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Magnesium in PDB 3gli: Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide

Enzymatic activity of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide

All present enzymatic activity of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide:
2.7.7.7;

Protein crystallography data

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

Resolution Low / High (Å) 73.03 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.690, 217.180, 275.320, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.7

Other elements in 3gli:

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

Magnesium binding site 1 out of 6 in 3gli

Go back to Magnesium Binding Sites List in 3gli
Magnesium binding site 1 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg412

b:86.0
occ:1.00
F1 B:BEF401 2.1 97.1 1.0
O1B B:ADP400 2.1 92.8 1.0
OG1 B:THR52 2.7 0.3 1.0
OD2 B:ASP126 2.9 88.5 1.0
OE2 B:GLU127 2.9 96.1 1.0
BE B:BEF401 3.3 96.9 1.0
CB B:THR52 3.4 0.9 1.0
OD1 B:ASP126 3.4 87.8 1.0
PB B:ADP400 3.5 93.5 1.0
CG B:ASP126 3.6 88.1 1.0
F3 B:BEF401 3.6 96.0 1.0
OE2 C:GLU144 3.7 92.3 1.0
NH2 C:ARG169 3.9 84.4 1.0
O3B B:ADP400 3.9 92.4 1.0
CD B:GLU127 4.1 95.3 1.0
O2A B:ADP400 4.2 95.6 1.0
CG2 B:THR52 4.3 0.6 1.0
O2B B:ADP400 4.6 94.2 1.0
N B:THR52 4.6 0.9 1.0
CA B:THR52 4.6 0.3 1.0
F2 B:BEF401 4.6 96.9 1.0
O3A B:ADP400 4.6 95.2 1.0
CD C:GLU144 4.7 93.7 1.0
OE1 C:GLU144 4.8 95.1 1.0
CG B:GLU127 4.9 95.3 1.0
NZ C:LYS141 5.0 83.6 1.0
NH1 B:ARG215 5.0 91.0 1.0

Magnesium binding site 2 out of 6 in 3gli

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Magnesium binding site 2 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:84.0
occ:1.00
F1 C:BEF403 2.1 85.4 1.0
O1B C:ADP402 2.1 87.2 1.0
OG1 C:THR52 2.2 84.2 1.0
CB C:THR52 3.0 85.3 1.0
BE C:BEF403 3.2 86.7 1.0
OE2 C:GLU127 3.3 0.1 1.0
F2 C:BEF403 3.4 87.1 1.0
NH2 D:ARG169 3.4 94.1 1.0
PB C:ADP402 3.5 88.6 1.0
O2A C:ADP402 3.6 88.9 1.0
OD1 C:ASP126 3.7 95.7 1.0
CG2 C:THR52 3.8 85.0 1.0
O3B C:ADP402 3.8 88.4 1.0
OE2 D:GLU144 3.9 0.5 1.0
OE1 D:GLU144 4.0 0.4 1.0
NH2 C:ARG215 4.1 87.9 1.0
OD2 C:ASP126 4.1 95.1 1.0
CG C:ASP126 4.3 95.0 1.0
CD D:GLU144 4.3 0.8 1.0
CA C:THR52 4.4 86.1 1.0
O3A C:ADP402 4.4 90.1 1.0
F3 C:BEF403 4.5 86.7 1.0
N C:THR52 4.5 86.8 1.0
CD C:GLU127 4.5 0.5 1.0
PA C:ADP402 4.6 90.3 1.0
CZ D:ARG169 4.6 93.4 1.0
O2B C:ADP402 4.7 89.3 1.0
CD D:LYS141 4.7 93.0 1.0

Magnesium binding site 3 out of 6 in 3gli

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Magnesium binding site 3 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg414

b:84.0
occ:1.00
F1 D:BEF405 2.1 82.7 1.0
O1B D:ADP404 2.1 85.7 1.0
OG1 D:THR52 2.8 92.2 1.0
OE2 D:GLU127 3.1 88.3 1.0
OD2 D:ASP126 3.1 1.0 1.0
CB D:THR52 3.4 93.9 1.0
BE D:BEF405 3.5 82.9 1.0
PB D:ADP404 3.5 86.0 1.0
NH2 E:ARG158 3.6 95.2 1.0
OE1 E:GLU133 3.7 0.6 1.0
OD1 D:ASP126 3.8 0.9 1.0
CG D:ASP126 3.9 0.3 1.0
O3B D:ADP404 3.9 85.0 1.0
O2A D:ADP404 4.1 89.1 1.0
F2 D:BEF405 4.2 83.3 1.0
CG2 D:THR52 4.2 94.8 1.0
CD D:GLU127 4.3 87.5 1.0
NH2 D:ARG215 4.4 0.4 1.0
NZ E:LYS130 4.5 0.2 1.0
N D:THR52 4.6 94.0 1.0
O2B D:ADP404 4.6 85.7 1.0
CA D:THR52 4.6 94.7 1.0
F3 D:BEF405 4.6 81.8 1.0
O3A D:ADP404 4.7 87.8 1.0
CD E:GLU133 4.7 0.5 1.0
CZ E:ARG158 4.7 94.6 1.0
OE2 E:GLU133 4.9 0.1 1.0

Magnesium binding site 4 out of 6 in 3gli

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Magnesium binding site 4 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg415

b:92.4
occ:1.00
F1 G:BEF407 2.1 95.0 1.0
O1B G:ADP406 2.1 95.0 1.0
OG1 G:THR52 2.7 0.9 1.0
OE2 G:GLU127 2.9 0.3 1.0
OD2 G:ASP126 3.1 0.7 1.0
BE G:BEF407 3.2 94.5 1.0
CB G:THR52 3.4 0.2 1.0
OD1 G:ASP126 3.4 0.7 1.0
F3 G:BEF407 3.5 94.1 1.0
PB G:ADP406 3.5 95.0 1.0
CG G:ASP126 3.6 0.3 1.0
O3B G:ADP406 3.8 94.0 1.0
OE2 H:GLU144 3.9 0.5 1.0
NH2 H:ARG169 4.0 0.2 1.0
CD G:GLU127 4.1 0.0 1.0
O2A G:ADP406 4.2 97.3 1.0
CG2 G:THR52 4.4 0.3 1.0
N G:THR52 4.5 0.3 1.0
O2B G:ADP406 4.5 95.5 1.0
CA G:THR52 4.6 0.1 1.0
F2 G:BEF407 4.6 94.3 1.0
O3A G:ADP406 4.6 96.0 1.0
CG G:GLU127 4.8 0.5 1.0
NZ H:LYS141 4.8 99.3 1.0
CD H:GLU144 4.9 0.9 1.0
OE1 G:GLU127 5.0 0.6 1.0

Magnesium binding site 5 out of 6 in 3gli

Go back to Magnesium Binding Sites List in 3gli
Magnesium binding site 5 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg416

b:66.6
occ:1.00
F1 H:BEF409 2.1 74.6 1.0
O1B H:ADP408 2.1 70.7 1.0
OG1 H:THR52 2.2 66.2 1.0
CB H:THR52 3.0 66.7 1.0
BE H:BEF409 3.2 74.6 1.0
OE2 H:GLU127 3.3 78.8 1.0
NH2 I:ARG169 3.3 68.4 1.0
F2 H:BEF409 3.4 74.4 1.0
O2A H:ADP408 3.5 70.9 1.0
PB H:ADP408 3.5 71.0 1.0
OD1 H:ASP126 3.7 86.8 1.0
CG2 H:THR52 3.7 67.0 1.0
OE2 I:GLU144 3.9 69.5 1.0
O3B H:ADP408 3.9 70.8 1.0
OE1 I:GLU144 4.0 70.8 1.0
NH2 H:ARG215 4.1 73.7 1.0
OD2 H:ASP126 4.2 86.8 1.0
CD I:GLU144 4.3 69.8 1.0
CG H:ASP126 4.3 86.9 1.0
CA H:THR52 4.3 67.5 1.0
O3A H:ADP408 4.4 71.2 1.0
N H:THR52 4.5 67.5 1.0
F3 H:BEF409 4.5 75.0 1.0
PA H:ADP408 4.5 71.4 1.0
CD H:GLU127 4.6 79.2 1.0
CZ I:ARG169 4.6 67.7 1.0
O2B H:ADP408 4.7 71.8 1.0
CD I:LYS141 4.8 76.2 1.0

Magnesium binding site 6 out of 6 in 3gli

Go back to Magnesium Binding Sites List in 3gli
Magnesium binding site 6 out of 6 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


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 E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg417

b:67.3
occ:1.00
F1 I:BEF411 2.1 81.9 1.0
O1B I:ADP410 2.1 68.1 1.0
OG1 I:THR52 2.8 72.5 1.0
OD2 I:ASP126 3.1 72.1 1.0
OE2 I:GLU127 3.2 75.5 1.0
NH2 J:ARG158 3.3 78.4 1.0
CB I:THR52 3.3 73.5 1.0
OE1 J:GLU133 3.4 89.9 1.0
BE I:BEF411 3.5 82.3 1.0
PB I:ADP410 3.6 68.3 1.0
OD1 I:ASP126 3.9 70.8 1.0
CG I:ASP126 3.9 71.3 1.0
O3B I:ADP410 4.0 68.4 1.0
O2A I:ADP410 4.0 70.2 1.0
CG2 I:THR52 4.2 74.0 1.0
F2 I:BEF411 4.2 83.3 1.0
NZ J:LYS130 4.3 76.0 1.0
NH2 I:ARG215 4.4 70.3 1.0
CD J:GLU133 4.4 90.8 1.0
CD I:GLU127 4.4 75.6 1.0
CZ J:ARG158 4.5 78.2 1.0
N I:THR52 4.6 73.4 1.0
O2B I:ADP410 4.6 68.0 1.0
CA I:THR52 4.6 73.6 1.0
OE2 J:GLU133 4.6 91.3 1.0
O3A I:ADP410 4.7 69.6 1.0
F3 I:BEF411 4.7 81.9 1.0
NH1 J:ARG158 4.9 78.1 1.0
PA I:ADP410 5.0 70.4 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: Wed Aug 14 14:50:11 2024

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