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:
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
Go back to
Magnesium Binding Sites List in 3gli
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
Go back to
Magnesium Binding Sites List in 3gli
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
Go back to
Magnesium Binding Sites List in 3gli
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
|