Magnesium in PDB 5da8: Crystal Structure of Chaperonin Groel From
Protein crystallography data
The structure of Crystal Structure of Chaperonin Groel From, PDB code: 5da8
was solved by
C.Chang,
N.Marshall,
B.Feldmann,
A.Joachimiak,
Midwest Center Forstructural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.60 /
3.00
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.996,
159.781,
228.823,
75.46,
90.51,
91.22
|
R / Rfree (%)
|
23 /
26.3
|
Other elements in 5da8:
The structure of Crystal Structure of Chaperonin Groel From also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Chaperonin Groel From
(pdb code 5da8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Crystal Structure of Chaperonin Groel From, PDB code: 5da8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 1 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg601
b:51.2
occ:1.00
|
O
|
H:THR30
|
2.1
|
36.7
|
1.0
|
O
|
H:LYS51
|
3.0
|
28.3
|
1.0
|
O
|
H:GLY32
|
3.0
|
44.4
|
1.0
|
C
|
H:THR30
|
3.3
|
31.8
|
1.0
|
CA
|
H:GLY35
|
3.9
|
32.4
|
1.0
|
CA
|
H:THR30
|
4.0
|
27.4
|
1.0
|
CB
|
H:THR30
|
4.1
|
31.9
|
1.0
|
C
|
H:LYS51
|
4.1
|
25.7
|
1.0
|
C
|
H:GLY32
|
4.2
|
41.0
|
1.0
|
N
|
H:GLY32
|
4.2
|
43.3
|
1.0
|
N
|
H:LEU31
|
4.3
|
32.2
|
1.0
|
N
|
H:GLY35
|
4.3
|
31.7
|
1.0
|
C
|
H:LEU31
|
4.4
|
37.1
|
1.0
|
CB
|
H:LYS51
|
4.4
|
28.2
|
1.0
|
CA
|
H:LEU31
|
4.5
|
29.5
|
1.0
|
OG1
|
H:THR30
|
4.6
|
34.0
|
1.0
|
OD2
|
H:ASP87
|
4.6
|
35.6
|
1.0
|
C
|
H:GLY35
|
4.7
|
33.6
|
1.0
|
CA
|
H:GLY32
|
4.8
|
35.1
|
1.0
|
CA
|
H:LYS51
|
4.8
|
29.6
|
1.0
|
O
|
H:LEU31
|
4.9
|
40.8
|
1.0
|
O
|
H:GLY35
|
4.9
|
37.0
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 2 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg601
b:53.0
occ:1.00
|
O
|
M:THR30
|
2.1
|
51.5
|
1.0
|
O
|
M:LYS51
|
2.3
|
45.4
|
1.0
|
C
|
M:THR30
|
3.2
|
39.1
|
1.0
|
C
|
M:LYS51
|
3.5
|
36.5
|
1.0
|
CB
|
M:THR30
|
3.5
|
39.8
|
1.0
|
CA
|
M:THR30
|
3.8
|
35.5
|
1.0
|
O
|
M:GLY32
|
4.0
|
46.4
|
1.0
|
OG1
|
M:THR30
|
4.2
|
39.7
|
1.0
|
CB
|
M:LYS51
|
4.3
|
26.1
|
1.0
|
N
|
M:LEU31
|
4.4
|
34.5
|
1.0
|
CA
|
M:LYS51
|
4.4
|
33.5
|
1.0
|
N
|
M:ASP52
|
4.4
|
32.4
|
1.0
|
CA
|
M:ASP52
|
4.5
|
36.3
|
1.0
|
N
|
M:GLY53
|
4.5
|
39.1
|
1.0
|
N
|
M:GLY32
|
4.6
|
44.6
|
1.0
|
CG2
|
M:THR30
|
4.7
|
37.0
|
1.0
|
CA
|
M:LEU31
|
4.7
|
30.8
|
1.0
|
CA
|
M:GLY35
|
4.7
|
39.0
|
1.0
|
O4
|
M:SO4602
|
4.7
|
55.0
|
0.7
|
C
|
M:LEU31
|
4.8
|
33.7
|
1.0
|
C
|
M:ASP52
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 3 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Mg601
b:67.1
occ:1.00
|
O
|
Q:LYS51
|
2.0
|
22.6
|
1.0
|
O
|
Q:THR30
|
2.1
|
31.0
|
1.0
|
CB
|
Q:THR30
|
2.1
|
21.2
|
1.0
|
C
|
Q:THR30
|
2.6
|
22.6
|
1.0
|
CA
|
Q:THR30
|
2.7
|
16.8
|
1.0
|
OG1
|
Q:THR30
|
2.8
|
17.2
|
1.0
|
C
|
Q:LYS51
|
3.2
|
18.1
|
1.0
|
CG2
|
Q:THR30
|
3.3
|
18.7
|
1.0
|
N
|
Q:GLY53
|
3.8
|
18.5
|
1.0
|
N
|
Q:LEU31
|
3.9
|
22.1
|
1.0
|
N
|
Q:THR30
|
4.1
|
19.1
|
1.0
|
N
|
Q:ASP52
|
4.1
|
16.9
|
1.0
|
CA
|
Q:LYS51
|
4.1
|
18.8
|
1.0
|
OD1
|
Q:ASP87
|
4.2
|
58.4
|
1.0
|
C
|
Q:ASP52
|
4.2
|
20.0
|
1.0
|
CA
|
Q:ASP52
|
4.2
|
13.2
|
1.0
|
CB
|
Q:LYS51
|
4.3
|
13.9
|
1.0
|
CA
|
Q:GLY53
|
4.5
|
16.7
|
1.0
|
CA
|
Q:LEU31
|
4.6
|
20.4
|
1.0
|
CA
|
Q:GLY35
|
4.7
|
24.9
|
1.0
|
O
|
Q:GLY32
|
4.9
|
30.8
|
1.0
|
O
|
Q:ARG36
|
5.0
|
27.1
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 4 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Mg601
b:34.5
occ:1.00
|
O
|
R:THR30
|
2.1
|
23.7
|
1.0
|
O
|
R:GLY32
|
3.0
|
26.7
|
1.0
|
O
|
R:LYS51
|
3.0
|
17.6
|
1.0
|
C
|
R:THR30
|
3.3
|
22.0
|
1.0
|
CA
|
R:THR30
|
4.1
|
22.6
|
1.0
|
N
|
R:GLY32
|
4.1
|
20.4
|
1.0
|
C
|
R:GLY32
|
4.1
|
22.1
|
1.0
|
C
|
R:LYS51
|
4.2
|
15.7
|
1.0
|
CB
|
R:THR30
|
4.2
|
24.3
|
1.0
|
CA
|
R:GLY35
|
4.2
|
22.1
|
1.0
|
C
|
R:LEU31
|
4.3
|
19.5
|
1.0
|
N
|
R:LEU31
|
4.3
|
19.7
|
1.0
|
CB
|
R:LYS51
|
4.4
|
15.6
|
1.0
|
CA
|
R:LEU31
|
4.5
|
13.8
|
1.0
|
N
|
R:GLY35
|
4.5
|
19.9
|
1.0
|
CA
|
R:GLY32
|
4.7
|
18.6
|
1.0
|
O
|
R:LEU31
|
4.8
|
26.2
|
1.0
|
OG1
|
R:THR30
|
4.9
|
21.1
|
1.0
|
CA
|
R:LYS51
|
4.9
|
14.4
|
1.0
|
C
|
R:GLY35
|
4.9
|
23.0
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 5 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Mg601
b:54.4
occ:1.00
|
O
|
S:THR30
|
2.1
|
37.4
|
1.0
|
O
|
S:GLY32
|
2.9
|
50.8
|
1.0
|
O
|
S:LYS51
|
2.9
|
30.6
|
1.0
|
C
|
S:THR30
|
3.3
|
32.3
|
1.0
|
C
|
S:GLY32
|
4.0
|
46.6
|
1.0
|
C
|
S:LYS51
|
4.1
|
25.9
|
1.0
|
CA
|
S:THR30
|
4.1
|
35.9
|
1.0
|
N
|
S:GLY32
|
4.1
|
37.8
|
1.0
|
CA
|
S:GLY35
|
4.2
|
46.9
|
1.0
|
CB
|
S:THR30
|
4.2
|
31.5
|
1.0
|
C
|
S:LEU31
|
4.2
|
40.4
|
1.0
|
N
|
S:LEU31
|
4.3
|
30.4
|
1.0
|
CB
|
S:LYS51
|
4.3
|
26.1
|
1.0
|
CA
|
S:LEU31
|
4.4
|
32.6
|
1.0
|
N
|
S:GLY35
|
4.5
|
43.5
|
1.0
|
CA
|
S:GLY32
|
4.7
|
38.3
|
1.0
|
O
|
S:LEU31
|
4.7
|
51.3
|
1.0
|
CA
|
S:LYS51
|
4.7
|
26.1
|
1.0
|
O
|
S:GLY35
|
4.7
|
48.4
|
1.0
|
OG1
|
S:THR30
|
4.8
|
28.6
|
1.0
|
C
|
S:GLY35
|
4.8
|
42.6
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 6 out
of 7 in the Crystal Structure of Chaperonin Groel From
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 Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg601
b:58.1
occ:1.00
|
O
|
T:GLY32
|
3.7
|
57.9
|
1.0
|
O
|
T:THR30
|
3.7
|
47.1
|
1.0
|
O
|
T:LYS51
|
4.0
|
42.3
|
1.0
|
C
|
T:GLY32
|
4.4
|
54.9
|
1.0
|
N
|
T:GLY32
|
4.6
|
53.2
|
1.0
|
CA
|
T:GLY32
|
4.9
|
53.6
|
1.0
|
C
|
T:THR30
|
5.0
|
45.9
|
1.0
|
C
|
T:LYS51
|
5.0
|
39.6
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 5da8
Go back to
Magnesium Binding Sites List in 5da8
Magnesium binding site 7 out
of 7 in the Crystal Structure of Chaperonin Groel From
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Chaperonin Groel From within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg601
b:61.6
occ:1.00
|
O
|
V:LYS51
|
2.0
|
26.7
|
1.0
|
O
|
V:THR30
|
2.1
|
31.2
|
1.0
|
CB
|
V:THR30
|
2.1
|
26.4
|
1.0
|
C
|
V:THR30
|
2.6
|
28.8
|
1.0
|
CA
|
V:THR30
|
2.7
|
27.4
|
1.0
|
OG1
|
V:THR30
|
2.8
|
20.5
|
1.0
|
C
|
V:LYS51
|
3.3
|
23.2
|
1.0
|
CG2
|
V:THR30
|
3.3
|
25.4
|
1.0
|
N
|
V:GLY53
|
3.7
|
24.5
|
1.0
|
N
|
V:LEU31
|
3.9
|
21.8
|
1.0
|
N
|
V:THR30
|
4.1
|
25.4
|
1.0
|
N
|
V:ASP52
|
4.1
|
24.4
|
1.0
|
CA
|
V:ASP52
|
4.1
|
25.0
|
1.0
|
C
|
V:ASP52
|
4.2
|
28.0
|
1.0
|
CA
|
V:LYS51
|
4.2
|
26.2
|
1.0
|
CB
|
V:LYS51
|
4.4
|
24.5
|
1.0
|
CA
|
V:GLY53
|
4.4
|
22.0
|
1.0
|
CA
|
V:LEU31
|
4.6
|
18.1
|
1.0
|
CA
|
V:GLY35
|
4.8
|
25.7
|
1.0
|
O
|
V:GLY32
|
5.0
|
26.0
|
1.0
|
|
Reference:
C.Chang,
N.Marshall,
B.Feldmann,
A.Joachimiak,
Midwest Center For Structural Genomics (Mcsg).
Crystal Structure of Chaperonin Groel From To Be Published.
Page generated: Sun Sep 29 02:39:52 2024
|