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Magnesium in PDB 2flc: Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions

Enzymatic activity of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions

All present enzymatic activity of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions:
3.1.21.4;

Protein crystallography data

The structure of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions, PDB code: 2flc was solved by J.R.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.10 / 2.59
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.387, 100.387, 139.369, 90.00, 90.00, 120.00
R / Rfree (%) 27.5 / 32.4

Other elements in 2flc:

The structure of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions (pdb code 2flc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions, PDB code: 2flc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2flc

Go back to Magnesium Binding Sites List in 2flc
Magnesium binding site 1 out of 2 in the Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2

b:68.0
occ:1.00
O3' C:DG4 2.0 64.8 1.0
OD1 A:ASP62 2.2 62.6 1.0
O A:HOH250 2.3 80.4 1.0
O5' D:DC5 2.6 66.8 1.0
OP2 D:DC5 2.7 66.2 1.0
C3' C:DG4 2.9 64.2 1.0
P D:DC5 2.9 68.0 1.0
OP1 D:DC5 2.9 69.0 1.0
CG A:ASP62 3.0 62.7 1.0
OD2 A:ASP62 3.2 62.2 1.0
OE2 A:GLU18 3.2 87.9 1.0
MG A:MG248 3.6 58.5 1.0
C2' C:DG4 3.7 63.6 1.0
C5' D:DC5 4.0 65.8 1.0
C4' C:DG4 4.1 64.0 1.0
CD A:GLU18 4.2 86.7 1.0
OP3 D:DC5 4.3 68.4 1.0
CB A:ASP62 4.4 63.0 1.0
OE1 A:GLU18 4.4 88.0 1.0
OE1 A:GLN81 4.6 47.1 1.0
C1' C:DG4 4.6 62.5 1.0
C4' D:DC5 4.7 65.9 1.0
NE2 A:GLN81 4.9 49.6 1.0
O A:TYR59 4.9 60.3 1.0

Magnesium binding site 2 out of 2 in 2flc

Go back to Magnesium Binding Sites List in 2flc
Magnesium binding site 2 out of 2 in the Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Reactive Complex of Restriction Endonuclease HINP1I with Nicked Cognate Dna and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg248

b:58.5
occ:1.00
OP1 D:DC5 1.9 69.0 1.0
OE1 A:GLN81 1.9 47.1 1.0
O A:VAL82 2.0 60.6 1.0
OD2 A:ASP62 2.1 62.2 1.0
CD A:GLN81 2.8 48.3 1.0
P D:DC5 2.9 68.0 1.0
C A:VAL82 3.1 59.5 1.0
OP2 D:DC5 3.1 66.2 1.0
N A:VAL82 3.2 55.5 1.0
CG A:ASP62 3.3 62.7 1.0
CE A:LYS83 3.4 64.8 1.0
NE2 A:GLN81 3.4 49.6 1.0
MG D:MG2 3.6 68.0 1.0
CA A:VAL82 3.6 57.1 1.0
OP3 D:DC5 3.8 68.4 1.0
OD1 A:ASP62 3.8 62.6 1.0
CG A:GLN81 3.9 47.5 1.0
NZ A:LYS83 3.9 63.8 1.0
O A:HOH250 4.0 80.4 1.0
OE2 A:GLU18 4.0 87.9 1.0
O5' D:DC5 4.2 66.8 1.0
N A:LYS83 4.2 62.1 1.0
C A:GLN81 4.2 53.4 1.0
CB A:VAL82 4.4 56.8 1.0
CB A:ASP62 4.4 63.0 1.0
OP2 D:DG6 4.5 70.7 1.0
CD A:LYS83 4.6 63.9 1.0
CA A:LYS83 4.6 65.0 1.0
CA A:GLN81 4.6 51.5 1.0
CG A:LYS83 4.7 65.0 1.0
CB A:GLN81 4.8 49.7 1.0
CD A:GLU18 4.9 86.7 1.0
OP1 D:DG6 5.0 71.2 1.0

Reference:

J.R.Horton, X.Zhang, R.Maunus, Z.Yang, G.G.Wilson, R.J.Roberts, X.Cheng. Dna Nicking By HINP1I Endonuclease: Bending, Base Flipping and Minor Groove Expansion. Nucleic Acids Res. V. 34 939 2006.
ISSN: ISSN 0305-1048
PubMed: 16473850
DOI: 10.1093/NAR/GKJ484
Page generated: Mon Dec 14 07:23:07 2020

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