Magnesium in PDB 6duq: Structure of A Rho-Nusg Kow Domain Complex

Protein crystallography data

The structure of Structure of A Rho-Nusg Kow Domain Complex, PDB code: 6duq was solved by J.M.Berger, M.R.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.03 / 3.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 126.350, 126.320, 166.820, 89.94, 89.90, 60.01
R / Rfree (%) 28.7 / 30

Other elements in 6duq:

The structure of Structure of A Rho-Nusg Kow Domain Complex also contains other interesting chemical elements:

Fluorine (F) 36 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Rho-Nusg Kow Domain Complex (pdb code 6duq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of A Rho-Nusg Kow Domain Complex, PDB code: 6duq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6duq

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Magnesium binding site 1 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1001

b:0.0
occ:1.00
F3 L:BEF1002 1.8 0.8 1.0
OG1 L:THR185 2.0 0.5 1.0
O1B L:ADP1000 2.2 0.4 1.0
CB L:THR185 3.1 0.6 1.0
BE L:BEF1002 3.2 0.0 1.0
PB L:ADP1000 3.3 0.0 1.0
O2B L:ADP1000 3.3 0.0 1.0
NH1 L:ARG212 3.8 0.8 1.0
F2 L:BEF1002 3.8 0.0 1.0
O1A L:ADP1000 3.8 0.6 1.0
OD2 L:ASP265 3.9 0.9 1.0
N L:THR185 4.0 0.4 1.0
OE2 L:GLU215 4.0 0.1 1.0
CA L:THR185 4.1 0.6 1.0
CG2 L:THR185 4.2 1.0 1.0
OE2 L:GLU211 4.2 0.9 1.0
F1 L:BEF1002 4.3 0.0 1.0
O3B L:ADP1000 4.3 0.0 1.0
O3A L:ADP1000 4.3 0.6 1.0
OE1 L:GLU215 4.4 0.4 1.0
OD1 L:ASP265 4.4 0.7 1.0
PA L:ADP1000 4.5 0.1 1.0
CD L:GLU215 4.5 0.1 1.0
CG L:ASP265 4.6 0.3 1.0
CD L:GLU211 4.6 0.3 1.0
O2A L:ADP1000 4.7 0.9 1.0
NH2 K:ARG366 4.8 0.6 1.0
OE1 L:GLU211 5.0 0.5 1.0

Magnesium binding site 2 out of 12 in 6duq

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Magnesium binding site 2 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:0.3
occ:1.00
F3 A:BEF1002 1.9 0.3 1.0
OG1 A:THR185 2.0 0.8 1.0
O1B A:ADP1000 2.2 0.0 1.0
CB A:THR185 3.1 0.3 1.0
BE A:BEF1002 3.2 0.1 1.0
PB A:ADP1000 3.3 0.3 1.0
O2B A:ADP1000 3.4 0.2 1.0
NH1 A:ARG212 3.8 0.2 1.0
F2 A:BEF1002 3.8 0.7 1.0
OD2 A:ASP265 3.9 0.6 1.0
O1A A:ADP1000 3.9 0.6 1.0
N A:THR185 4.0 0.1 1.0
OE2 A:GLU215 4.0 0.1 1.0
CA A:THR185 4.1 0.8 1.0
CG2 A:THR185 4.1 0.3 1.0
OE2 A:GLU211 4.2 1.0 1.0
F1 A:BEF1002 4.3 0.1 1.0
OD1 A:ASP265 4.3 0.6 1.0
O3B A:ADP1000 4.4 0.8 1.0
O3A A:ADP1000 4.4 0.3 1.0
OE1 A:GLU215 4.4 0.8 1.0
PA A:ADP1000 4.5 0.2 1.0
CG A:ASP265 4.5 0.2 1.0
CD A:GLU215 4.6 0.7 1.0
CD A:GLU211 4.6 0.7 1.0
O2A A:ADP1000 4.8 1.0 1.0
NH2 F:ARG366 4.8 0.7 1.0
OE1 A:GLU211 5.0 0.1 1.0

Magnesium binding site 3 out of 12 in 6duq

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Magnesium binding site 3 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1001

b:0.0
occ:1.00
F3 G:BEF1002 1.8 0.0 1.0
OG1 G:THR185 2.0 0.1 1.0
O1B G:ADP1000 2.2 0.5 1.0
CB G:THR185 3.1 0.4 1.0
BE G:BEF1002 3.2 0.8 1.0
PB G:ADP1000 3.3 0.2 1.0
O2B G:ADP1000 3.3 0.3 1.0
NH1 G:ARG212 3.8 0.9 1.0
F2 G:BEF1002 3.8 0.2 1.0
OD2 G:ASP265 3.9 0.2 1.0
O1A G:ADP1000 3.9 0.7 1.0
N G:THR185 4.0 0.1 1.0
OE2 G:GLU215 4.0 0.2 1.0
CA G:THR185 4.1 0.8 1.0
CG2 G:THR185 4.1 0.8 1.0
OE2 G:GLU211 4.2 0.5 1.0
F1 G:BEF1002 4.3 0.7 1.0
OD1 G:ASP265 4.3 0.7 1.0
O3B G:ADP1000 4.4 0.7 1.0
O3A G:ADP1000 4.4 0.8 1.0
OE1 G:GLU215 4.4 0.5 1.0
PA G:ADP1000 4.5 0.2 1.0
CG G:ASP265 4.5 0.7 1.0
CD G:GLU215 4.6 0.5 1.0
CD G:GLU211 4.6 0.0 1.0
NH2 L:ARG366 4.7 0.4 1.0
O2A G:ADP1000 4.8 0.9 1.0
OE1 G:GLU211 4.9 0.1 1.0

Magnesium binding site 4 out of 12 in 6duq

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Magnesium binding site 4 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:0.5
occ:1.00
F3 B:BEF1002 1.8 0.5 1.0
OG1 B:THR185 2.0 0.5 1.0
O1B B:ADP1000 2.2 0.7 1.0
BE B:BEF1002 3.2 0.5 1.0
CB B:THR185 3.2 0.4 1.0
PB B:ADP1000 3.2 0.5 1.0
O2B B:ADP1000 3.3 0.5 1.0
NH1 B:ARG212 3.8 0.6 1.0
F2 B:BEF1002 3.8 0.5 1.0
O1A B:ADP1000 3.8 0.5 1.0
OD2 B:ASP265 3.9 0.5 1.0
OE2 B:GLU215 4.0 0.6 1.0
N B:THR185 4.0 0.3 1.0
CA B:THR185 4.1 0.1 1.0
OE2 B:GLU211 4.2 0.1 1.0
CG2 B:THR185 4.2 0.9 1.0
F1 B:BEF1002 4.3 0.5 1.0
O3B B:ADP1000 4.3 0.5 1.0
O3A B:ADP1000 4.4 1.0 1.0
OE1 B:GLU215 4.4 0.4 1.0
OD1 B:ASP265 4.4 0.8 1.0
PA B:ADP1000 4.5 0.1 1.0
CD B:GLU215 4.5 0.7 1.0
CG B:ASP265 4.6 0.3 1.0
CD B:GLU211 4.6 0.9 1.0
NH2 A:ARG366 4.7 0.6 1.0
O2A B:ADP1000 4.7 0.5 1.0
OE1 B:GLU211 4.9 0.2 1.0
CZ B:ARG212 5.0 0.0 1.0

Magnesium binding site 5 out of 12 in 6duq

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Magnesium binding site 5 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1001

b:1.0
occ:1.00
F3 H:BEF1002 1.8 0.5 1.0
OG1 H:THR185 2.0 0.8 1.0
O1B H:ADP1000 2.2 0.4 1.0
CB H:THR185 3.1 0.6 1.0
BE H:BEF1002 3.2 1.0 1.0
PB H:ADP1000 3.2 1.0 1.0
O2B H:ADP1000 3.3 1.0 1.0
NH1 H:ARG212 3.8 0.8 1.0
O1A H:ADP1000 3.8 1.0 1.0
F2 H:BEF1002 3.8 1.0 1.0
OD2 H:ASP265 3.9 0.2 1.0
OE2 H:GLU215 4.0 0.5 1.0
N H:THR185 4.0 0.7 1.0
CA H:THR185 4.1 0.2 1.0
OE2 H:GLU211 4.2 0.3 1.0
CG2 H:THR185 4.2 0.8 1.0
F1 H:BEF1002 4.3 1.0 1.0
O3B H:ADP1000 4.3 0.5 1.0
O3A H:ADP1000 4.3 0.0 1.0
OE1 H:GLU215 4.4 0.7 1.0
OD1 H:ASP265 4.4 0.9 1.0
PA H:ADP1000 4.4 0.1 1.0
CD H:GLU215 4.5 0.1 1.0
CG H:ASP265 4.6 0.3 1.0
CD H:GLU211 4.6 0.1 1.0
O2A H:ADP1000 4.7 1.0 1.0
NH2 G:ARG366 4.7 0.2 1.0
OE1 H:GLU211 5.0 0.6 1.0

Magnesium binding site 6 out of 12 in 6duq

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Magnesium binding site 6 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:0.9
occ:1.00
F3 C:BEF1002 1.8 0.9 1.0
OG1 C:THR185 2.0 0.8 1.0
O1B C:ADP1000 2.2 0.9 1.0
CB C:THR185 3.1 0.5 1.0
BE C:BEF1002 3.2 0.6 1.0
PB C:ADP1000 3.3 0.3 1.0
O2B C:ADP1000 3.3 0.3 1.0
NH1 C:ARG212 3.8 1.0 1.0
F2 C:BEF1002 3.8 0.5 1.0
O1A C:ADP1000 3.9 0.7 1.0
OD2 C:ASP265 3.9 0.3 1.0
OE2 C:GLU215 4.0 0.5 1.0
N C:THR185 4.0 1.0 1.0
CA C:THR185 4.1 0.8 1.0
CG2 C:THR185 4.2 0.4 1.0
OE2 C:GLU211 4.2 0.2 1.0
F1 C:BEF1002 4.3 0.1 1.0
O3B C:ADP1000 4.3 0.8 1.0
O3A C:ADP1000 4.4 0.9 1.0
OD1 C:ASP265 4.4 0.6 1.0
OE1 C:GLU215 4.4 0.4 1.0
PA C:ADP1000 4.5 0.9 1.0
CD C:GLU215 4.6 0.8 1.0
CG C:ASP265 4.6 0.7 1.0
CD C:GLU211 4.6 0.5 1.0
NH2 B:ARG366 4.7 0.1 1.0
O2A C:ADP1000 4.8 0.8 1.0
OE1 C:GLU211 5.0 1.0 1.0

Magnesium binding site 7 out of 12 in 6duq

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Magnesium binding site 7 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1001

b:0.2
occ:1.00
F3 I:BEF1002 1.8 0.2 1.0
OG1 I:THR185 2.0 0.6 1.0
O1B I:ADP1000 2.2 0.4 1.0
CB I:THR185 3.1 0.2 1.0
BE I:BEF1002 3.2 0.0 1.0
PB I:ADP1000 3.3 0.6 1.0
O2B I:ADP1000 3.3 0.8 1.0
NH1 I:ARG212 3.8 0.6 1.0
F2 I:BEF1002 3.8 0.2 1.0
O1A I:ADP1000 3.9 0.7 1.0
OD2 I:ASP265 3.9 0.8 1.0
N I:THR185 4.0 0.6 1.0
OE2 I:GLU215 4.0 0.3 1.0
CA I:THR185 4.1 0.1 1.0
CG2 I:THR185 4.2 0.1 1.0
OE2 I:GLU211 4.2 1.0 1.0
F1 I:BEF1002 4.3 0.5 1.0
O3B I:ADP1000 4.3 0.2 1.0
OD1 I:ASP265 4.4 0.0 1.0
O3A I:ADP1000 4.4 0.2 1.0
OE1 I:GLU215 4.4 0.8 1.0
PA I:ADP1000 4.5 0.0 1.0
CD I:GLU215 4.6 0.8 1.0
CG I:ASP265 4.6 0.1 1.0
CD I:GLU211 4.6 0.9 1.0
NH2 H:ARG366 4.7 0.1 1.0
O2A I:ADP1000 4.8 0.2 1.0
OE1 I:GLU211 5.0 0.8 1.0

Magnesium binding site 8 out of 12 in 6duq

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Magnesium binding site 8 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:0.4
occ:1.00
F3 D:BEF1002 1.8 0.4 1.0
OG1 D:THR185 2.0 0.1 1.0
O1B D:ADP1000 2.2 0.4 1.0
CB D:THR185 3.2 1.0 1.0
BE D:BEF1002 3.2 0.4 1.0
PB D:ADP1000 3.3 0.4 1.0
O2B D:ADP1000 3.4 0.4 1.0
F2 D:BEF1002 3.8 0.4 1.0
NH1 D:ARG212 3.8 0.0 1.0
O1A D:ADP1000 3.9 0.4 1.0
OD2 D:ASP265 3.9 0.3 1.0
N D:THR185 4.0 0.6 1.0
OE2 D:GLU215 4.0 1.0 1.0
CA D:THR185 4.1 0.9 1.0
OE2 D:GLU211 4.2 0.2 1.0
CG2 D:THR185 4.2 0.7 1.0
O3B D:ADP1000 4.3 0.3 1.0
F1 D:BEF1002 4.3 0.4 1.0
OD1 D:ASP265 4.3 0.8 1.0
O3A D:ADP1000 4.4 0.6 1.0
OE1 D:GLU215 4.4 0.1 1.0
PA D:ADP1000 4.5 0.8 1.0
CD D:GLU215 4.6 0.4 1.0
CG D:ASP265 4.6 0.9 1.0
CD D:GLU211 4.6 0.7 1.0
O2A D:ADP1000 4.8 0.4 1.0
NH2 C:ARG366 4.8 0.1 1.0
OE1 D:GLU211 5.0 0.2 1.0

Magnesium binding site 9 out of 12 in 6duq

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Magnesium binding site 9 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1001

b:1.0
occ:1.00
F3 K:BEF1002 1.8 1.0 1.0
OG1 K:THR185 2.0 0.4 1.0
O1B K:ADP1000 2.2 0.2 1.0
CB K:THR185 3.1 0.1 1.0
BE K:BEF1002 3.2 0.1 1.0
PB K:ADP1000 3.3 0.3 1.0
O2B K:ADP1000 3.4 0.9 1.0
NH1 K:ARG212 3.8 0.3 1.0
F2 K:BEF1002 3.8 0.5 1.0
OD2 K:ASP265 3.9 0.9 1.0
O1A K:ADP1000 3.9 0.7 1.0
N K:THR185 4.0 0.9 1.0
OE2 K:GLU215 4.0 0.7 1.0
CA K:THR185 4.1 0.9 1.0
CG2 K:THR185 4.1 0.4 1.0
OE2 K:GLU211 4.2 0.4 1.0
F1 K:BEF1002 4.3 0.6 1.0
OD1 K:ASP265 4.3 0.7 1.0
O3B K:ADP1000 4.4 0.8 1.0
O3A K:ADP1000 4.4 0.7 1.0
OE1 K:GLU215 4.4 0.0 1.0
PA K:ADP1000 4.5 0.9 1.0
CG K:ASP265 4.6 0.3 1.0
CD K:GLU215 4.6 0.2 1.0
CD K:GLU211 4.6 1.0 1.0
O2A K:ADP1000 4.8 0.3 1.0
NH2 J:ARG366 4.8 0.4 1.0
OE1 K:GLU211 5.0 0.0 1.0

Magnesium binding site 10 out of 12 in 6duq

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Magnesium binding site 10 out of 12 in the Structure of A Rho-Nusg Kow Domain Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Rho-Nusg Kow Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:0.6
occ:1.00
F3 F:BEF1002 1.8 0.6 1.0
OG1 F:THR185 2.0 0.1 1.0
O1B F:ADP1000 2.2 0.6 1.0
BE F:BEF1002 3.1 0.6 1.0
CB F:THR185 3.2 0.9 1.0
PB F:ADP1000 3.2 0.6 1.0
O2B F:ADP1000 3.3 0.6 1.0
F2 F:BEF1002 3.8 0.6 1.0
NH1 F:ARG212 3.8 0.2 1.0
O1A F:ADP1000 3.8 0.1 1.0
OD2 F:ASP265 4.0 0.7 1.0
OE2 F:GLU215 4.0 0.2 1.0
N F:THR185 4.0 0.4 1.0
CA F:THR185 4.1 0.8 1.0
OE2 F:GLU211 4.2 0.7 1.0
CG2 F:THR185 4.2 0.8 1.0
F1 F:BEF1002 4.3 0.6 1.0
O3B F:ADP1000 4.3 0.0 1.0
O3A F:ADP1000 4.3 0.4 1.0
OE1 F:GLU215 4.4 0.8 1.0
OD1 F:ASP265 4.4 0.6 1.0
PA F:ADP1000 4.5 0.3 1.0
CD F:GLU215 4.6 0.8 1.0
CG F:ASP265 4.6 0.5 1.0
CD F:GLU211 4.6 0.8 1.0
NH2 E:ARG366 4.7 0.6 1.0
O2A F:ADP1000 4.8 0.6 1.0
OE1 F:GLU211 4.9 0.6 1.0

Reference:

M.R.Lawson, W.Ma, M.J.Bellecourt, I.Artsimovitch, A.Martin, R.Landick, K.Schulten, J.M.Berger. Mechanism For the Regulated Control of Bacterial Transcription Termination By A Universal Adaptor Protein. Mol. Cell V. 71 911 2018.
ISSN: ISSN 1097-4164
PubMed: 30122535
DOI: 10.1016/J.MOLCEL.2018.07.014
Page generated: Mon Dec 14 22:37:16 2020

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