Atomistry » Magnesium » PDB 5cr0-5d2h » 5cz2
Atomistry »
  Magnesium »
    PDB 5cr0-5d2h »
      5cz2 »

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: Mon Dec 14 20:08:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy