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Magnesium in PDB 3glg: Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna

Enzymatic activity of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna

All present enzymatic activity of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glg was solved by K.R.Simonetta, S.N.Seyedin, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 3.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.102, 219.104, 274.664, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.3

Other elements in 3glg:

The structure of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna (pdb code 3glg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3glg

Go back to Magnesium Binding Sites List in 3glg
Magnesium binding site 1 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg412

b:89.5
occ:1.00
F1 B:BEF401 2.1 95.3 1.0
O1B B:ADP400 2.1 0.7 1.0
CG2 B:THR52 2.3 0.4 1.0
OD1 B:ASP126 3.3 87.4 1.0
OD2 B:ASP126 3.3 88.4 1.0
BE B:BEF401 3.3 95.4 1.0
PB B:ADP400 3.5 0.5 1.0
OE2 B:GLU127 3.6 90.2 1.0
CB B:THR52 3.6 1.0 1.0
F3 B:BEF401 3.6 94.6 1.0
CG B:ASP126 3.7 87.8 1.0
OG1 B:THR52 3.7 0.5 1.0
O3B B:ADP400 3.9 0.7 1.0
OE2 C:GLU144 4.2 0.3 1.0
NH2 C:ARG169 4.2 85.3 1.0
O2A B:ADP400 4.3 0.1 1.0
N B:THR52 4.5 1.0 1.0
O2B B:ADP400 4.5 0.1 1.0
CD B:GLU127 4.5 89.6 1.0
O3A B:ADP400 4.6 1.0 1.0
F2 B:BEF401 4.6 95.6 1.0
CA B:THR52 4.7 0.2 1.0
CG B:GLU127 4.7 89.5 1.0
NZ C:LYS141 5.0 90.1 1.0

Magnesium binding site 2 out of 6 in 3glg

Go back to Magnesium Binding Sites List in 3glg
Magnesium binding site 2 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:89.0
occ:1.00
OG1 C:THR52 2.0 90.2 1.0
F1 C:BEF403 2.1 95.9 1.0
O1B C:ADP402 2.1 90.3 1.0
OE2 C:GLU127 3.1 92.8 1.0
OD1 C:ASP126 3.1 97.6 1.0
CB C:THR52 3.2 91.6 1.0
BE C:BEF403 3.5 96.8 1.0
PB C:ADP402 3.5 91.3 1.0
O2A C:ADP402 3.7 92.8 1.0
NH2 D:ARG169 3.8 91.7 1.0
CG2 C:THR52 3.9 91.7 1.0
O3B C:ADP402 4.0 90.8 1.0
CG C:ASP126 4.0 96.6 1.0
F2 C:BEF403 4.0 97.7 1.0
OD2 C:ASP126 4.1 96.4 1.0
OE2 D:GLU144 4.2 0.1 1.0
CD C:GLU127 4.3 92.0 1.0
CA C:THR52 4.4 92.2 1.0
N C:THR52 4.5 92.2 1.0
O3A C:ADP402 4.5 93.1 1.0
OE1 D:GLU144 4.5 0.8 1.0
F3 C:BEF403 4.6 96.1 1.0
O2B C:ADP402 4.7 91.8 1.0
NH2 C:ARG215 4.7 99.4 1.0
PA C:ADP402 4.7 94.0 1.0
CD D:GLU144 4.8 0.5 1.0
OE1 C:GLU127 4.9 91.8 1.0
CD D:LYS141 5.0 97.4 1.0

Magnesium binding site 3 out of 6 in 3glg

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Magnesium binding site 3 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg414

b:85.8
occ:1.00
F1 D:BEF405 2.1 1.0 1.0
O1B D:ADP404 2.1 93.2 1.0
CG2 D:THR52 2.3 89.3 1.0
OD2 D:ASP126 2.9 97.9 1.0
OE2 D:GLU127 3.3 85.1 1.0
CB D:THR52 3.4 91.2 1.0
BE D:BEF405 3.5 0.7 1.0
OG1 D:THR52 3.5 92.3 1.0
PB D:ADP404 3.5 93.8 1.0
OD1 D:ASP126 3.7 96.4 1.0
CG D:ASP126 3.7 97.0 1.0
NH2 E:ARG158 3.9 87.7 1.0
O2A D:ADP404 3.9 96.5 1.0
O3B D:ADP404 4.0 92.8 1.0
F2 D:BEF405 4.1 0.2 1.0
OE1 E:GLU133 4.4 0.2 1.0
N D:THR52 4.4 92.1 1.0
NZ E:LYS130 4.5 0.6 1.0
O2B D:ADP404 4.5 93.7 1.0
CD D:GLU127 4.6 84.0 1.0
CA D:THR52 4.6 92.5 1.0
O3A D:ADP404 4.7 96.1 1.0
NH2 D:ARG215 4.7 95.8 1.0
F3 D:BEF405 4.7 0.7 1.0
PA D:ADP404 4.9 97.7 1.0

Magnesium binding site 4 out of 6 in 3glg

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Magnesium binding site 4 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg415

b:89.5
occ:1.00
F1 G:BEF407 2.1 97.8 1.0
O1B G:ADP406 2.1 93.2 1.0
CG2 G:THR52 2.3 94.0 1.0
BE G:BEF407 3.3 97.1 1.0
OD1 G:ASP126 3.4 93.5 1.0
PB G:ADP406 3.4 93.1 1.0
OD2 G:ASP126 3.5 94.9 1.0
OE2 G:GLU127 3.5 95.1 1.0
CB G:THR52 3.6 95.8 1.0
F3 G:BEF407 3.6 96.7 1.0
CG G:ASP126 3.8 94.2 1.0
O3B G:ADP406 3.8 91.6 1.0
OG1 G:THR52 3.8 96.2 1.0
OE2 H:GLU144 4.2 0.2 1.0
NH2 H:ARG169 4.2 96.4 1.0
O2A G:ADP406 4.2 95.2 1.0
CD G:GLU127 4.4 94.8 1.0
O2B G:ADP406 4.5 93.5 1.0
N G:THR52 4.5 96.1 1.0
O3A G:ADP406 4.6 94.0 1.0
F2 G:BEF407 4.6 96.5 1.0
CA G:THR52 4.7 96.9 1.0
CG G:GLU127 4.7 95.2 1.0
NZ H:LYS141 4.8 89.0 1.0
CE G:LYS51 4.9 91.2 1.0

Magnesium binding site 5 out of 6 in 3glg

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Magnesium binding site 5 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg416

b:63.9
occ:1.00
OG1 H:THR52 1.9 66.2 1.0
F1 I:BEF409 2.1 72.7 1.0
O1B H:ADP408 2.1 74.2 1.0
OE2 H:GLU127 3.1 71.6 1.0
OD1 H:ASP126 3.1 75.7 1.0
CB H:THR52 3.2 66.8 1.0
BE I:BEF409 3.4 72.7 1.0
PB H:ADP408 3.6 74.4 1.0
O2A H:ADP408 3.7 74.7 1.0
NH2 I:ARG169 3.8 72.4 1.0
CG H:ASP126 3.9 75.9 1.0
CG2 H:THR52 3.9 67.5 1.0
OD2 H:ASP126 3.9 75.6 1.0
O3B H:ADP408 4.0 74.1 1.0
F2 I:BEF409 4.0 72.6 1.0
CD H:GLU127 4.3 71.8 1.0
CA H:THR52 4.3 67.5 1.0
N H:THR52 4.3 67.2 1.0
OE2 I:GLU144 4.4 86.1 1.0
O3A H:ADP408 4.5 74.6 1.0
F3 I:BEF409 4.5 72.9 1.0
OE1 I:GLU144 4.5 86.8 1.0
O2B H:ADP408 4.7 75.0 1.0
NH2 H:ARG215 4.7 67.6 1.0
PA H:ADP408 4.7 75.0 1.0
OE1 H:GLU127 4.9 71.8 1.0
CD I:GLU144 4.9 86.0 1.0

Magnesium binding site 6 out of 6 in 3glg

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Magnesium binding site 6 out of 6 in the Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Mutant (GAMMAT157A) E. Coli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg417

b:67.6
occ:1.00
F1 I:BEF411 2.1 76.3 1.0
O1B I:ADP410 2.1 67.6 1.0
CG2 I:THR52 2.4 73.6 1.0
OD2 I:ASP126 3.2 87.0 1.0
BE I:BEF411 3.4 77.1 1.0
NH2 J:ARG158 3.4 73.7 1.0
OG1 I:THR52 3.4 75.5 1.0
OE2 I:GLU127 3.5 90.2 1.0
CB I:THR52 3.5 74.5 1.0
PB I:ADP410 3.5 68.0 1.0
O2A I:ADP410 3.6 69.8 1.0
O3B I:ADP410 3.9 68.0 1.0
F2 I:BEF411 3.9 78.1 1.0
OE1 J:GLU133 4.0 95.5 1.0
OD1 I:ASP126 4.0 85.5 1.0
CG I:ASP126 4.0 86.2 1.0
NZ J:LYS130 4.3 93.2 1.0
NH2 I:ARG215 4.4 74.7 1.0
N I:THR52 4.5 74.7 1.0
O2B I:ADP410 4.6 67.6 1.0
O3A I:ADP410 4.6 69.4 1.0
OE2 J:GLU133 4.6 96.5 1.0
CA I:THR52 4.6 74.9 1.0
CZ J:ARG158 4.7 73.4 1.0
F3 I:BEF411 4.7 76.7 1.0
CD J:GLU133 4.7 96.1 1.0
PA I:ADP410 4.7 70.3 1.0
CD I:GLU127 4.7 90.1 1.0

Reference:

K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.Mcnally, S.N.Seyedin, D.L.Makino, M.O'donnell, J.Kuriyan. The Mechanism of Atp-Dependent Primer-Template Recognition By A Clamp Loader Complex. Cell(Cambridge,Mass.) V. 137 659 2009.
ISSN: ISSN 0092-8674
PubMed: 19450514
DOI: 10.1016/J.CELL.2009.03.044
Page generated: Sun Aug 10 21:43:04 2025

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