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Magnesium in PDB 5a78: Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved

Protein crystallography data

The structure of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved, PDB code: 5a78 was solved by R.Molina, P.Redondo, B.Lopezmendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.539 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.573, 95.079, 52.145, 90.00, 103.71, 90.00
R / Rfree (%) 21.51 / 28.02

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved (pdb code 5a78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved, PDB code: 5a78:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5a78

Go back to Magnesium Binding Sites List in 5a78
Magnesium binding site 1 out of 2 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved


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 Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1164

b:51.1
occ:1.00
OP1 C:DC514 2.1 46.2 1.0
O B:ALA22 2.3 42.3 1.0
OD2 A:ASP23 2.5 45.7 1.0
O A:HOH2009 2.6 30.0 1.0
OP1 D:DG615 2.9 58.4 1.0
C B:ALA22 3.3 38.7 1.0
O B:HOH2001 3.4 30.0 1.0
P C:DC514 3.5 47.2 1.0
CG A:ASP23 3.7 49.4 1.0
CA B:ALA22 3.8 39.6 1.0
O3' C:DA513 4.0 42.2 1.0
NE2 A:GLN50 4.1 52.2 1.0
P D:DG615 4.2 69.7 1.0
C5' C:DC514 4.2 39.7 1.0
OD1 A:ASP23 4.3 50.5 1.0
OD1 B:ASP23 4.3 50.0 1.0
O5' C:DC514 4.4 47.9 1.0
OE1 A:GLN50 4.4 47.6 1.0
CB B:ALA22 4.5 39.7 1.0
N B:ASP23 4.5 38.7 1.0
CD A:GLN50 4.5 46.2 1.0
OP2 D:DG615 4.6 54.2 1.0
OP2 C:DC514 4.6 42.2 1.0
O B:ASP21 4.7 42.9 1.0
CB A:ASP23 4.8 39.1 1.0
C4' C:DC514 4.8 43.0 1.0
CA B:ASP23 4.9 46.6 1.0
C5' D:DG615 4.9 49.1 1.0
O5' D:DG615 4.9 54.1 1.0

Magnesium binding site 2 out of 2 in 5a78

Go back to Magnesium Binding Sites List in 5a78
Magnesium binding site 2 out of 2 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved


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 Homing Endonuclease I-Cvui in Complex with I-Crei Target (C1221) in the Presence of 2 Mm Mg Revealing Dna Not Cleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1625

b:53.3
occ:1.00
OP1 D:DC614 2.2 42.9 1.0
O A:ALA22 2.2 41.6 1.0
OD2 B:ASP23 2.9 49.0 1.0
OD1 A:ASP23 3.2 50.5 1.0
OP2 C:DG515 3.2 48.6 1.0
O A:HOH2003 3.3 30.0 1.0
O A:HOH2002 3.3 30.0 1.0
C A:ALA22 3.3 36.5 1.0
P D:DC614 3.5 49.8 1.0
CG B:ASP23 3.7 50.9 1.0
OD1 B:ASP23 3.8 50.0 1.0
OP1 C:DG515 3.8 54.5 1.0
C5' D:DC614 3.9 44.7 1.0
O3' D:DA613 3.9 49.1 1.0
P C:DG515 3.9 58.9 1.0
CA A:ALA22 4.2 35.0 1.0
O5' D:DC614 4.2 51.8 1.0
N A:ASP23 4.2 33.8 1.0
CA A:ASP23 4.3 39.0 1.0
CG A:ASP23 4.3 49.4 1.0
C4' D:DC614 4.4 47.9 1.0
NE2 B:GLN50 4.6 49.6 1.0
C5' C:DG515 4.7 44.3 1.0
OP2 D:DC614 4.7 47.2 1.0
O5' C:DG515 4.8 50.2 1.0
CB A:ALA22 4.9 38.6 1.0
CB A:ASP23 4.9 39.1 1.0

Reference:

R.Molina, P.Redondo, B.Lopez-Mendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya. Crystal Structure of the Homing Endonuclease I-Cvui Provides A New Template For Genome Modification J.Biol.Chem. V. 290 28727 2015.
ISSN: ISSN 0021-9258
PubMed: 26363068
DOI: 10.1074/JBC.M115.678342
Page generated: Mon Dec 14 19:59:40 2020

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