Magnesium in PDB 4cyj: Chaetomium Thermophilum PAN2:PAN3 Complex

The structure of Chaetomium Thermophilum PAN2:PAN3 Complex, PDB code: 4cyj was solved by J.Wolf, E.Valkov, M.D.Allen, B.Meineke, Y.Gordiyenko, S.H.Mclaughlin, T.M.Olsen, C.V.Robinson, M.Bycroft, M.Stewart, L.A.Passmore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.890 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.094, 145.359, 101.811, 90.00, 94.86, 90.00
R / Rfree (%)	18.3 / 22.06

The binding sites of Magnesium atom in the Chaetomium Thermophilum PAN2:PAN3 Complex (pdb code 4cyj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Chaetomium Thermophilum PAN2:PAN3 Complex, PDB code: 4cyj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Chaetomium Thermophilum PAN2:PAN3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chaetomium Thermophilum PAN2:PAN3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:71.9 occ:1.00 OD2 A:ASP257 2.6 73.8 1.0 O3G A:ATP900 2.8 0.8 1.0 O1A A:ATP900 2.8 73.8 1.0 O3A A:ATP900 2.8 55.4 1.0 O A:SER271 2.9 50.5 1.0 PA A:ATP900 3.5 56.6 1.0 OG A:SER271 3.7 73.0 1.0 HA A:TRP272 3.7 52.4 1.0 CG A:ASP257 3.8 78.9 1.0 O3B A:ATP900 3.8 0.7 1.0 C A:SER271 3.9 50.4 1.0 PG A:ATP900 3.9 0.6 1.0 H5'2 A:ATP900 4.0 67.1 1.0 HG21 A:VAL273 4.0 53.2 1.0 HG A:SER271 4.0 87.6 1.0 PB A:ATP900 4.1 78.2 1.0 HB3 A:ASP257 4.1 91.9 1.0 H5'1 A:ATP900 4.1 67.1 1.0 C5' A:ATP900 4.4 55.9 1.0 O5' A:ATP900 4.5 57.6 1.0 CA A:TRP272 4.5 43.6 1.0 CB A:ASP257 4.6 76.6 1.0 N A:TRP272 4.6 47.7 1.0 H A:SER271 4.6 51.5 1.0 OD1 A:ASP257 4.7 82.2 1.0 O2A A:ATP900 4.7 45.3 1.0 HH12 A:ARG288 4.7 84.1 1.0 O2B A:ATP900 4.7 88.5 1.0 H A:VAL273 4.8 58.6 1.0 O2G A:ATP900 4.8 0.6 1.0 CB A:SER271 4.8 58.9 1.0 CA A:SER271 4.9 49.8 1.0 CG2 A:VAL273 4.9 44.4 1.0 HA A:ASP257 5.0 88.8 1.0

Magnesium binding site 2 out of 4 in the Chaetomium Thermophilum PAN2:PAN3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Chaetomium Thermophilum PAN2:PAN3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1000 b:87.5 occ:1.00 O1A B:ATP900 2.1 0.7 1.0 OD1 B:ASP257 2.6 97.9 1.0 HH21 B:ARG288 3.0 0.1 1.0 O3A B:ATP900 3.2 1.0 1.0 PA B:ATP900 3.2 0.0 1.0 H5'2 B:ATP900 3.3 0.7 1.0 HG21 B:VAL273 3.5 63.2 1.0 NH2 B:ARG288 3.7 88.4 1.0 CG B:ASP257 3.8 98.1 1.0 HH22 B:ARG288 3.8 0.1 1.0 O B:SER271 3.8 75.4 1.0 OG B:SER271 3.9 73.3 1.0 H5'1 B:ATP900 3.9 0.7 1.0 C5' B:ATP900 3.9 0.4 1.0 O5' B:ATP900 4.0 94.0 1.0 HG B:SER271 4.0 87.9 1.0 HB3 B:ASP257 4.2 0.2 1.0 HA B:TRP272 4.3 76.1 1.0 O3B B:ATP900 4.3 1.0 1.0 CG2 B:VAL273 4.3 52.7 1.0 HG22 B:VAL273 4.4 63.2 1.0 O2A B:ATP900 4.5 0.9 1.0 PB B:ATP900 4.5 0.8 1.0 C B:SER271 4.5 71.7 1.0 CB B:ASP257 4.6 98.5 1.0 OD2 B:ASP257 4.6 91.2 1.0 HE B:ARG288 4.8 81.3 1.0 H B:VAL273 4.8 54.0 1.0 HG23 B:VAL273 4.8 63.2 1.0 HA B:ASP257 4.9 0.2 1.0 CZ B:ARG288 4.9 80.2 1.0 CA B:TRP272 5.0 63.4 1.0

Magnesium binding site 3 out of 4 in the Chaetomium Thermophilum PAN2:PAN3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Chaetomium Thermophilum PAN2:PAN3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1000 b:75.7 occ:1.00 OD1 C:ASP257 2.7 74.8 1.0 O2B C:ATP900 2.8 85.1 1.0 HB3 C:ASP257 2.8 0.0 1.0 H5'1 C:ATP900 2.8 71.6 1.0 O3B C:ATP900 3.0 0.4 1.0 HA C:ASP257 3.1 0.4 1.0 O3A C:ATP900 3.1 70.5 1.0 PB C:ATP900 3.2 79.5 1.0 H5'2 C:ATP900 3.3 71.6 1.0 O1A C:ATP900 3.4 76.1 1.0 CB C:ASP257 3.4 84.2 1.0 CG C:ASP257 3.4 76.8 1.0 C5' C:ATP900 3.5 59.6 1.0 CA C:ASP257 3.7 85.3 1.0 PA C:ATP900 3.7 58.8 1.0 H C:THR258 4.0 0.7 1.0 O5' C:ATP900 4.1 63.4 1.0 HB2 C:ASP257 4.3 0.0 1.0 PG C:ATP900 4.5 0.9 1.0 N C:THR258 4.5 0.8 1.0 O2G C:ATP900 4.5 0.9 1.0 C C:ASP257 4.6 89.8 1.0 H C:SER259 4.6 1.0 1.0 O1B C:ATP900 4.7 84.2 1.0 OD2 C:ASP257 4.7 75.5 1.0 N C:ASP257 4.8 72.3 1.0 C4' C:ATP900 4.8 58.5 1.0 O C:SER259 5.0 0.8 1.0 H4' C:ATP900 5.0 70.1 1.0

Magnesium binding site 4 out of 4 in the Chaetomium Thermophilum PAN2:PAN3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Chaetomium Thermophilum PAN2:PAN3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1000 b:76.3 occ:1.00 O1A D:ATP900 2.3 0.1 1.0 OD1 D:ASP257 2.4 83.7 1.0 O3B D:ATP900 2.4 0.3 1.0 O2G D:ATP900 3.1 0.1 1.0 PG D:ATP900 3.2 0.6 1.0 O D:SER271 3.3 95.6 1.0 PA D:ATP900 3.5 95.0 1.0 CG D:ASP257 3.5 85.5 1.0 PB D:ATP900 3.6 0.5 1.0 O3A D:ATP900 3.6 0.1 1.0 O3G D:ATP900 3.6 0.1 1.0 H5'2 D:ATP900 3.8 95.0 1.0 HB3 D:ASP257 3.8 0.9 1.0 H5'1 D:ATP900 3.8 95.0 1.0 HA D:TRP272 3.9 97.7 1.0 HG21 D:VAL273 4.1 71.5 1.0 OG D:SER271 4.2 0.7 1.0 O2B D:ATP900 4.2 0.7 1.0 C5' D:ATP900 4.2 79.2 1.0 CB D:ASP257 4.2 91.6 1.0 O5' D:ATP900 4.3 80.9 1.0 C D:SER271 4.3 91.7 1.0 OD2 D:ASP257 4.4 80.5 1.0 HG D:SER271 4.5 1.0 1.0 HD1 D:TRP272 4.5 0.7 1.0 O1G D:ATP900 4.6 0.1 1.0 O2A D:ATP900 4.7 96.2 1.0 HA D:ASP257 4.7 0.3 1.0 HH12 D:ARG288 4.7 0.7 1.0 O1B D:ATP900 4.8 0.9 1.0 CA D:TRP272 4.8 81.4 1.0 H D:VAL273 4.8 72.0 1.0 HB2 D:ASP257 4.9 0.9 1.0 N D:TRP272 5.0 86.5 1.0

J.Wolf, E.Valkov, M.D.Allen, B.Meineke, Y.Gordiyenko, S.H.Mclaughlin, T.M.Olsen, C.V.Robinson, M.Bycroft, M.Stewart, L.A.Passmore. Structural Basis For PAN3 Binding to PAN2 and Its Function in Mrna Recruitment and Deadenylation Embo J. V. 33 1514 2014.
ISSN: ISSN 0261-4189
PubMed: 24872509
DOI: 10.15252/EMBJ.201488373