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Magnesium in PDB 3n78: Sgrai Bound to Secondary Site Dna and Mg(II)

Enzymatic activity of Sgrai Bound to Secondary Site Dna and Mg(II)

All present enzymatic activity of Sgrai Bound to Secondary Site Dna and Mg(II):
3.1.21.4;

Protein crystallography data

The structure of Sgrai Bound to Secondary Site Dna and Mg(II), PDB code: 3n78 was solved by N.C.Horton, E.J.Little, P.W.Dunten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.35 / 2.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.794, 133.002, 64.623, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sgrai Bound to Secondary Site Dna and Mg(II) (pdb code 3n78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sgrai Bound to Secondary Site Dna and Mg(II), PDB code: 3n78:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3n78

Go back to Magnesium Binding Sites List in 3n78
Magnesium binding site 1 out of 2 in the Sgrai Bound to Secondary Site Dna and Mg(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sgrai Bound to Secondary Site Dna and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:19.6
occ:1.00
OD2 A:ASP188 2.1 11.7 1.0
O A:PHE241 2.1 24.8 1.0
OP1 C:DC8 2.1 27.8 0.5
OP1 D:DC8 2.1 27.8 0.5
O A:HOH367 3.0 11.8 1.0
CG A:ASP188 3.1 14.4 1.0
O A:HOH344 3.1 11.9 1.0
C A:PHE241 3.2 16.9 1.0
OD1 A:ASP188 3.4 16.7 1.0
P C:DC8 3.4 20.4 0.5
P D:DC8 3.4 20.4 0.5
N A:PHE241 3.6 16.0 1.0
C5' C:DC8 3.7 14.9 0.5
C5' D:DC8 3.7 14.9 0.5
CA A:PHE241 3.9 12.5 1.0
OP2 C:DC8 3.9 22.7 0.5
OP2 D:DC8 3.9 22.7 0.5
CG A:LYS242 4.0 12.9 1.0
O5' C:DC8 4.1 16.9 0.5
O5' D:DC8 4.1 16.9 0.5
OP2 C:DC9 4.1 13.0 0.5
OP2 D:DC9 4.1 13.0 0.5
NZ A:LYS242 4.2 16.4 1.0
N A:LYS242 4.3 15.1 1.0
CB A:PHE241 4.4 11.8 1.0
CE A:LYS242 4.4 12.8 1.0
CB A:ASP188 4.5 11.8 1.0
O3' C:DA7 4.5 21.8 0.5
O3' D:DC7 4.5 21.8 0.5
C A:ALA240 4.6 16.0 1.0
CA A:LYS242 4.7 14.6 1.0
OE1 A:GLU103 4.8 30.9 1.0
CD A:LYS242 4.9 13.0 1.0
CA A:ALA240 4.9 12.9 1.0
CB A:ALA240 4.9 11.8 1.0
CB A:LYS242 4.9 11.9 1.0

Magnesium binding site 2 out of 2 in 3n78

Go back to Magnesium Binding Sites List in 3n78
Magnesium binding site 2 out of 2 in the Sgrai Bound to Secondary Site Dna and Mg(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sgrai Bound to Secondary Site Dna and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:25.0
occ:1.00
OD2 B:ASP188 2.1 27.8 1.0
OP1 C:DC8 2.1 40.9 0.5
OP1 D:DC8 2.1 40.9 0.5
O B:PHE241 2.1 41.5 1.0
CG B:ASP188 3.1 25.5 1.0
C B:PHE241 3.1 24.3 1.0
P C:DC8 3.4 24.0 0.5
P D:DC8 3.4 24.0 0.5
OD1 B:ASP188 3.4 27.5 1.0
N B:PHE241 3.7 17.8 1.0
C5' C:DC8 3.8 20.1 0.5
C5' D:DC8 3.8 20.1 0.5
O5' C:DC8 3.9 13.7 0.5
O5' D:DC8 3.9 13.7 0.5
CA B:PHE241 3.9 17.2 1.0
CG B:LYS242 3.9 12.7 1.0
OP2 C:DC8 4.0 31.2 0.5
OP2 D:DC8 4.0 31.2 0.5
OP2 C:DC9 4.0 9.0 0.5
OP2 D:DC9 4.0 9.0 0.5
N B:LYS242 4.1 11.6 1.0
CA B:LYS242 4.4 15.8 1.0
C B:ALA240 4.4 18.9 1.0
CB B:ASP188 4.5 18.2 1.0
CB B:PHE241 4.5 18.6 1.0
O3' D:DC7 4.5 30.9 0.5
O3' C:DA7 4.6 31.2 0.5
CB B:LYS242 4.7 15.7 1.0
NZ B:LYS242 4.8 21.8 1.0
OE1 B:GLU103 4.8 37.1 1.0
CB B:ALA240 4.9 22.7 1.0
CA B:ALA240 4.9 18.4 1.0
P C:DC9 4.9 13.8 0.5
P D:DC9 4.9 13.8 0.5
CD B:LYS242 4.9 15.1 1.0
O C:HOH24 4.9 10.1 1.0
CE B:LYS242 5.0 18.6 1.0

Reference:

E.J.Little, P.W.Dunten, J.Bitinaite, N.C.Horton. New Clues in the Allosteric Activation of Dna Cleavage By Sgrai: Structures of Sgrai Bound to Cleaved Primary-Site Dna and Uncleaved Secondary-Site Dna. Acta Crystallogr.,Sect.D V. 67 67 2011.
ISSN: ISSN 0907-4449
PubMed: 21206063
DOI: 10.1107/S0907444910047785
Page generated: Mon Dec 14 08:27:46 2020

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