97.3 1.0
N F:VAL66 4.1 76.8 1.0
O F:VAL66 4.2 71.2 1.0
CB F:ASP65 4.3 80.4 1.0
CB F:ASP122 4.4 95.3 1.0
CA F:ASP65 4.6 74.0 1.0
CE1 F:TYR127 4.7 0.1 1.0
CB F:ALA124 4.7 83.8 1.0
C F:ASP65 4.9 70.7 1.0
CA F:VAL66 4.9 75.9 1.0
CB F:VAL66 5.0 76.9 1.0
C F:VAL66 5.0 73.9 1.0

Reference:

A.Ballandras-Colas, M.Brown, N.J.Cook, T.G.Dewdney, B.Demeler, P.Cherepanov, D.Lyumkis, A.N.Engelman. Cryo-Em Reveals A Novel Octameric Integrase Structure For Betaretroviral Intasome Function. Nature V. 530 358 2016.
ISSN: ESSN 1476-4687
PubMed: 26887496
DOI: 10.1038/NATURE16955
Page generated: Sun Sep 29 02:20:09 2024

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