Aluminium in PDB 8uk9: Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog

The structure of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 8uk9 was solved by K.Marcus, S.Ghaffari-Kashani, C.L.Gee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.13 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.243, 231.991, 264.511, 90, 90, 90
R / Rfree (%)	25.3 / 26.5

The structure of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog also contains other interesting chemical elements:

Fluorine	(F)	18 atoms
Magnesium	(Mg)	8 atoms

The binding sites of Aluminium atom in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog (pdb code 8uk9). This binding sites where shown within 5.0 Angstroms radius around Aluminium atom.
In total 6 binding sites of Aluminium where determined in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 8uk9:
Jump to Aluminium binding site number: 1; 2; 3; 4; 5; 6;

Aluminium binding site 1 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 1 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Al901 b:67.9 occ:1.00 AL B:AF3901 0.0 67.9 1.0 F3 B:AF3901 1.6 68.5 1.0 F2 B:AF3901 1.6 68.5 1.0 F1 B:AF3901 1.6 66.9 1.0 O3B B:ADP902 1.7 69.0 1.0 NZ B:LYS56 2.8 71.5 1.0 PB B:ADP902 2.9 70.1 1.0 O2B B:ADP902 3.2 70.8 1.0 OE2 B:GLU108 3.4 74.9 1.0 NH2 C:ARG151 3.4 64.3 1.0 NH2 B:ARG205 3.5 67.7 1.0 NH1 C:ARG151 3.6 63.8 1.0 MG B:MG903 3.7 65.0 1.0 ND2 B:ASN139 3.8 77.2 1.0 O3A B:ADP902 3.9 69.8 1.0 O1B B:ADP902 3.9 70.7 1.0 CZ C:ARG151 4.0 63.1 1.0 OE1 B:GLU108 4.0 75.2 1.0 CE B:LYS56 4.1 72.5 1.0 CD B:GLU108 4.1 75.1 1.0 CB B:PRO52 4.3 68.2 1.0 N B:GLY53 4.4 69.0 1.0 OD1 B:ASN139 4.4 77.7 1.0 CG B:ASN139 4.5 77.7 1.0 CA B:PRO52 4.6 69.2 1.0 CB C:PRO147 4.7 63.6 1.0 CZ B:ARG205 4.8 67.3 1.0

Aluminium binding site 2 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 2 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Al402 b:55.0 occ:1.00 AL C:AF3402 0.0 55.0 1.0 F3 C:AF3402 1.6 55.1 1.0 F2 C:AF3402 1.6 55.8 1.0 F1 C:AF3402 1.6 54.6 1.0 O1B C:ADP403 1.7 54.9 1.0 PB C:ADP403 2.7 55.2 1.0 O2B C:ADP403 2.9 54.6 1.0 OE2 C:GLU108 3.3 69.4 1.0 MG C:MG401 3.5 48.3 1.0 OD1 C:ASN139 3.7 60.4 1.0 CE C:LYS56 3.7 53.0 1.0 NZ C:LYS56 3.8 53.8 1.0 ND2 C:ASN139 3.8 60.9 1.0 O3B C:ADP403 3.8 55.7 1.0 O3A C:ADP403 3.9 56.3 1.0 N C:GLY53 3.9 54.9 1.0 NH2 C:ARG205 4.0 54.8 1.0 NH2 D:ARG151 4.2 54.6 1.0 CG C:ASN139 4.2 60.1 1.0 CD C:GLU108 4.2 67.1 1.0 OE1 C:GLU108 4.3 62.7 1.0 NH1 D:ARG151 4.4 54.3 1.0 CA C:PRO52 4.5 56.6 1.0 CA C:GLY53 4.7 55.8 1.0 CZ D:ARG151 4.8 54.0 1.0 OG1 C:THR57 4.8 55.8 1.0 C C:PRO52 4.8 57.2 1.0 CB C:PRO52 4.8 56.7 1.0 CB D:PRO147 4.9 57.1 1.0

Aluminium binding site 3 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 3 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Al402 b:56.1 occ:1.00 AL D:AF3402 0.0 56.1 1.0 F2 D:AF3402 1.6 52.3 1.0 F3 D:AF3402 1.6 70.3 1.0 F1 D:AF3402 1.6 62.8 1.0 O1B D:ADP403 1.7 56.5 1.0 PB D:ADP403 2.9 72.7 1.0 O2B D:ADP403 3.1 58.3 1.0 OE2 D:GLU108 3.3 70.9 1.0 NH1 E:ARG151 3.5 61.3 1.0 MG D:MG401 3.6 59.2 1.0 NH2 D:ARG205 3.6 65.6 1.0 NZ D:LYS56 3.6 58.2 1.0 OE1 D:GLU108 3.7 72.3 1.0 O3A D:ADP403 3.8 70.1 1.0 NH2 E:ARG151 3.8 61.5 1.0 OD1 D:ASN139 3.8 62.3 1.0 CD D:GLU108 3.9 71.6 1.0 O3B D:ADP403 4.0 61.5 1.0 ND2 D:ASN139 4.1 62.0 1.0 CZ E:ARG151 4.1 61.3 1.0 CE D:LYS56 4.2 57.6 1.0 CG D:ASN139 4.3 61.6 1.0 N D:GLY53 4.4 62.5 1.0 CB D:PRO52 4.4 61.3 1.0 CB E:PRO147 4.4 59.5 1.0 CA D:PRO52 4.5 61.6 1.0 CZ D:ARG205 4.8 69.2 1.0 OG1 D:THR57 4.9 58.6 1.0

Aluminium binding site 4 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 4 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ K:Al402 b:101.1 occ:1.00 AL K:AF3402 0.0 101.1 1.0 F3 K:AF3402 1.6 100.9 1.0 F2 K:AF3402 1.6 102.0 1.0 F1 K:AF3402 1.6 100.9 1.0 O2B K:ADP403 2.4 103.6 1.0 O1B K:ADP403 2.6 104.8 1.0 PB K:ADP403 3.0 105.1 1.0 OE2 K:GLU108 3.3 105.7 1.0 NZ K:LYS56 3.3 107.2 1.0 ND2 K:ASN139 3.4 108.2 1.0 MG K:MG401 3.5 96.7 1.0 NH2 L:ARG151 3.5 101.8 1.0 CE K:LYS56 3.8 106.0 1.0 OE1 K:GLU108 3.9 104.2 1.0 CD K:GLU108 3.9 104.8 1.0 NH2 K:ARG205 4.1 104.1 1.0 O3A K:ADP403 4.1 106.7 1.0 O3B K:ADP403 4.2 106.2 1.0 NH1 L:ARG151 4.2 94.9 1.0 CZ L:ARG151 4.3 97.2 1.0 N K:GLY53 4.3 108.5 1.0 CG K:ASN139 4.4 107.9 1.0 OD1 K:ASN139 4.6 108.3 1.0 CA K:PRO52 4.6 105.0 1.0 CB L:PRO147 4.7 95.0 1.0 CB K:PRO52 4.8 104.2 1.0 NH1 K:ARG205 4.9 104.5 1.0 CG2 K:THR57 4.9 106.1 1.0 CZ K:ARG205 5.0 105.1 1.0

Aluminium binding site 5 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 5 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ L:Al402 b:86.3 occ:1.00 AL L:AF3402 0.0 86.3 1.0 F3 L:AF3402 1.6 85.8 1.0 F1 L:AF3402 1.6 87.4 1.0 F2 L:AF3402 1.6 85.5 1.0 O2B L:ADP403 1.7 89.0 1.0 PB L:ADP403 2.7 89.9 1.0 OE2 L:GLU108 2.9 94.6 1.0 O1B L:ADP403 3.0 90.0 1.0 MG L:MG401 3.1 84.8 1.0 NZ L:LYS56 3.2 89.3 1.0 NH2 L:ARG205 3.5 88.1 1.0 O3B L:ADP403 3.6 89.7 1.0 CE L:LYS56 3.9 90.3 1.0 CD L:GLU108 3.9 93.6 1.0 O3A L:ADP403 4.0 91.6 1.0 NH2 M:ARG151 4.0 86.3 1.0 NH1 M:ARG151 4.0 84.2 1.0 ND2 L:ASN139 4.1 92.2 1.0 OG1 L:THR57 4.2 89.8 1.0 OE1 L:GLU108 4.2 93.0 1.0 NH1 L:ARG205 4.2 88.7 1.0 CZ L:ARG205 4.3 89.0 1.0 OD1 L:ASN139 4.4 93.6 1.0 CB L:PRO52 4.4 90.8 1.0 CZ M:ARG151 4.5 85.2 1.0 N L:GLY53 4.6 90.9 1.0 CG L:ASN139 4.7 92.6 1.0 O2A L:ADP403 4.8 91.8 1.0 CA L:PRO52 4.9 91.5 1.0 CG2 L:THR137 4.9 95.6 1.0

Aluminium binding site 6 out of 6 in the Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 6 of Structure of T4 Bacteriophage Clamp Loader Mutant D110C Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ M:Al402 b:84.2 occ:1.00 AL M:AF3402 0.0 84.2 1.0 F3 M:AF3402 1.6 83.3 1.0 F2 M:AF3402 1.6 84.2 1.0 F1 M:AF3402 1.6 85.5 1.0 O2B M:ADP403 1.7 88.3 1.0 PB M:ADP403 2.9 91.6 1.0 OE2 M:GLU108 3.0 90.0 1.0 O M:PRO52 3.3 93.3 1.0 NZ M:LYS56 3.3 88.5 1.0 MG M:MG401 3.4 84.7 1.0 NH2 M:ARG205 3.4 96.3 1.0 O3B M:ADP403 3.5 90.3 1.0 ND2 M:ASN139 3.5 90.8 1.0 O1B M:ADP403 3.6 87.5 1.0 CD M:GLU108 3.8 89.8 1.0 NH2 N:ARG151 3.8 91.0 1.0 OE1 M:GLU108 3.9 88.0 1.0 CE M:LYS56 3.9 87.6 1.0 O3A M:ADP403 4.2 94.3 1.0 OD1 M:ASN139 4.3 88.7 1.0 C M:PRO52 4.3 95.5 1.0 CG M:ASN139 4.3 91.6 1.0 OG1 M:THR57 4.4 88.1 1.0 CZ M:ARG205 4.7 96.0 1.0 CB N:PRO147 4.7 92.9 1.0 CG2 M:THR137 4.7 83.0 1.0 CA M:PRO52 4.8 95.8 1.0

K.Marcus, Y.Huang, S.Subramanian, C.L.Gee, K.Gorday, S.Ghaffari-Kashani, X.R.Luo, L.Zheng, M.O'donnel, S.Subramanian, J.Kuriyan. Autoinhibition of A Clamp-Loader Atpase Revealed By Deep Mutagenesis and Cryo-Em To Be Published.