Magnesium in PDB 5hml: Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

All present enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions:
3.1.11.3;

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml was solved by C.S.Flemming, M.Feng, S.E.Sedelnikova, J.Zhang, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.60 / 1.48
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.380, 58.380, 59.720, 66.53, 79.48, 73.71
R / Rfree (%)	14.1 / 19.6

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions also contains other interesting chemical elements:

Iodine	(I)	3 atoms
Chlorine	(Cl)	13 atoms

The binding sites of Magnesium atom in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions (pdb code 5hml). 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 T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:21.0 occ:1.00 OD2 A:ASP204 2.0 23.7 1.0 O A:HOH529 2.0 19.4 1.0 O A:HOH403 2.0 26.1 1.0 OD2 A:ASP155 2.1 19.4 1.0 O A:HOH484 2.1 22.5 1.0 O A:HOH552 2.1 25.6 1.0 CG A:ASP204 3.0 25.7 1.0 CG A:ASP155 3.1 17.7 1.0 OD1 A:ASP155 3.4 15.4 1.0 OD1 A:ASP204 3.4 28.9 1.0 O A:HOH594 3.8 36.3 1.0 O A:HOH415 4.0 19.2 1.0 O A:HOH498 4.2 23.0 1.0 OD2 A:ASP201 4.3 36.3 1.0 CB A:ASP204 4.3 22.3 1.0 CB A:ASP155 4.4 18.1 1.0 O A:HOH424 4.5 20.4 1.0 O A:HOH505 4.5 43.4 1.0 NZ A:LYS196 4.7 18.6 1.0 O A:HOH582 4.7 20.7 1.0 OH A:TYR82 4.7 13.9 1.0 CG A:ASP201 4.9 33.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:35.6 occ:1.00 O B:HOH616 2.1 34.5 0.5 O B:HOH597 2.1 28.6 1.0 O B:HOH447 2.1 32.2 1.0 O B:HOH408 2.2 33.1 1.0 OD2 B:ASP204 2.2 34.5 1.0 OD2 B:ASP155 2.2 20.7 1.0 CG B:ASP155 3.3 25.2 1.0 CG B:ASP204 3.3 23.2 1.0 OD1 B:ASP155 3.7 19.2 1.0 O B:HOH427 3.8 25.8 1.0 OD1 B:ASP204 3.9 27.5 1.0 O B:HOH492 4.1 31.0 1.0 O B:HOH405 4.2 32.9 1.0 OD2 B:ASP201 4.3 23.6 1.0 CB B:ASP204 4.5 20.7 1.0 CB B:ASP155 4.6 17.7 1.0 O B:HOH510 4.6 39.5 1.0 CG B:ASP201 4.7 17.8 1.0 OH B:TYR82 4.8 15.3 1.0 O B:HOH424 4.9 29.0 1.0 O B:HOH571 5.0 20.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:45.0 occ:1.00 O B:HOH431 2.0 64.4 1.0 O B:HOH670 2.1 41.7 1.0 O B:HOH416 2.1 33.8 1.0 O B:HOH512 2.1 40.3 1.0 OD1 B:ASP87 2.2 49.5 1.0 O B:HOH470 2.3 35.5 1.0 CG B:ASP87 3.0 35.7 1.0 OD2 B:ASP87 3.2 38.7 1.0 OE1 B:GLU88 4.1 41.9 1.0 CB B:ASP87 4.4 25.7 1.0 OD1 B:ASN85 4.5 37.0 1.0 O B:HOH626 4.5 28.1 1.0 N B:ASP87 4.6 23.2 1.0 N B:GLU88 4.6 23.8 1.0 CA B:ASP87 4.9 24.2 1.0

F.A.Almalki, C.S.Flemming, J.Zhang, M.Feng, S.E.Sedelnikova, T.Ceska, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk. Direct Observation of Dna Threading in Flap Endonuclease Complexes. Nat.Struct.Mol.Biol. V. 23 640 2016.
ISSN: ESSN 1545-9985
PubMed: 27273516
DOI: 10.1038/NSMB.3241