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Magnesium in PDB 3mqy: Sgrai with Cleaved Dna and Magnesium Bound

Enzymatic activity of Sgrai with Cleaved Dna and Magnesium Bound

All present enzymatic activity of Sgrai with Cleaved Dna and Magnesium Bound:
3.1.21.4;

Protein crystallography data

The structure of Sgrai with Cleaved Dna and Magnesium Bound, PDB code: 3mqy was solved by P.W.Dunten, N.C.Horton, E.J.Little, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.163, 119.980, 69.857, 90.00, 102.68, 90.00
R / Rfree (%) 19.6 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sgrai with Cleaved Dna and Magnesium Bound (pdb code 3mqy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Sgrai with Cleaved Dna and Magnesium Bound, PDB code: 3mqy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 1 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:19.2
occ:1.00
 O A:HOH340 1.8 24.8 1.0
OP2 F:DC8 2.0 31.0 1.0
O A:PHE241 2.1 27.4 1.0
O A:HOH342 2.2 23.5 1.0
OD2 A:ASP188 2.2 33.6 1.0
O A:HOH341 2.2 18.4 1.0
CG A:ASP188 3.1 33.5 1.0
C A:PHE241 3.3 27.8 1.0
OD1 A:ASP188 3.3 41.9 1.0
P F:DC8 3.3 35.0 1.0
OP1 F:DC8 3.7 32.8 1.0
O A:HOH365 3.8 41.4 1.0
N A:PHE241 3.9 26.8 1.0
O5' F:DC8 4.0 27.0 1.0
CA A:PHE241 4.0 25.9 1.0
C5' F:DC8 4.1 28.1 1.0
OE2 A:GLU103 4.2 48.8 1.0
O F:HOH7 4.3 29.5 1.0
OP2 F:DC9 4.3 30.4 1.0
N A:LYS242 4.4 29.2 1.0
CB A:PHE241 4.4 24.9 1.0
MG F:MG502 4.4 38.9 1.0
O A:HOH397 4.4 49.7 1.0
OP3 F:DC8 4.4 37.5 1.0
CB A:ASP188 4.5 32.0 1.0
CG A:LYS242 4.6 33.4 1.0
C A:ALA240 4.8 27.3 1.0
O3' F:DC8 4.8 25.4 1.0
O A:HOH344 4.9 41.1 1.0
CA A:LYS242 4.9 29.7 1.0
CD A:GLU103 5.0 45.2 1.0

Magnesium binding site 2 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 2 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:43.1
occ:1.00
 OE1 A:GLU103 2.0 48.4 1.0
O A:LEU150 2.3 29.0 1.0
O A:ASP188 2.5 30.6 1.0
OD1 A:ASN149 2.5 35.0 1.0
O A:HOH393 2.8 38.5 1.0
CD A:GLU103 3.2 45.2 1.0
O A:HOH394 3.3 50.3 1.0
N A:LEU150 3.3 28.7 1.0
C A:LEU150 3.3 28.7 1.0
C A:ASP188 3.4 31.5 1.0
CA A:ASP188 3.6 31.4 1.0
CG A:ASN149 3.7 31.3 1.0
CA A:LEU150 3.8 29.6 1.0
CB A:ASP188 3.8 32.0 1.0
CG A:GLU103 4.0 38.3 1.0
O A:HOH397 4.0 49.7 1.0
OE2 A:GLU103 4.1 48.8 1.0
C A:ASN149 4.2 29.0 1.0
O A:HOH452 4.3 37.9 1.0
OD1 A:ASP188 4.3 41.9 1.0
CB A:LEU150 4.3 27.5 1.0
CG A:ASP188 4.5 33.5 1.0
N A:PRO151 4.5 31.0 1.0
ND2 A:ASN149 4.5 32.6 1.0
CA A:ASN149 4.5 28.2 1.0
N A:LEU189 4.6 28.6 1.0
CB A:ASN149 4.8 28.5 1.0
C A:PRO151 4.8 33.8 1.0
O A:HOH477 4.9 46.2 1.0
CA A:PRO151 4.9 33.2 1.0
O A:PRO151 4.9 34.1 1.0
MG F:MG502 4.9 38.9 1.0

Magnesium binding site 3 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 3 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:23.4
occ:1.00
 O B:HOH340 1.8 30.7 1.0
O B:HOH1 1.9 28.1 1.0
OP2 D:DC8 2.0 28.8 1.0
O B:PHE241 2.2 22.7 1.0
OD1 B:ASP188 2.4 30.6 1.0
O B:HOH341 2.4 27.1 1.0
P D:DC8 3.1 36.4 1.0
CG B:ASP188 3.3 34.8 1.0
C B:PHE241 3.4 26.8 1.0
OP1 D:DC8 3.5 38.8 1.0
O5' D:DC8 3.6 30.7 1.0
OD2 B:ASP188 3.6 39.0 1.0
C5' D:DC8 3.9 29.5 1.0
N B:PHE241 3.9 26.3 1.0
CA B:PHE241 4.2 27.1 1.0
OE1 B:GLU103 4.2 45.3 1.0
MG D:MG502 4.2 63.9 1.0
O B:HOH359 4.3 31.5 1.0
OP3 D:DC8 4.4 38.8 1.0
O B:HOH345 4.4 39.3 1.0
OP2 D:DC9 4.4 22.5 1.0
CB B:PHE241 4.4 27.7 1.0
N B:LYS242 4.4 28.9 1.0
CG B:LYS242 4.5 35.6 1.0
O3' D:DC8 4.6 19.3 1.0
CB B:ASP188 4.7 34.1 1.0
CA B:LYS242 4.7 30.8 1.0
P D:DC9 4.7 21.9 1.0
O B:HOH352 4.8 43.2 1.0
C4' D:DC8 4.9 30.9 1.0
C3' D:DC8 4.9 24.4 1.0
C B:ALA240 4.9 25.8 1.0
OP1 D:DC9 5.0 18.3 1.0

Magnesium binding site 4 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 4 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:56.5
occ:1.00
 OE2 B:GLU103 2.0 44.2 1.0
O B:LEU150 2.4 33.4 1.0
O B:ASP188 2.5 31.3 1.0
OD1 B:ASN149 2.7 36.0 1.0
O B:HOH353 2.7 44.9 1.0
O B:HOH454 3.0 42.0 1.0
CD B:GLU103 3.2 39.8 1.0
C B:ASP188 3.3 33.5 1.0
C B:LEU150 3.4 33.5 1.0
N B:LEU150 3.5 32.1 1.0
CA B:ASP188 3.5 33.0 1.0
O B:HOH455 3.6 60.5 1.0
OD2 B:ASP188 3.9 39.0 1.0
CG B:ASN149 3.9 31.4 1.0
CB B:ASP188 3.9 34.1 1.0
CA B:LEU150 3.9 32.8 1.0
OE1 B:GLU103 4.0 45.3 1.0
CG B:GLU103 4.0 37.0 1.0
C B:ASN149 4.2 31.8 1.0
CG B:ASP188 4.3 34.8 1.0
CB B:LEU150 4.4 32.3 1.0
N B:PRO151 4.6 35.1 1.0
N B:LEU189 4.6 33.6 1.0
CA B:ASN149 4.7 31.5 1.0
ND2 B:ASN149 4.7 36.5 1.0
C B:PRO151 4.8 36.4 1.0
CA B:PRO151 4.8 35.6 1.0
O B:PRO187 4.8 36.0 1.0
N B:ASP188 4.9 33.8 1.0
MG D:MG502 4.9 63.9 1.0
O B:PRO151 4.9 34.6 1.0
CB B:ASN149 4.9 31.5 1.0
O B:ASN149 5.0 33.6 1.0

Magnesium binding site 5 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 5 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:63.9
occ:1.00
 O B:HOH465 2.1 45.3 1.0
OD2 B:ASP188 2.2 39.0 1.0
O B:HOH464 2.4 48.5 1.0
OP2 D:DC8 2.5 28.8 1.0
OP3 D:DC8 2.5 38.8 1.0
O B:HOH455 2.7 60.5 1.0
O B:HOH353 2.9 44.9 1.0
P D:DC8 2.9 36.4 1.0
CG B:ASP188 3.3 34.8 1.0
OD1 B:ASP188 3.9 30.6 1.0
OP1 D:DC8 4.0 38.8 1.0
MG B:MG500 4.2 23.4 1.0
O5' D:DC8 4.3 30.7 1.0
CA B:ASP188 4.4 33.0 1.0
CB B:ASP188 4.4 34.1 1.0
OE1 B:GLU103 4.4 45.3 1.0
O B:HOH341 4.5 27.1 1.0
O B:HOH352 4.5 43.2 1.0
C5' D:DC8 4.5 29.5 1.0
O B:HOH340 4.6 30.7 1.0
O3' C:DA7 4.6 37.4 1.0
O B:ARG152 4.7 40.7 1.0
O B:PRO187 4.7 36.0 1.0
N B:ASP188 4.7 33.8 1.0
CG2 B:THR186 4.8 38.3 1.0
MG B:MG501 4.9 56.5 1.0
OE2 B:GLU103 4.9 44.2 1.0
C B:PRO187 4.9 35.7 1.0

Magnesium binding site 6 out of 6 in 3mqy

Go back to Magnesium Binding Sites List in 3mqy
Magnesium binding site 6 out of 6 in the Sgrai with Cleaved Dna and Magnesium Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sgrai with Cleaved Dna and Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:38.9
occ:1.00
 O A:HOH397 2.2 49.7 1.0
O A:HOH395 2.2 38.4 1.0
OD1 A:ASP188 2.2 41.9 1.0
O A:HOH396 2.3 33.3 1.0
O A:HOH394 2.4 50.3 1.0
OP3 F:DC8 2.5 37.5 1.0
OP2 F:DC8 2.8 31.0 1.0
P F:DC8 3.2 35.0 1.0
CG A:ASP188 3.4 33.5 1.0
OD2 A:ASP188 4.2 33.6 1.0
OP1 F:DC8 4.3 32.8 1.0
MG A:MG500 4.4 19.2 1.0
O3' E:DA7 4.4 39.1 1.0
CA A:ASP188 4.4 31.4 1.0
CB A:ASP188 4.4 32.0 1.0
OE1 A:GLU103 4.5 48.4 1.0
O A:ARG152 4.5 39.3 1.0
OE2 A:GLU103 4.5 48.8 1.0
O5' F:DC8 4.5 27.0 1.0
C5' F:DC8 4.7 28.1 1.0
O A:HOH475 4.8 52.6 1.0
CG2 A:THR186 4.8 28.9 1.0
O A:HOH341 4.8 18.4 1.0
N A:ASP188 4.8 30.6 1.0
C4' E:DA7 4.8 40.4 1.0
O A:HOH344 4.9 41.1 1.0
MG A:MG501 4.9 43.1 1.0
CD A:GLU103 5.0 45.2 1.0
O A:PRO187 5.0 30.5 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: Wed Aug 14 19:23:14 2024

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