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

Protein crystallography data

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

Magnesium Binding Sites:

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 4cyj

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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 4cyj

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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 4cyj

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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 4cyj

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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

Reference:

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
Page generated: Thu Aug 15 16:54:50 2024

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