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Magnesium in PDB 4gmj: Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1

Protein crystallography data

The structure of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1, PDB code: 4gmj was solved by P.Petit, O.Weichenrieder, L.Wohlbold, E.Izaurralde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.70 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.470, 101.740, 142.200, 90.00, 101.10, 90.00
R / Rfree (%) 21.4 / 24.9

Other elements in 4gmj:

The structure of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 (pdb code 4gmj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1, PDB code: 4gmj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4gmj

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Magnesium binding site 1 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:37.0
occ:1.00
 O B:HOH409 2.1 40.1 1.0
O B:HOH410 2.1 38.3 1.0
OE1 B:GLU278 2.1 39.0 1.0
O B:HOH407 2.1 40.1 1.0
O B:HOH408 2.1 37.7 1.0
OD1 B:ASP40 2.1 36.5 1.0
CG B:ASP40 3.0 39.4 1.0
CD B:GLU278 3.2 42.3 1.0
OD2 B:ASP40 3.3 43.7 1.0
H2 B:GOL303 3.5 55.4 1.0
O1 B:GOL303 3.6 47.0 1.0
O B:HOH412 3.6 37.0 1.0
OE2 B:GLU278 3.6 38.9 1.0
H B:THR41 3.8 39.7 1.0
OD2 B:ASP161 3.8 42.5 1.0
MG B:MG302 3.9 37.9 1.0
O B:THR41 3.9 35.1 1.0
O B:HOH442 4.0 41.7 1.0
OD1 B:ASP161 4.0 41.6 1.0
HO1 B:GOL303 4.1 56.5 1.0
C2 B:GOL303 4.3 46.1 1.0
CG B:ASP161 4.4 41.7 1.0
CB B:ASP40 4.4 38.9 1.0
HA B:ASP40 4.4 46.0 1.0
HB3 B:GLU278 4.4 53.3 1.0
O B:PHE156 4.5 40.2 1.0
CG B:GLU278 4.5 42.1 1.0
C1 B:GOL303 4.5 44.7 1.0
N B:THR41 4.5 33.0 1.0
O2 B:GOL303 4.6 49.5 1.0
HB2 B:ASP40 4.6 46.7 1.0
HB2 B:GLU278 4.7 53.3 1.0
HG2 B:GLU278 4.8 50.6 1.0
HO2 B:GOL303 4.8 59.5 1.0
CB B:GLU278 4.8 44.4 1.0
HG1 B:THR41 4.8 36.6 1.0
CA B:ASP40 4.9 38.3 1.0
H11 B:GOL303 4.9 53.7 1.0
O B:HOH411 4.9 48.0 1.0

Magnesium binding site 2 out of 8 in 4gmj

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Magnesium binding site 2 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:37.9
occ:1.00
 OD2 B:ASP230 2.0 49.8 1.0
O B:HOH412 2.0 37.0 1.0
O B:HOH411 2.1 48.0 1.0
O B:HOH409 2.1 40.1 1.0
OE2 B:GLU42 2.1 42.8 1.0
OD2 B:ASP40 2.3 43.7 1.0
CG B:ASP230 3.0 46.4 1.0
CD B:GLU42 3.1 43.5 1.0
CG B:ASP40 3.4 39.4 1.0
HB2 B:ASP230 3.5 53.0 1.0
HA B:HIS225 3.5 55.6 1.0
HB3 B:ASP230 3.5 53.0 1.0
OE1 B:GLU42 3.5 44.0 1.0
CB B:ASP230 3.6 44.2 1.0
OD1 B:ASP40 3.9 36.5 1.0
MG B:MG301 3.9 37.0 1.0
O B:THR41 3.9 35.1 1.0
O B:HOH410 4.0 38.3 1.0
HA B:ALA227 4.0 48.1 1.0
OD1 B:ASP230 4.0 44.8 1.0
HO2 B:GOL303 4.1 59.5 1.0
HG2 B:GLU42 4.2 46.2 1.0
O B:GLN226 4.3 39.5 1.0
C B:HIS225 4.3 46.5 1.0
CG B:GLU42 4.3 38.4 1.0
CA B:HIS225 4.3 46.3 1.0
HO3 B:GOL303 4.3 57.7 1.0
H2 B:GOL303 4.4 55.4 1.0
O B:HOH441 4.4 44.0 1.0
C B:GLN226 4.5 41.9 1.0
HB3 B:ASP40 4.6 46.7 1.0
HD1 B:HIS225 4.6 69.2 1.0
N B:GLN226 4.6 45.5 1.0
CB B:ASP40 4.6 38.9 1.0
O B:HIS225 4.6 41.9 1.0
O2 B:GOL303 4.7 49.5 1.0
ND1 B:HIS225 4.7 57.7 1.0
HG3 B:GLU42 4.8 46.2 1.0
CA B:ALA227 4.8 40.1 1.0
N B:ALA227 4.8 42.2 1.0
OE1 B:GLU278 4.8 39.0 1.0
HA B:GLN226 4.8 51.9 1.0
H B:HIS225 4.8 61.8 1.0
O B:HOH408 4.9 37.7 1.0
H B:GLN226 4.9 54.7 1.0
C B:THR41 4.9 36.0 1.0
CA B:GLN226 5.0 43.2 1.0

Magnesium binding site 3 out of 8 in 4gmj

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Magnesium binding site 3 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:63.1
occ:1.00
 O B:HOH402 2.1 54.0 1.0
O B:HOH401 2.1 52.0 1.0
O B:HOH406 2.1 53.6 1.0
O B:HOH404 2.1 52.5 1.0
O B:HOH405 2.1 53.9 1.0
O B:HOH403 2.1 58.1 1.0
OE2 B:GLU53 3.9 57.2 1.0
OE1 B:GLU53 4.1 56.2 1.0
OD2 B:ASP59 4.2 42.4 1.0
CD B:GLU53 4.4 55.5 1.0
OE2 B:GLU177 4.5 51.6 1.0
OE1 B:GLU177 4.6 51.0 1.0
HE21 B:GLN63 4.7 51.0 1.0
HG3 B:GLN63 4.8 49.8 1.0
OD1 B:ASP59 4.9 49.3 1.0
CG B:ASP59 5.0 44.2 1.0

Magnesium binding site 4 out of 8 in 4gmj

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Magnesium binding site 4 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:55.0
occ:1.00
 OD1 D:ASP40 2.0 49.1 1.0
O D:HOH403 2.0 54.3 1.0
O D:HOH404 2.1 55.5 1.0
O D:HOH402 2.1 51.6 1.0
O D:HOH401 2.1 51.0 1.0
OE1 D:GLU278 2.1 63.5 1.0
CG D:ASP40 2.7 50.1 1.0
OD2 D:ASP40 2.8 48.3 1.0
CD D:GLU278 3.0 59.5 1.0
OE2 D:GLU278 3.3 60.2 1.0
O D:HOH406 3.6 57.8 1.0
H D:THR41 3.8 48.2 1.0
MG D:MG302 4.0 55.7 1.0
OD2 D:ASP161 4.0 51.9 1.0
O D:THR41 4.0 42.5 1.0
CB D:ASP40 4.1 49.3 1.0
OD1 D:ASP161 4.3 46.2 1.0
HB2 D:ASP40 4.3 59.2 1.0
O1 D:GOL303 4.3 56.8 1.0
HA D:ASP40 4.4 53.8 1.0
O D:PHE156 4.4 56.7 1.0
HO1 D:GOL303 4.4 68.2 1.0
CG D:GLU278 4.5 56.6 1.0
N D:THR41 4.5 40.1 1.0
CG D:ASP161 4.6 49.5 1.0
HB2 D:GLU278 4.6 77.7 1.0
HB3 D:GLU278 4.6 77.7 1.0
O D:HOH419 4.7 50.7 1.0
HB3 D:ASP40 4.7 59.2 1.0
CA D:ASP40 4.8 44.8 1.0
OE2 D:GLU42 4.8 48.5 1.0
O D:HOH405 4.8 57.6 1.0
CB D:GLU278 4.9 64.7 1.0
HG2 D:GLU278 4.9 68.0 1.0
O D:HIS157 5.0 57.1 1.0

Magnesium binding site 5 out of 8 in 4gmj

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Magnesium binding site 5 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:55.7
occ:1.00
 OE2 D:GLU42 1.9 48.5 1.0
OD2 D:ASP230 2.0 55.6 1.0
O D:HOH406 2.0 57.8 1.0
O D:HOH403 2.1 54.3 1.0
O D:HOH405 2.1 57.6 1.0
OD2 D:ASP40 2.4 48.3 1.0
CD D:GLU42 2.9 49.9 1.0
CG D:ASP230 3.1 56.5 1.0
HA D:HIS225 3.2 71.8 1.0
OE1 D:GLU42 3.3 53.5 1.0
HB2 D:ASP230 3.6 63.4 1.0
CG D:ASP40 3.7 50.1 1.0
HB3 D:ASP230 3.7 63.4 1.0
CB D:ASP230 3.7 52.8 1.0
MG D:MG301 4.0 55.0 1.0
CA D:HIS225 4.0 59.8 1.0
HA D:ALA227 4.1 56.8 1.0
O D:HOH404 4.1 55.5 1.0
OD1 D:ASP230 4.1 62.3 1.0
C D:HIS225 4.1 55.4 1.0
O D:THR41 4.2 42.5 1.0
CG D:GLU42 4.2 50.4 1.0
HG2 D:GLU42 4.2 60.5 1.0
HD2 D:HIS225 4.3 89.0 1.0
N D:GLN226 4.4 51.8 1.0
OD1 D:ASP40 4.4 49.1 1.0
HB3 D:ASP40 4.5 59.2 1.0
O D:HIS225 4.6 51.6 1.0
H D:GLN226 4.6 62.2 1.0
O2 D:GOL303 4.6 51.9 1.0
HG3 D:GLU42 4.6 60.5 1.0
C D:GLN226 4.7 52.2 1.0
H D:HIS225 4.7 70.7 1.0
CB D:ASP40 4.7 49.3 1.0
O D:GLN226 4.8 51.8 1.0
HB3 D:HIS225 4.8 72.0 1.0
N D:ALA227 4.8 46.5 1.0
O D:HOH402 4.8 51.6 1.0
CA D:ALA227 4.9 47.3 1.0
HA D:GLN226 4.9 62.1 1.0
N D:HIS225 4.9 58.9 1.0
CB D:HIS225 4.9 59.9 1.0
CA D:GLN226 5.0 51.8 1.0
CD2 D:HIS225 5.0 74.1 1.0

Magnesium binding site 6 out of 8 in 4gmj

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Magnesium binding site 6 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:47.2
occ:1.00
 OD1 F:ASP40 2.0 47.5 1.0
O F:HOH408 2.1 43.9 1.0
O F:HOH409 2.1 44.1 1.0
O F:HOH407 2.1 47.8 1.0
O F:HOH410 2.1 50.0 1.0
OE1 F:GLU278 2.2 48.8 1.0
CG F:ASP40 2.8 45.2 1.0
OD2 F:ASP40 2.9 45.7 1.0
CD F:GLU278 3.3 51.8 1.0
HO3 F:GOL303 3.4 62.4 1.0
O F:HOH412 3.5 43.1 1.0
O3 F:GOL303 3.6 51.9 1.0
OE2 F:GLU278 3.6 52.5 1.0
H F:THR41 3.7 49.4 1.0
MG F:MG302 3.9 49.4 1.0
O F:THR41 3.9 41.7 1.0
OD1 F:ASP161 4.0 37.8 1.0
OD2 F:ASP161 4.1 47.0 1.0
CB F:ASP40 4.3 42.0 1.0
HA F:ASP40 4.5 47.1 1.0
CG F:ASP161 4.5 42.8 1.0
O F:PHE156 4.5 44.6 1.0
HB3 F:GLU278 4.5 66.9 1.0
N F:THR41 4.5 41.1 1.0
O F:HOH447 4.6 53.5 1.0
CG F:GLU278 4.6 55.1 1.0
HB2 F:ASP40 4.6 50.4 1.0
HO2 F:GOL303 4.7 53.9 1.0
O F:HOH411 4.8 52.1 1.0
HB3 F:ASP40 4.8 50.4 1.0
HG1 F:THR41 4.9 45.1 1.0
HG2 F:GLU278 4.9 66.2 1.0
CA F:ASP40 4.9 39.2 1.0
HB2 F:GLU278 4.9 66.9 1.0
C3 F:GOL303 4.9 46.3 1.0
CB F:GLU278 4.9 55.7 1.0

Magnesium binding site 7 out of 8 in 4gmj

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Magnesium binding site 7 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:49.4
occ:1.00
 OE2 F:GLU42 1.9 43.3 1.0
O F:HOH412 2.1 43.1 1.0
O F:HOH409 2.1 44.1 1.0
OD2 F:ASP230 2.1 49.4 1.0
O F:HOH411 2.1 52.1 1.0
OD2 F:ASP40 2.1 45.7 1.0
CD F:GLU42 3.0 44.5 1.0
CG F:ASP230 3.1 49.3 1.0
HB2 F:ASP230 3.3 57.9 1.0
HB3 F:ASP230 3.4 57.9 1.0
CG F:ASP40 3.4 45.2 1.0
CB F:ASP230 3.5 48.2 1.0
OE1 F:GLU42 3.6 46.5 1.0
HA F:HIS225 3.7 62.9 1.0
HA F:ALA227 3.8 55.6 1.0
O F:HOH410 3.8 50.0 1.0
MG F:MG301 3.9 47.2 1.0
O F:THR41 3.9 41.7 1.0
O F:HIS225 4.0 45.4 1.0
OD1 F:ASP40 4.1 47.5 1.0
C F:HIS225 4.1 50.6 1.0
OD1 F:ASP230 4.2 55.6 1.0
HB3 F:ASP40 4.2 50.4 1.0
HG2 F:GLU42 4.2 49.7 1.0
CG F:GLU42 4.3 41.4 1.0
HO2 F:GOL303 4.3 53.9 1.0
CA F:HIS225 4.4 52.4 1.0
CB F:ASP40 4.4 42.0 1.0
C F:GLN226 4.4 45.9 1.0
O F:GLN226 4.5 42.5 1.0
N F:ALA227 4.6 41.3 1.0
N F:GLN226 4.6 47.2 1.0
CA F:ALA227 4.6 46.3 1.0
HG3 F:GLU42 4.7 49.7 1.0
HA F:GLN226 4.7 53.2 1.0
C F:THR41 4.8 38.8 1.0
H F:THR41 4.8 49.4 1.0
HB2 F:ASP40 4.9 50.4 1.0
CA F:GLN226 4.9 44.3 1.0
O F:HOH408 4.9 43.9 1.0
HB2 F:ALA227 4.9 50.9 1.0
H F:ALA227 5.0 49.6 1.0
HA F:GLU42 5.0 43.8 1.0

Magnesium binding site 8 out of 8 in 4gmj

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Magnesium binding site 8 out of 8 in the Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Human NOT1 MIF4G Domain Co-Crystallized with CAF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg305

b:73.6
occ:1.00
 O F:HOH406 2.1 58.7 1.0
O F:HOH401 2.1 65.7 1.0
O F:HOH403 2.1 66.4 1.0
O F:HOH402 2.1 61.5 1.0
O F:HOH405 2.1 62.1 1.0
O F:HOH404 2.1 63.3 1.0
OE2 F:GLU53 4.2 62.0 1.0
OE1 F:GLU53 4.3 65.5 1.0
OD2 F:ASP59 4.5 51.6 1.0
OE2 F:GLU177 4.6 61.8 1.0
OD1 F:ASP59 4.6 56.3 1.0
CD F:GLU53 4.7 61.5 1.0
OE1 F:GLU177 4.8 61.5 1.0
HG3 F:GLN63 4.9 60.7 1.0
CG F:ASP59 5.0 53.3 1.0

Reference:

A.P.Petit, L.Wohlbold, P.Bawankar, E.Huntzinger, S.Schmidt, E.Izaurralde, O.Weichenrieder. The Structural Basis For the Interaction Between the CAF1 Nuclease and the NOT1 Scaffold of the Human CCR4-Not Deadenylase Complex Nucleic Acids Res. V. 40 11058 2012.
ISSN: ISSN 0305-1048
PubMed: 22977175
DOI: 10.1093/NAR/GKS883
Page generated: Fri Aug 16 15:34:09 2024

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