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Magnesium in PDB 3glf: Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna

Enzymatic activity of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna

All present enzymatic activity of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glf was solved by K.R.Simonetta, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.97 / 3.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.264, 219.947, 273.150, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26

Other elements in 3glf:

The structure of Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna (pdb code 3glf). 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 the Ecoli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 1 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg412

b:79.5
occ:1.00
F1 B:BEF401 2.1 80.6 1.0
O1B B:ADP400 2.1 86.6 1.0
CG2 B:THR52 2.3 85.3 1.0
OE2 B:GLU127 3.2 92.0 1.0
OD2 B:ASP126 3.2 86.3 1.0
OD1 B:ASP126 3.3 85.2 1.0
BE B:BEF401 3.3 80.6 1.0
OG1 B:THR52 3.3 87.1 1.0
CB B:THR52 3.4 86.5 1.0
PB B:ADP400 3.5 87.3 1.0
F3 B:BEF401 3.6 79.9 1.0
CG B:ASP126 3.6 85.7 1.0
O3B B:ADP400 3.9 86.8 1.0
OE2 C:GLU144 4.0 96.9 1.0
O2A B:ADP400 4.1 88.7 1.0
NH2 C:ARG169 4.1 75.6 1.0
N B:THR52 4.4 87.2 1.0
CD B:GLU127 4.4 91.6 1.0
CA B:THR52 4.5 87.4 1.0
O2B B:ADP400 4.6 87.7 1.0
F2 B:BEF401 4.6 81.1 1.0
O3A B:ADP400 4.6 88.7 1.0
CD C:GLU144 4.9 98.0 1.0
PA B:ADP400 5.0 89.5 1.0
OE1 C:GLU144 5.0 99.0 1.0

Magnesium binding site 2 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 2 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:77.9
occ:1.00
OG1 C:THR52 2.0 79.5 1.0
F1 C:BEF403 2.1 77.2 1.0
O1B C:ADP402 2.1 78.2 1.0
CB C:THR52 3.0 80.8 1.0
OD1 C:ASP126 3.2 97.7 1.0
OE2 C:GLU127 3.3 0.1 1.0
BE C:BEF403 3.3 78.4 1.0
PB C:ADP402 3.5 79.3 1.0
O2A C:ADP402 3.6 80.4 1.0
NH2 D:ARG169 3.6 77.4 1.0
CG2 C:THR52 3.7 80.8 1.0
OE2 D:GLU144 3.8 0.4 1.0
F2 C:BEF403 3.8 79.2 1.0
O3B C:ADP402 3.9 79.1 1.0
OE1 D:GLU144 4.2 0.9 1.0
CG C:ASP126 4.2 96.8 1.0
OD2 C:ASP126 4.3 96.7 1.0
CA C:THR52 4.3 81.3 1.0
CD D:GLU144 4.4 0.1 1.0
NH2 C:ARG215 4.5 80.5 1.0
CD C:GLU127 4.5 0.4 1.0
N C:THR52 4.5 81.7 1.0
O3A C:ADP402 4.6 81.0 1.0
F3 C:BEF403 4.6 78.0 1.0
O2B C:ADP402 4.6 79.6 1.0
PA C:ADP402 4.7 81.5 1.0
CD D:LYS141 4.8 81.7 1.0
CZ D:ARG169 4.9 76.6 1.0

Magnesium binding site 3 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 3 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg414

b:75.9
occ:1.00
F1 D:BEF405 2.1 86.0 1.0
O1B D:ADP404 2.1 80.3 1.0
CG2 D:THR52 2.4 75.8 1.0
OD2 D:ASP126 2.9 99.1 1.0
OG1 D:THR52 3.3 78.5 1.0
CB D:THR52 3.4 77.3 1.0
BE D:BEF405 3.5 86.5 1.0
OE2 D:GLU127 3.5 80.3 1.0
PB D:ADP404 3.6 80.8 1.0
CG D:ASP126 3.8 98.1 1.0
O2A D:ADP404 3.9 83.5 1.0
OD1 D:ASP126 3.9 97.6 1.0
F2 D:BEF405 4.0 87.3 1.0
NH2 E:ARG158 4.0 79.3 1.0
O3B D:ADP404 4.1 80.1 1.0
NZ E:LYS130 4.3 0.7 1.0
OE1 E:GLU133 4.3 0.2 1.0
NH2 D:ARG215 4.5 87.3 1.0
O2B D:ADP404 4.6 80.7 1.0
CA D:THR52 4.6 78.3 1.0
N D:THR52 4.6 78.1 1.0
O3A D:ADP404 4.7 82.8 1.0
F3 D:BEF405 4.7 85.6 1.0
CD D:GLU127 4.7 79.5 1.0
OE2 E:GLU133 4.7 0.3 1.0
PA D:ADP404 4.9 84.3 1.0
CD E:GLU133 4.9 0.8 1.0
CZ E:ARG158 5.0 79.1 1.0
NH1 E:ARG158 5.0 79.3 1.0

Magnesium binding site 4 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 4 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg415

b:79.2
occ:1.00
F1 G:BEF407 2.1 80.9 1.0
O1B G:ADP406 2.1 82.7 1.0
CG2 G:THR52 2.3 81.4 1.0
OE2 G:GLU127 3.0 0.7 1.0
BE G:BEF407 3.2 80.2 1.0
OD1 G:ASP126 3.3 94.1 1.0
OD2 G:ASP126 3.3 95.6 1.0
CB G:THR52 3.4 83.0 1.0
OG1 G:THR52 3.4 83.2 1.0
F3 G:BEF407 3.4 79.7 1.0
PB G:ADP406 3.5 82.6 1.0
CG G:ASP126 3.7 94.9 1.0
O3B G:ADP406 3.8 81.4 1.0
OE2 H:GLU144 4.2 0.5 1.0
O2A G:ADP406 4.2 84.8 1.0
NH2 H:ARG169 4.2 85.4 1.0
CD G:GLU127 4.3 0.4 1.0
N G:THR52 4.3 83.0 1.0
CA G:THR52 4.5 83.8 1.0
O2B G:ADP406 4.5 82.8 1.0
O3A G:ADP406 4.6 83.5 1.0
F2 G:BEF407 4.6 79.8 1.0
PA G:ADP406 5.0 84.9 1.0

Magnesium binding site 5 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 5 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg416

b:57.6
occ:1.00
OG1 H:THR52 1.9 57.5 1.0
F1 H:BEF409 2.1 57.8 1.0
O1B H:ADP408 2.1 60.2 1.0
CB H:THR52 3.0 58.0 1.0
OD1 H:ASP126 3.1 78.5 1.0
OE2 H:GLU127 3.2 73.9 1.0
BE H:BEF409 3.4 57.8 1.0
PB H:ADP408 3.6 60.4 1.0
NH2 I:ARG169 3.6 65.2 1.0
CG2 H:THR52 3.6 58.6 1.0
O2A H:ADP408 3.7 60.6 1.0
F2 H:BEF409 3.9 57.8 1.0
OE2 I:GLU144 4.0 78.9 1.0
O3B H:ADP408 4.0 60.2 1.0
CG H:ASP126 4.0 78.6 1.0
OD2 H:ASP126 4.1 78.4 1.0
CA H:THR52 4.2 58.5 1.0
OE1 I:GLU144 4.2 80.0 1.0
N H:THR52 4.4 58.4 1.0
CD H:GLU127 4.4 74.3 1.0
CD I:GLU144 4.5 78.9 1.0
NH2 H:ARG215 4.6 60.6 1.0
F3 H:BEF409 4.6 58.1 1.0
O3A H:ADP408 4.6 60.6 1.0
O2B H:ADP408 4.7 60.9 1.0
PA H:ADP408 4.7 60.9 1.0
CD I:LYS141 4.9 80.9 1.0
CZ I:ARG169 4.9 63.9 1.0

Magnesium binding site 6 out of 6 in 3glf

Go back to Magnesium Binding Sites List in 3glf
Magnesium binding site 6 out of 6 in the Crystal Structure of the Ecoli 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 the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg417

b:58.4
occ:1.00
F1 I:BEF411 2.1 62.8 1.0
O1B I:ADP410 2.1 62.3 1.0
CG2 I:THR52 2.4 67.1 1.0
OD2 I:ASP126 3.2 78.1 1.0
OG1 I:THR52 3.3 68.5 1.0
CB I:THR52 3.4 67.6 1.0
BE I:BEF411 3.4 63.5 1.0
PB I:ADP410 3.6 62.7 1.0
OE2 I:GLU127 3.7 90.6 1.0
O2A I:ADP410 3.7 64.0 1.0
NH2 J:ARG158 3.7 66.6 1.0
F2 I:BEF411 3.9 64.3 1.0
O3B I:ADP410 4.0 62.8 1.0
OE1 J:GLU133 4.0 83.5 1.0
NZ J:LYS130 4.0 88.1 1.0
CG I:ASP126 4.0 77.5 1.0
OD1 I:ASP126 4.1 77.1 1.0
NH2 I:ARG215 4.4 61.0 1.0
OE2 J:GLU133 4.4 84.5 1.0
O3A I:ADP410 4.5 63.9 1.0
O2B I:ADP410 4.6 62.5 1.0
CD J:GLU133 4.6 83.9 1.0
CA I:THR52 4.6 68.0 1.0
N I:THR52 4.6 68.0 1.0
CZ J:ARG158 4.7 66.3 1.0
F3 I:BEF411 4.7 63.3 1.0
PA I:ADP410 4.7 64.4 1.0
NH1 J:ARG158 4.8 66.4 1.0
CD I:GLU127 4.9 90.8 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: Mon Dec 14 08:11:46 2020

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