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Magnesium in PDB 1d3y: Structure of the Dna Topoisomerase VI A Subunit

Enzymatic activity of Structure of the Dna Topoisomerase VI A Subunit

All present enzymatic activity of Structure of the Dna Topoisomerase VI A Subunit:
5.99.1.3;

Protein crystallography data

The structure of Structure of the Dna Topoisomerase VI A Subunit, PDB code: 1d3y was solved by M.D.Nichols, K.A.Deangelis, J.L.Keck, J.M.Berger, 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 (°) 66.510, 59.040, 87.260, 90.00, 94.05, 90.00
R / Rfree (%) 19.7 / 24.2

Other elements in 1d3y:

The structure of Structure of the Dna Topoisomerase VI A Subunit also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Dna Topoisomerase VI A Subunit (pdb code 1d3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Dna Topoisomerase VI A Subunit, PDB code: 1d3y:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1d3y

Go back to Magnesium Binding Sites List in 1d3y
Magnesium binding site 1 out of 3 in the Structure of the Dna Topoisomerase VI A Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Dna Topoisomerase VI A Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg371

b:21.8
occ:1.00
OE2 A:GLU197 2.0 16.4 1.0
OD2 A:ASP249 2.1 17.8 1.0
O A:HOH511 2.1 18.9 1.0
O A:HOH381 2.2 12.0 1.0
O A:HOH463 2.2 16.5 1.0
O A:HOH399 2.2 13.8 1.0
CD A:GLU197 3.0 15.2 1.0
CG A:ASP249 3.2 17.2 1.0
OE1 A:GLU197 3.4 14.8 1.0
CB A:ASP249 3.7 13.8 1.0
O A:HOH421 3.9 15.2 1.0
O A:HOH414 4.0 19.3 1.0
OD2 A:ASP251 4.1 16.7 1.0
OD1 A:ASP249 4.3 15.1 1.0
O A:HOH471 4.3 45.2 1.0
CG A:GLU197 4.3 15.2 1.0
O A:HOH515 4.4 25.2 1.0
OD1 A:ASP251 4.4 14.5 1.0
CD1 A:ILE258 4.7 18.3 1.0
CG A:ASP251 4.7 18.2 1.0
CG2 A:THR198 4.9 11.5 1.0
CD2 A:TYR253 4.9 22.6 1.0
CA A:ASP249 5.0 13.8 1.0

Magnesium binding site 2 out of 3 in 1d3y

Go back to Magnesium Binding Sites List in 1d3y
Magnesium binding site 2 out of 3 in the Structure of the Dna Topoisomerase VI A Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Dna Topoisomerase VI A Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg372

b:21.8
occ:1.00
O B:HOH379 2.1 17.0 1.0
O A:HOH394 2.1 15.4 1.0
O A:HOH490 2.2 15.4 1.0
O B:HOH376 2.2 15.2 1.0
O B:HOH451 2.2 17.9 1.0
O A:HOH426 2.3 19.3 1.0
O A:HOH430 4.0 17.0 1.0
NZ B:LYS350 4.0 13.6 1.0
OE1 B:GLU208 4.0 14.6 1.0
O A:THR92 4.1 19.7 1.0
OE2 B:GLU208 4.1 17.1 1.0
O B:HOH537 4.2 26.4 1.0
OD2 A:ASP94 4.2 15.9 1.0
CE B:LYS350 4.4 21.0 1.0
CG A:ASP94 4.4 17.6 1.0
CD B:GLU208 4.6 15.4 1.0
O A:ASP93 4.6 21.0 1.0
OD1 A:ASP94 4.8 13.8 1.0
CB A:ASP94 4.8 15.0 1.0

Magnesium binding site 3 out of 3 in 1d3y

Go back to Magnesium Binding Sites List in 1d3y
Magnesium binding site 3 out of 3 in the Structure of the Dna Topoisomerase VI A Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Dna Topoisomerase VI A Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg374

b:19.1
occ:1.00
OE2 B:GLU197 2.0 16.4 1.0
OD2 B:ASP249 2.1 14.1 1.0
O B:HOH426 2.1 15.4 1.0
O B:HOH413 2.2 19.2 1.0
O B:HOH417 2.2 14.0 1.0
O B:HOH501 2.2 15.2 1.0
CD B:GLU197 3.0 15.7 1.0
CG B:ASP249 3.2 15.4 1.0
OE1 B:GLU197 3.3 13.2 1.0
CB B:ASP249 3.7 13.7 1.0
O B:HOH538 3.8 18.1 1.0
O B:HOH457 4.0 23.3 1.0
OD2 B:ASP251 4.1 16.9 1.0
OD1 B:ASP249 4.2 13.5 1.0
O B:HOH443 4.3 19.2 1.0
CG B:GLU197 4.3 13.0 1.0
OD1 B:ASP251 4.4 12.6 1.0
CG B:ASP251 4.7 18.2 1.0
O B:HOH544 4.9 39.3 1.0
CG2 B:THR198 4.9 14.3 1.0
CD1 B:ILE258 4.9 16.0 1.0
CA B:ASP249 5.0 13.2 1.0

Reference:

M.D.Nichols, K.Deangelis, J.L.Keck, J.M.Berger. Structure and Function of An Archaeal Topoisomerase VI Subunit with Homology to the Meiotic Recombination Factor SPO11. Embo J. V. 18 6177 1999.
ISSN: ISSN 0261-4189
PubMed: 10545127
DOI: 10.1093/EMBOJ/18.21.6177
Page generated: Tue Aug 13 02:35:03 2024

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