Magnesium in PDB 4ndn: Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp

All present enzymatic activity of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp:
2.5.1.6;

The structure of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp, PDB code: 4ndn was solved by B.Murray, S.V.Antonyuk, A.Marina, S.C.Lu, J.M.Mato, S.S.Hasnain, A.L.Rojas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.140, 122.178, 298.423, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.1

The binding sites of Magnesium atom in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp (pdb code 4ndn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp, PDB code: 4ndn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:44.5 occ:1.00 O A:HOH600 2.0 36.4 1.0 O1A A:PPK406 2.1 60.4 1.0 O3G A:PPK406 2.2 58.0 1.0 OD2 A:ASP31 2.3 40.3 1.0 O A:HOH529 2.8 34.9 1.0 O2G A:PPK406 3.1 63.4 1.0 MG A:MG402 3.1 37.2 1.0 PG A:PPK406 3.1 65.3 1.0 PA A:PPK406 3.3 57.0 1.0 CG A:ASP31 3.3 38.0 1.0 O4A A:PPK406 3.4 61.0 1.0 O B:HOH597 3.6 29.3 1.0 OD1 A:ASP31 3.6 35.3 1.0 NZ A:LYS265 3.7 41.0 1.0 NH2 A:ARG264 3.8 40.7 1.0 OD2 A:ASP258 4.1 41.1 1.0 N3B A:PPK406 4.2 68.2 1.0 O3A A:PPK406 4.3 64.8 1.0 NE A:ARG264 4.3 41.3 1.0 O2A A:PPK406 4.4 56.5 1.0 CZ A:ARG264 4.4 40.8 1.0 O1G A:PPK406 4.4 65.6 1.0 CE1 A:HIS29 4.5 40.3 1.0 OE2 B:GLU57 4.6 44.2 1.0 O A:ALA259 4.6 35.8 1.0 CB A:ASP31 4.6 37.1 1.0 CB A:ARG264 4.7 38.0 1.0 CE A:LYS265 4.8 39.6 1.0 PB A:PPK406 4.9 74.9 1.0 O A:ARG264 4.9 33.2 1.0

Magnesium binding site 2 out of 4 in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:37.2 occ:1.00 O2G A:PPK406 1.7 63.4 1.0 O4A A:PPK406 2.0 61.0 1.0 O B:HOH595 3.0 57.3 1.0 MG A:MG401 3.1 44.5 1.0 PA A:PPK406 3.2 57.0 1.0 PG A:PPK406 3.2 65.3 1.0 O1A A:PPK406 3.4 60.4 1.0 NZ B:LYS285 3.6 51.9 1.0 O3G A:PPK406 3.7 58.0 1.0 O2B A:PPK406 3.8 72.6 1.0 O B:HOH597 3.9 29.3 1.0 O A:HOH600 4.0 36.4 1.0 OD2 A:ASP258 4.1 41.1 1.0 CE B:LYS285 4.1 49.5 1.0 CG A:SAM407 4.1 56.6 1.0 O3A A:PPK406 4.2 64.8 1.0 N3B A:PPK406 4.3 68.2 1.0 OD2 B:ASP291 4.3 39.8 1.0 O1G A:PPK406 4.3 65.6 1.0 PB A:PPK406 4.3 74.9 1.0 NH2 A:ARG264 4.3 40.7 1.0 O2A A:PPK406 4.3 56.5 1.0 OD1 A:ASP258 4.5 40.6 1.0 OD2 B:ASP134 4.5 38.8 1.0 O B:HOH590 4.5 53.9 1.0 C5' A:SAM407 4.7 51.9 1.0 CG A:ASP258 4.7 42.0 1.0 CB A:SAM407 4.9 56.2 1.0

Magnesium binding site 3 out of 4 in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:43.6 occ:1.00 O3G C:PPK404 2.1 59.4 1.0 O C:HOH552 2.2 41.0 1.0 O1A C:PPK404 2.2 56.2 1.0 O C:HOH507 2.4 35.6 1.0 OD2 C:ASP31 2.4 38.4 1.0 MG D:MG401 2.8 32.9 1.0 O2G C:PPK404 2.9 59.1 1.0 PG C:PPK404 3.0 64.4 1.0 PA C:PPK404 3.3 52.0 1.0 O4A C:PPK404 3.4 61.7 1.0 CG C:ASP31 3.4 39.6 1.0 NH2 C:ARG264 3.6 43.6 1.0 O D:HOH615 3.7 27.8 1.0 OD1 C:ASP31 3.7 37.9 1.0 NZ C:LYS265 3.8 43.0 1.0 NE C:ARG264 4.1 40.5 1.0 OD2 C:ASP258 4.1 43.1 1.0 O1G C:PPK404 4.1 63.2 1.0 CZ C:ARG264 4.2 42.4 1.0 O3A C:PPK404 4.2 62.9 1.0 N3B C:PPK404 4.3 65.9 1.0 OE1 D:GLU57 4.4 49.0 1.0 O2A C:PPK404 4.5 57.2 1.0 CB C:ARG264 4.6 36.9 1.0 O C:ALA259 4.7 41.0 1.0 CE1 C:HIS29 4.7 45.8 1.0 CE C:LYS265 4.8 41.5 1.0 CB C:ASP31 4.8 39.8 1.0 O C:ARG264 4.8 37.5 1.0 PB C:PPK404 4.9 73.3 1.0

Magnesium binding site 4 out of 4 in the Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insights of Mat Enzymes: MATA2B Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:32.9 occ:1.00 O2G C:PPK404 1.8 59.1 1.0 O4A C:PPK404 1.9 61.7 1.0 O C:HOH567 2.5 78.1 1.0 MG C:MG401 2.8 43.6 1.0 PA C:PPK404 3.1 52.0 1.0 PG C:PPK404 3.2 64.4 1.0 O1A C:PPK404 3.3 56.2 1.0 O3G C:PPK404 3.6 59.4 1.0 O D:HOH615 3.8 27.8 1.0 NZ D:LYS285 3.8 46.3 1.0 O C:HOH552 3.9 41.0 1.0 OD2 C:ASP258 4.1 43.1 1.0 O3A C:PPK404 4.2 62.9 1.0 NH2 C:ARG264 4.2 43.6 1.0 O2A C:PPK404 4.2 57.2 1.0 CE D:LYS285 4.2 45.8 1.0 O1G C:PPK404 4.2 63.2 1.0 O2B C:PPK404 4.2 67.7 1.0 N3B C:PPK404 4.3 65.9 1.0 OD1 C:ASP258 4.3 43.1 1.0 CG C:SAM405 4.4 56.8 1.0 OD2 D:ASP291 4.4 39.9 1.0 PB C:PPK404 4.4 73.3 1.0 O D:HOH521 4.5 45.6 1.0 O C:HOH507 4.6 35.6 1.0 CG C:ASP258 4.6 42.7 1.0 C5' C:SAM405 4.7 51.4 1.0 OD2 D:ASP134 4.8 45.0 1.0 OE1 D:GLU57 4.9 49.0 1.0

B.Murray, S.V.Antonyuk, A.Marina, S.M.Van Liempd, S.C.Lu, J.M.Mato, S.S.Hasnain, A.L.Rojas. Structure and Function Study of the Complex That Synthesizes S-Adenosylmethionine. Iucrj V. 1 240 2014.
ISSN: ESSN 2052-2525
PubMed: 25075345
DOI: 10.1107/S2052252514012585