Magnesium in PDB 6fb5: Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium

Protein crystallography data

The structure of Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium, PDB code: 6fb5 was solved by R.Molina, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.73 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.290, 68.005, 83.030, 90.00, 96.55, 90.00
R / Rfree (%) 18.9 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium (pdb code 6fb5). 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 A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium, PDB code: 6fb5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fb5

Go back to Magnesium Binding Sites List in 6fb5
Magnesium binding site 1 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium


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 Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:9.9
occ:1.00
 O F:HOH710 2.0 26.0 1.0
O A:HOH309 2.0 18.5 1.0
OD2 A:ASP20 2.1 19.0 1.0
O B:GLY19 2.2 16.4 1.0
OP2 F:DA615 2.3 24.1 1.0
OP1 D:DC514 2.3 24.1 1.0
OD1 A:ASP20 2.5 11.7 1.0
CG A:ASP20 2.6 13.9 1.0
C B:GLY19 3.2 22.1 1.0
O B:HOH301 3.4 30.0 1.0
P F:DA615 3.6 24.2 1.0
P D:DC514 3.7 20.3 1.0
CA B:GLY19 3.7 20.3 1.0
O3' D:DA513 4.1 17.9 1.0
CB A:ASP20 4.1 13.2 1.0
O5' F:DA615 4.2 25.6 1.0
NE2 A:GLN47 4.2 16.5 1.0
C5' F:DA615 4.3 26.0 1.0
N B:ASP20 4.4 19.9 1.0
OP1 F:DA615 4.4 24.5 1.0
O B:ASP18 4.4 21.2 1.0
C5' D:DC514 4.4 16.5 1.0
OE1 A:GLN47 4.4 19.4 1.0
C4' D:DC514 4.4 17.0 1.0
O5' D:DC514 4.6 15.5 1.0
OD1 B:ASP20 4.6 16.1 1.0
O3' F:DG614 4.7 21.0 1.0
CD A:GLN47 4.7 20.7 1.0
OP2 D:DC514 4.7 19.1 1.0
CA B:ASP20 4.8 19.3 1.0
N B:GLY19 4.8 19.4 1.0
O3' D:DC514 4.8 16.8 1.0

Magnesium binding site 2 out of 4 in 6fb5

Go back to Magnesium Binding Sites List in 6fb5
Magnesium binding site 2 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium


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 Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:30.0
occ:1.00
 O A:HOH310 2.4 27.5 1.0
O A:HOH313 2.4 35.4 1.0
O A:ASN136 2.4 21.8 1.0
O A:HOH332 2.4 41.4 1.0
O A:ALA134 2.4 36.8 1.0
O B:HOH317 3.0 43.5 1.0
C A:ALA134 3.5 33.1 1.0
C A:ASN136 3.5 25.5 1.0
O A:LEU135 4.0 27.4 1.0
C A:LEU135 4.0 25.9 1.0
O A:ALA133 4.2 29.2 1.0
CA A:ASP137 4.3 22.9 1.0
CA A:ALA134 4.3 32.0 1.0
N A:ASN136 4.3 24.7 1.0
N A:ASP137 4.3 27.9 1.0
N A:LEU135 4.4 27.8 1.0
OD1 A:ASP137 4.4 24.2 1.0
CA A:LEU135 4.5 27.3 1.0
CA A:ASN136 4.5 23.4 1.0
NE2 B:GLN50 4.6 61.6 1.0
N A:SER138 4.6 20.7 1.0
OE1 B:GLN50 4.9 64.0 1.0
C A:ASP137 5.0 23.5 1.0

Magnesium binding site 3 out of 4 in 6fb5

Go back to Magnesium Binding Sites List in 6fb5
Magnesium binding site 3 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium


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 Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:30.0
occ:1.00
 O B:ALA134 2.3 30.6 1.0
O B:HOH318 2.3 28.3 1.0
O B:HOH343 2.3 52.1 1.0
O B:HOH341 2.4 38.1 1.0
O B:HOH315 2.4 29.5 1.0
O B:ASN136 2.4 36.6 1.0
C B:ALA134 3.4 30.5 1.0
C B:ASN136 3.6 33.2 1.0
O B:LEU135 4.1 28.2 1.0
C B:LEU135 4.1 30.2 1.0
O B:HOH308 4.2 43.9 1.0
CA B:ALA134 4.2 36.7 1.0
O B:ALA133 4.3 37.6 1.0
CA B:ASP137 4.3 29.4 1.0
N B:LEU135 4.4 31.2 1.0
N B:ASN136 4.4 32.2 1.0
N B:ASP137 4.4 29.2 1.0
OD1 B:ASP137 4.5 33.4 1.0
CA B:LEU135 4.6 34.4 1.0
N B:SER138 4.6 29.3 1.0
CA B:ASN136 4.7 30.0 1.0
NE2 A:GLN50 4.8 50.7 1.0

Magnesium binding site 4 out of 4 in 6fb5

Go back to Magnesium Binding Sites List in 6fb5
Magnesium binding site 4 out of 4 in the Crystal Structure of A Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium


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 Tailored I-Crei Homing Endonuclease Protein (3115 Variant) in Complex with An Altered Version of Its Target Dna (Haemoglobin Beta Subunit Gene) at 5NNN Region in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:8.9
occ:1.00
 O B:HOH314 2.0 16.3 1.0
O D:HOH704 2.1 27.6 1.0
OD2 B:ASP20 2.1 15.8 1.0
O A:SER19 2.2 19.7 1.0
OP1 F:DG614 2.2 14.6 1.0
OP2 D:DA515 2.3 18.6 1.0
OD1 B:ASP20 2.5 16.1 1.0
CG B:ASP20 2.6 17.5 1.0
C A:SER19 3.2 21.6 1.0
O B:HOH301 3.5 30.0 1.0
O D:HOH709 3.6 60.7 1.0
P D:DA515 3.6 21.3 1.0
P F:DG614 3.6 19.8 1.0
CA A:SER19 3.7 25.4 1.0
O1 D:PGO601 4.0 41.3 1.0
O3' F:DG613 4.1 14.0 1.0
CB B:ASP20 4.1 15.5 1.0
NE2 B:GLN47 4.1 10.9 1.0
O5' D:DA515 4.2 18.9 1.0
O A:ASP18 4.3 18.3 1.0
OP1 D:DA515 4.3 19.2 1.0
C5' D:DA515 4.3 19.7 1.0
C5' F:DG614 4.3 11.1 1.0
C4' F:DG614 4.3 21.4 1.0
N A:ASP20 4.4 15.4 1.0
OE1 B:GLN47 4.5 17.1 1.0
O5' F:DG614 4.5 11.5 1.0
C1 D:PGO601 4.5 41.8 1.0
CB A:SER19 4.5 38.4 1.0
OP2 F:DG614 4.6 17.4 1.0
CD B:GLN47 4.7 18.9 1.0
OD1 A:ASP20 4.7 11.7 1.0
O3' D:DC514 4.8 16.8 1.0
N A:SER19 4.8 19.3 1.0
CA A:ASP20 4.9 17.8 1.0
O3' F:DG614 4.9 21.0 1.0
C3' F:DG614 5.0 22.7 1.0

Reference:

J.Prieto, P.Redondo, B.Lopez-Mendez, M.D'abramo, N.Merino, F.J.Blanco, P.Duchateau, G.Montoya, R.Molina. Understanding the Indirect Dna Read-Out Specificity of I-Crei Meganuclease. Sci Rep V. 8 10286 2018.
ISSN: ESSN 2045-2322
PubMed: 29980759
DOI: 10.1038/S41598-018-28599-0
Page generated: Mon Dec 14 22:40:53 2020

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