Magnesium in PDB 3m6z: Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride

The structure of Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride, PDB code: 3m6z was solved by R.Rajan, B.Taneja, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.640, 80.110, 137.220, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.4

The structure of Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride (pdb code 3m6z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride, PDB code: 3m6z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride


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 An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg384 b:24.7 occ:1.00 O A:VAL349 2.9 12.5 1.0 N A:VAL211 3.0 9.9 1.0 N A:ARG351 3.1 13.0 0.5 N A:ARG351 3.1 13.3 0.5 O A:HOH618 3.4 19.0 1.0 CA A:SER210 3.4 10.9 1.0 O A:HOH454 3.4 13.1 1.0 CG A:ARG351 3.6 14.3 0.5 CA A:ASN350 3.7 12.9 1.0 C A:SER210 3.7 10.6 1.0 CB A:SER210 3.7 12.0 1.0 O A:ALA327 3.7 13.7 1.0 CB A:ALA327 3.8 12.1 1.0 CB A:ARG351 3.8 13.7 0.5 CG2 A:VAL211 3.8 10.7 1.0 C A:VAL349 3.9 13.1 1.0 C A:ASN350 3.9 13.0 1.0 CB A:ARG351 3.9 14.3 0.5 CB A:VAL211 4.0 9.7 1.0 CA A:ARG351 4.0 13.4 0.5 CA A:VAL211 4.1 10.2 1.0 CA A:ARG351 4.1 14.1 0.5 N A:ASN350 4.2 12.6 1.0 O A:HOH437 4.3 27.3 1.0 CG A:ARG351 4.3 15.4 0.5 CA A:ALA327 4.5 11.9 1.0 OD1 A:ASN350 4.5 13.6 1.0 C A:ALA327 4.5 12.6 1.0 O A:HOH462 4.6 14.9 1.0 O A:LEU209 4.6 12.0 1.0 N A:THR352 4.7 13.1 1.0 N A:SER210 4.7 11.6 1.0 OG A:SER210 4.9 13.0 1.0 CD A:ARG351 4.9 16.4 0.5 C A:ARG351 4.9 13.4 0.5 C A:ARG351 4.9 13.8 0.5 CB A:ASN350 4.9 13.3 1.0 O A:SER210 4.9 9.9 1.0 CD A:ARG351 4.9 17.2 0.5 N A:SER212 5.0 11.2 0.5

Magnesium binding site 2 out of 3 in the Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride


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 An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg385 b:15.0 occ:1.00 O A:GLU266 2.3 11.0 1.0 O A:LEU269 2.4 13.6 1.0 O A:HOH494 2.4 22.6 1.0 O A:HOH495 2.7 27.7 1.0 C A:GLU266 3.4 11.6 1.0 C A:LEU269 3.5 14.1 1.0 CA A:GLU266 3.8 11.7 1.0 CA A:ARG270 4.1 15.8 0.5 CA A:ARG270 4.1 15.5 0.5 N A:ARG270 4.2 14.9 0.5 N A:ARG270 4.2 14.7 0.5 O A:ARG270 4.3 15.8 0.5 CB A:GLU266 4.4 12.0 1.0 C A:ARG270 4.5 15.4 0.5 N A:LEU269 4.5 13.2 1.0 N A:ARG267 4.5 11.2 1.0 C A:ARG270 4.6 15.6 0.5 CA A:LEU269 4.6 13.8 1.0 O A:ARG270 4.7 16.4 0.5 CG A:PRO272 4.7 14.8 1.0 O A:SER265 4.8 10.7 1.0 CA A:ARG267 4.9 12.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride


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 An N-Terminal 44 kDa Fragment of Topoisomerase V in the Presence of Guanidium Hydrochloride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg385 b:33.4 occ:1.00 O3 B:PO4381 2.8 13.6 0.5 O B:HOH449 3.0 17.2 1.0 O B:HOH485 3.1 24.0 1.0 N B:SER324 3.1 16.6 0.5 N B:SER324 3.1 16.9 0.5 OG B:SER324 3.2 16.3 0.5 OG B:SER324 3.3 19.0 0.5 CB B:SER324 3.3 17.1 0.5 CB B:SER324 3.4 17.6 0.5 OD1 B:ASP201 3.6 19.7 1.0 N B:ILE323 3.6 16.4 1.0 O1 B:PO4381 3.6 19.7 0.5 P B:PO4381 3.7 13.6 0.5 O1 B:PO4381 3.7 15.6 0.5 OG B:SER322 3.7 15.4 1.0 CA B:SER324 3.8 16.5 0.5 CA B:SER324 3.8 17.0 0.5 O3 B:PO4381 3.9 19.7 0.5 O2 B:PO4381 3.9 11.3 0.5 C B:ILE323 4.1 16.2 1.0 C B:SER322 4.1 15.9 1.0 CA B:SER322 4.1 15.6 1.0 CA B:ILE323 4.1 16.7 1.0 P B:PO4381 4.2 18.5 0.5 CG B:ASP201 4.2 16.2 1.0 CB B:ILE323 4.3 17.4 1.0 O2 B:PO4381 4.4 18.6 0.5 O B:HOH542 4.4 25.4 1.0 CB B:SER322 4.4 15.5 1.0 CB B:ASP201 4.6 13.5 1.0 O B:HOH445 4.6 16.6 1.0 O B:HOH517 4.6 20.6 1.0 O B:HOH457 4.7 15.3 1.0 C B:SER324 4.9 16.3 0.5 N B:MET325 5.0 16.0 1.0 C B:SER324 5.0 16.5 0.5 OD2 B:ASP201 5.0 21.0 1.0 O B:SER322 5.0 15.7 1.0

R.Rajan, B.Taneja, A.Mondragon. Structures of Minimal Catalytic Fragments of Topoisomerase V Reveals Conformational Changes Relevant For Dna Binding. Structure V. 18 829 2010.
ISSN: ISSN 0969-2126
PubMed: 20637419
DOI: 10.1016/J.STR.2010.03.006