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Magnesium in PDB 3u5z: Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog

Protein crystallography data

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 3u5z was solved by B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.19 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.702, 239.177, 247.672, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 27.9

Other elements in 3u5z:

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog (pdb code 3u5z). 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 T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 3u5z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3u5z

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Magnesium binding site 1 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg800

b:71.4
occ:1.00
 OE2 B:GLU108 2.3 72.2 1.0
F1 B:08T700 2.4 72.2 1.0
CG2 B:THR57 2.7 70.4 1.0
O1B B:08T700 2.7 72.7 1.0
NH2 C:ARG151 3.1 68.3 1.0
OG1 B:THR57 3.1 70.4 1.0
OE1 C:GLU126 3.2 69.2 1.0
CD B:GLU108 3.3 72.0 1.0
CB B:THR57 3.4 70.7 1.0
BE B:08T700 3.6 71.9 1.0
OD2 B:ASP107 3.7 70.5 1.0
F2 B:08T700 3.8 71.4 1.0
CG B:GLU108 3.9 72.1 1.0
OD1 B:ASP107 3.9 70.7 1.0
NH2 B:ARG205 4.0 68.6 1.0
PB B:08T700 4.0 72.6 1.0
CG B:ASP107 4.2 70.7 1.0
O3B B:08T700 4.3 72.1 1.0
OE1 B:GLU108 4.3 71.7 1.0
CD C:GLU126 4.3 69.0 1.0
CZ C:ARG151 4.4 67.9 1.0
O2A B:08T700 4.6 72.9 1.0
F3 B:08T700 4.7 71.8 1.0
CG2 B:THR137 4.7 70.6 1.0
OE2 C:GLU126 4.8 69.1 1.0
CA B:THR57 4.8 71.2 1.0
O3A B:08T700 4.8 72.6 1.0
N B:THR57 5.0 71.0 1.0

Magnesium binding site 2 out of 8 in 3u5z

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Magnesium binding site 2 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg800

b:63.5
occ:1.00
 F1 C:08T700 2.3 64.4 1.0
OE2 C:GLU108 2.5 77.0 1.0
CG2 C:THR57 2.6 62.1 1.0
OG1 C:THR57 2.7 61.8 1.0
O1B C:08T700 2.9 64.5 1.0
NH2 D:ARG151 3.0 61.1 1.0
CB C:THR57 3.1 62.1 1.0
OE1 D:GLU126 3.2 61.4 1.0
BE C:08T700 3.3 64.2 1.0
F2 C:08T700 3.5 64.0 1.0
OD2 C:ASP107 3.5 62.4 1.0
CD C:GLU108 3.6 77.1 1.0
O2A C:08T700 4.0 64.2 1.0
CG C:GLU108 4.1 77.3 1.0
OD1 C:ASP107 4.1 62.5 1.0
NH2 C:ARG205 4.1 60.8 1.0
O3B C:08T700 4.1 64.1 1.0
PB C:08T700 4.1 64.3 1.0
CG C:ASP107 4.2 62.6 1.0
CD D:GLU126 4.2 61.3 1.0
CZ D:ARG151 4.2 60.9 1.0
F3 C:08T700 4.4 64.2 1.0
CA C:THR57 4.5 62.3 1.0
OE2 D:GLU126 4.6 61.1 1.0
CG2 C:THR137 4.7 62.4 1.0
OE1 C:GLU108 4.7 77.2 1.0
N C:THR57 4.8 62.2 1.0
NH1 D:ARG151 4.9 60.8 1.0

Magnesium binding site 3 out of 8 in 3u5z

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Magnesium binding site 3 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg800

b:63.9
occ:1.00
 OG1 D:THR57 2.5 70.8 1.0
CG2 D:THR57 2.5 70.7 1.0
F1 D:08T700 2.7 64.4 1.0
OE2 D:GLU108 2.7 89.7 1.0
F2 D:08T700 2.8 65.1 1.0
CB D:THR57 3.0 70.6 1.0
O1B D:08T700 3.1 64.0 1.0
OE1 E:GLU126 3.2 62.8 1.0
NH2 E:ARG151 3.2 62.9 1.0
BE D:08T700 3.2 64.7 1.0
OD2 D:ASP107 3.4 62.1 1.0
CD D:GLU108 3.8 89.8 1.0
O3B D:08T700 3.9 64.5 1.0
PB D:08T700 4.0 64.1 1.0
OD1 D:ASP107 4.1 61.4 1.0
CG D:ASP107 4.1 61.8 1.0
CD E:GLU126 4.1 63.0 1.0
CG D:GLU108 4.2 90.1 1.0
NH2 D:ARG205 4.3 62.3 1.0
OE2 E:GLU126 4.4 62.7 1.0
CZ E:ARG151 4.4 63.2 1.0
O2A D:08T700 4.4 64.4 1.0
CA D:THR57 4.4 60.7 1.0
F3 D:08T700 4.4 64.8 1.0
O3A D:08T700 4.5 64.3 1.0
N D:THR57 4.7 60.5 1.0
CG2 D:THR137 4.7 60.9 1.0
OE1 D:GLU108 4.9 89.8 1.0
O E:ARG122 4.9 63.8 1.0
NH1 E:ARG151 5.0 63.1 1.0

Magnesium binding site 4 out of 8 in 3u5z

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Magnesium binding site 4 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:81.3
occ:1.00
 CG2 E:THR57 2.8 95.5 1.0
OG1 E:THR57 2.9 97.1 1.0
O2A E:ADP700 3.0 82.8 1.0
O3B E:ADP700 3.0 81.8 1.0
OD2 E:ASP107 3.0 96.8 1.0
CB E:THR57 3.3 96.0 1.0
NH1 E:ARG205 3.6 81.9 1.0
CG E:ASP107 4.0 95.8 1.0
O1B E:ADP700 4.0 80.7 1.0
PB E:ADP700 4.0 81.6 1.0
OD1 E:ASP107 4.1 95.4 1.0
OE2 E:GLU108 4.1 0.9 1.0
PA E:ADP700 4.3 83.0 1.0
O3A E:ADP700 4.6 82.7 1.0
CA E:THR57 4.8 86.3 1.0
CZ E:ARG205 4.9 82.5 1.0
CG E:GLU108 4.9 1.0 1.0

Magnesium binding site 5 out of 8 in 3u5z

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Magnesium binding site 5 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg800

b:70.9
occ:1.00
 O1B L:08T700 2.5 72.0 1.0
OG1 L:THR57 2.7 81.0 1.0
CG2 L:THR57 2.7 81.0 1.0
F1 L:08T700 2.7 71.9 1.0
OE2 L:GLU108 2.8 0.1 1.0
NH2 M:ARG151 3.0 67.9 1.0
OE1 M:GLU126 3.0 68.5 1.0
CB L:THR57 3.2 81.3 1.0
O2A L:08T700 3.5 72.3 1.0
NH2 L:ARG205 3.6 68.5 1.0
BE L:08T700 3.6 71.8 1.0
PB L:08T700 3.7 72.6 1.0
O3B L:08T700 3.8 72.1 1.0
CD L:GLU108 3.9 99.9 1.0
F2 L:08T700 3.9 71.3 1.0
OD2 L:ASP107 4.0 69.5 1.0
CD M:GLU126 4.0 68.4 1.0
CZ M:ARG151 4.2 67.6 1.0
OE2 M:GLU126 4.3 68.6 1.0
OD1 L:ASP107 4.3 69.9 1.0
CG L:GLU108 4.5 99.8 1.0
PA L:08T700 4.5 72.8 1.0
CG L:ASP107 4.5 69.7 1.0
O3A L:08T700 4.6 72.8 1.0
CA L:THR57 4.6 70.7 1.0
N L:THR57 4.8 70.7 1.0
NH1 M:ARG151 4.8 67.6 1.0
OE1 L:GLU108 4.8 99.8 1.0
O1A L:08T700 4.8 73.2 1.0
F3 L:08T700 4.8 71.9 1.0
CZ L:ARG205 4.9 68.4 1.0
O2B L:08T700 5.0 73.0 1.0
CG2 L:THR137 5.0 70.2 1.0

Magnesium binding site 6 out of 8 in 3u5z

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Magnesium binding site 6 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg800

b:63.7
occ:1.00
 F1 M:08T700 2.4 65.2 1.0
OE2 M:GLU108 2.5 87.3 1.0
CG2 M:THR57 2.6 67.3 1.0
OG1 M:THR57 2.7 67.1 1.0
OE1 N:GLU126 2.9 61.2 1.0
O1B M:08T700 3.1 65.2 1.0
CB M:THR57 3.1 67.2 1.0
NH2 N:ARG151 3.1 61.5 1.0
BE M:08T700 3.4 65.3 1.0
OD2 M:ASP107 3.5 61.7 1.0
CD M:GLU108 3.6 87.3 1.0
O3B M:08T700 3.8 65.2 1.0
F2 M:08T700 3.9 65.1 1.0
CD N:GLU126 4.0 61.0 1.0
PB M:08T700 4.1 65.4 1.0
CG M:GLU108 4.1 87.2 1.0
OD1 M:ASP107 4.1 62.2 1.0
O2A M:08T700 4.1 64.7 1.0
NH2 M:ARG205 4.1 61.6 1.0
CG M:ASP107 4.2 61.9 1.0
CZ N:ARG151 4.4 61.4 1.0
OE2 N:GLU126 4.5 61.1 1.0
CA M:THR57 4.5 62.3 1.0
F3 M:08T700 4.6 65.6 1.0
OE1 M:GLU108 4.7 87.6 1.0
CG2 M:THR137 4.7 62.7 1.0
N M:THR57 4.8 62.6 1.0
O3A M:08T700 5.0 65.3 1.0

Magnesium binding site 7 out of 8 in 3u5z

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Magnesium binding site 7 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg800

b:65.4
occ:1.00
 F1 N:08T700 2.3 66.8 1.0
OE2 N:GLU108 2.5 91.3 1.0
CG2 N:THR57 2.6 62.5 1.0
OG1 N:THR57 2.8 62.8 1.0
O1B N:08T700 3.0 66.3 1.0
NH2 O:ARG151 3.1 64.7 1.0
CB N:THR57 3.2 62.3 1.0
OE1 O:GLU126 3.2 64.9 1.0
OD2 N:ASP107 3.2 62.5 1.0
CD N:GLU108 3.6 91.4 1.0
BE N:08T700 3.6 67.3 1.0
OD1 N:ASP107 3.9 62.2 1.0
CG N:GLU108 3.9 91.2 1.0
CG N:ASP107 3.9 62.3 1.0
F2 N:08T700 3.9 67.8 1.0
CD O:GLU126 4.2 65.2 1.0
PB N:08T700 4.3 66.7 1.0
CZ O:ARG151 4.3 65.2 1.0
O2A N:08T700 4.3 66.5 1.0
O3B N:08T700 4.4 67.3 1.0
OE2 O:GLU126 4.4 65.2 1.0
F3 N:08T700 4.5 67.4 1.0
CA N:THR57 4.6 62.0 1.0
NH2 N:ARG205 4.7 64.8 1.0
CG2 N:THR137 4.7 62.7 1.0
OE1 N:GLU108 4.7 91.6 1.0
O O:ARG122 4.8 64.8 1.0
N N:THR57 4.9 62.3 1.0
NH1 O:ARG151 4.9 65.6 1.0

Magnesium binding site 8 out of 8 in 3u5z

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Magnesium binding site 8 out of 8 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg801

b:83.8
occ:1.00
 CG2 O:THR57 2.4 0.5 1.0
O1B O:ADP700 2.6 84.3 1.0
O3B O:ADP700 3.0 85.9 1.0
O2A O:ADP700 3.1 85.6 1.0
OG1 O:THR57 3.1 0.0 1.0
OE2 O:GLU108 3.3 0.0 1.0
PB O:ADP700 3.3 85.5 1.0
CB O:THR57 3.4 0.8 1.0
OD2 O:ASP107 3.6 78.6 1.0
NH1 O:ARG205 3.8 91.7 1.0
OD1 O:ASP107 4.0 77.7 1.0
CG O:ASP107 4.2 77.7 1.0
O3A O:ADP700 4.3 86.5 1.0
PA O:ADP700 4.3 86.2 1.0
CD O:GLU108 4.3 0.3 1.0
NZ O:LYS56 4.5 80.7 1.0
CE O:LYS56 4.5 79.6 1.0
CG O:GLU108 4.6 0.6 1.0
CA O:THR57 4.6 81.2 1.0
N O:THR57 4.7 81.6 1.0
O2B O:ADP700 4.7 85.6 1.0
CZ O:ARG205 4.9 92.7 1.0

Reference:

B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan. How A Dna Polymerase Clamp Loader Opens A Sliding Clamp. Science V. 334 1675 2011.
ISSN: ISSN 0036-8075
PubMed: 22194570
DOI: 10.1126/SCIENCE.1211884
Page generated: Thu Aug 15 12:21:49 2024

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