Magnesium in PDB 3kdo: Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
Enzymatic activity of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
All present enzymatic activity of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp:
4.1.1.39;
Protein crystallography data
The structure of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp, PDB code: 3kdo
was solved by
Y.Nishitani,
M.Fujihashi,
T.Doi,
S.Yoshida,
H.Atomi,
T.Imanaka,
K.Miki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.46 /
2.36
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
97.481,
246.573,
134.830,
90.00,
104.73,
90.00
|
|
R / Rfree (%)
|
21.9 /
26.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
(pdb code 3kdo). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp, PDB code: 3kdo:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 1 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg500
b:28.8
occ:1.00
|
OE1
|
A:GLU192
|
1.9
|
29.9
|
1.0
|
|
OD1
|
A:ASP191
|
1.9
|
33.1
|
1.0
|
|
O7
|
A:CAP600
|
2.0
|
38.5
|
1.0
|
|
OQ2
|
A:KCX189
|
2.1
|
33.2
|
1.0
|
|
O3
|
A:CAP600
|
2.1
|
38.1
|
1.0
|
|
O2
|
A:CAP600
|
2.4
|
38.3
|
1.0
|
|
C
|
A:CAP600
|
2.7
|
38.4
|
1.0
|
|
C2
|
A:CAP600
|
2.8
|
38.4
|
1.0
|
|
CD
|
A:GLU192
|
2.9
|
30.4
|
1.0
|
|
C3
|
A:CAP600
|
3.0
|
38.3
|
1.0
|
|
CX
|
A:KCX189
|
3.1
|
33.4
|
1.0
|
|
CG
|
A:ASP191
|
3.1
|
32.7
|
1.0
|
|
OE2
|
A:GLU192
|
3.3
|
30.4
|
1.0
|
|
OQ1
|
A:KCX189
|
3.3
|
33.6
|
1.0
|
|
NZ
|
A:LYS165
|
3.6
|
33.8
|
1.0
|
|
ND2
|
H:ASN111
|
3.7
|
33.8
|
1.0
|
|
OD2
|
A:ASP191
|
3.7
|
33.4
|
1.0
|
|
N
|
A:GLU192
|
3.9
|
31.5
|
1.0
|
|
O6
|
A:CAP600
|
3.9
|
38.5
|
1.0
|
|
NZ
|
A:LYS163
|
4.0
|
33.3
|
1.0
|
|
NE2
|
A:HIS281
|
4.1
|
33.1
|
1.0
|
|
C4
|
A:CAP600
|
4.1
|
38.0
|
1.0
|
|
CA
|
A:ASP191
|
4.2
|
32.2
|
1.0
|
|
CB
|
A:ASP191
|
4.2
|
32.4
|
1.0
|
|
CG
|
A:GLU192
|
4.3
|
30.7
|
1.0
|
|
NZ
|
A:KCX189
|
4.3
|
33.2
|
1.0
|
|
C1
|
A:CAP600
|
4.3
|
38.5
|
1.0
|
|
CB
|
A:GLU192
|
4.5
|
31.0
|
1.0
|
|
C
|
A:ASP191
|
4.6
|
31.9
|
1.0
|
|
CG1
|
A:VAL161
|
4.6
|
36.3
|
1.0
|
|
C5
|
A:CAP600
|
4.7
|
37.8
|
1.0
|
|
O1
|
A:CAP600
|
4.7
|
38.9
|
1.0
|
|
CD2
|
A:HIS281
|
4.8
|
33.1
|
1.0
|
|
CA
|
A:GLU192
|
4.8
|
31.0
|
1.0
|
|
CE1
|
A:HIS281
|
4.9
|
33.2
|
1.0
|
|
CG
|
H:ASN111
|
4.9
|
33.8
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 2 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg500
b:31.6
occ:1.00
|
O7
|
B:CAP600
|
1.8
|
35.3
|
1.0
|
|
O3
|
B:CAP600
|
2.0
|
35.6
|
1.0
|
|
OQ2
|
B:KCX189
|
2.1
|
30.2
|
1.0
|
|
OD1
|
B:ASP191
|
2.1
|
32.2
|
1.0
|
|
OE1
|
B:GLU192
|
2.2
|
31.2
|
1.0
|
|
O2
|
B:CAP600
|
2.2
|
35.4
|
1.0
|
|
C
|
B:CAP600
|
2.4
|
35.5
|
1.0
|
|
C2
|
B:CAP600
|
2.5
|
35.5
|
1.0
|
|
C3
|
B:CAP600
|
2.7
|
35.2
|
1.0
|
|
CX
|
B:KCX189
|
3.1
|
30.3
|
1.0
|
|
CG
|
B:ASP191
|
3.2
|
31.9
|
1.0
|
|
CD
|
B:GLU192
|
3.2
|
31.3
|
1.0
|
|
OQ1
|
B:KCX189
|
3.3
|
30.1
|
1.0
|
|
OE2
|
B:GLU192
|
3.6
|
31.4
|
1.0
|
|
O6
|
B:CAP600
|
3.7
|
35.5
|
1.0
|
|
NZ
|
B:LYS163
|
3.7
|
38.6
|
1.0
|
|
OD2
|
B:ASP191
|
3.8
|
32.1
|
1.0
|
|
ND2
|
G:ASN111
|
3.9
|
28.0
|
1.0
|
|
NZ
|
B:LYS165
|
3.9
|
35.2
|
1.0
|
|
N
|
B:GLU192
|
4.0
|
31.5
|
1.0
|
|
C4
|
B:CAP600
|
4.0
|
34.8
|
1.0
|
|
C1
|
B:CAP600
|
4.0
|
35.7
|
1.0
|
|
NE2
|
B:HIS281
|
4.1
|
23.1
|
1.0
|
|
CA
|
B:ASP191
|
4.2
|
31.8
|
1.0
|
|
NZ
|
B:KCX189
|
4.3
|
30.4
|
1.0
|
|
CB
|
B:ASP191
|
4.3
|
31.8
|
1.0
|
|
CG1
|
B:VAL161
|
4.4
|
38.2
|
1.0
|
|
O1
|
B:CAP600
|
4.5
|
36.6
|
1.0
|
|
CG
|
B:GLU192
|
4.5
|
31.4
|
1.0
|
|
C5
|
B:CAP600
|
4.6
|
34.1
|
1.0
|
|
C
|
B:ASP191
|
4.7
|
31.7
|
1.0
|
|
CB
|
B:GLU192
|
4.7
|
31.3
|
1.0
|
|
CD2
|
B:HIS281
|
4.8
|
23.4
|
1.0
|
|
CE1
|
B:HIS281
|
4.9
|
23.5
|
1.0
|
|
CE
|
B:LYS163
|
4.9
|
38.7
|
1.0
|
|
CG2
|
B:VAL161
|
5.0
|
38.2
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 3 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg500
b:28.1
occ:1.00
|
O7
|
C:CAP600
|
1.8
|
31.8
|
1.0
|
|
OQ2
|
C:KCX189
|
1.9
|
24.6
|
1.0
|
|
OE1
|
C:GLU192
|
2.1
|
23.8
|
1.0
|
|
OD2
|
C:ASP191
|
2.4
|
26.6
|
1.0
|
|
O2
|
C:CAP600
|
2.4
|
32.0
|
1.0
|
|
O3
|
C:CAP600
|
2.5
|
31.8
|
1.0
|
|
C
|
C:CAP600
|
2.6
|
31.8
|
1.0
|
|
CG
|
C:ASP191
|
2.7
|
25.1
|
1.0
|
|
C2
|
C:CAP600
|
2.9
|
31.9
|
1.0
|
|
OD1
|
C:ASP191
|
2.9
|
26.2
|
1.0
|
|
CX
|
C:KCX189
|
3.1
|
24.3
|
1.0
|
|
CD
|
C:GLU192
|
3.2
|
23.9
|
1.0
|
|
C3
|
C:CAP600
|
3.2
|
31.8
|
1.0
|
|
OE2
|
C:GLU192
|
3.6
|
23.9
|
1.0
|
|
OQ1
|
C:KCX189
|
3.6
|
24.7
|
1.0
|
|
N
|
C:GLU192
|
3.7
|
24.0
|
1.0
|
|
NZ
|
C:LYS163
|
3.7
|
30.1
|
1.0
|
|
CA
|
C:ASP191
|
3.8
|
24.3
|
1.0
|
|
O6
|
C:CAP600
|
3.8
|
31.7
|
1.0
|
|
CB
|
C:ASP191
|
3.8
|
24.5
|
1.0
|
|
NZ
|
C:LYS165
|
3.8
|
26.5
|
1.0
|
|
ND2
|
F:ASN111
|
4.0
|
23.4
|
1.0
|
|
NZ
|
C:KCX189
|
4.1
|
24.1
|
1.0
|
|
CG1
|
C:VAL161
|
4.2
|
29.0
|
1.0
|
|
C
|
C:ASP191
|
4.2
|
24.2
|
1.0
|
|
NE2
|
C:HIS281
|
4.3
|
18.2
|
1.0
|
|
C1
|
C:CAP600
|
4.3
|
31.9
|
1.0
|
|
C4
|
C:CAP600
|
4.4
|
31.7
|
1.0
|
|
CG
|
C:GLU192
|
4.5
|
23.9
|
1.0
|
|
CB
|
C:GLU192
|
4.6
|
23.9
|
1.0
|
|
O1
|
C:CAP600
|
4.7
|
32.3
|
1.0
|
|
CA
|
C:GLU192
|
4.8
|
23.9
|
1.0
|
|
CG2
|
C:VAL161
|
5.0
|
29.1
|
1.0
|
|
CD2
|
C:HIS281
|
5.0
|
18.2
|
1.0
|
|
C5
|
C:CAP600
|
5.0
|
31.6
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 4 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg500
b:15.9
occ:1.00
|
OD1
|
D:ASP191
|
1.8
|
19.3
|
1.0
|
|
O7
|
D:CAP600
|
1.9
|
20.9
|
1.0
|
|
OE1
|
D:GLU192
|
2.0
|
18.2
|
1.0
|
|
OQ2
|
D:KCX189
|
2.1
|
16.9
|
1.0
|
|
O3
|
D:CAP600
|
2.2
|
20.9
|
1.0
|
|
O2
|
D:CAP600
|
2.4
|
20.9
|
1.0
|
|
C
|
D:CAP600
|
2.7
|
21.0
|
1.0
|
|
C2
|
D:CAP600
|
2.8
|
21.1
|
1.0
|
|
CD
|
D:GLU192
|
3.0
|
18.4
|
1.0
|
|
CG
|
D:ASP191
|
3.0
|
19.0
|
1.0
|
|
C3
|
D:CAP600
|
3.0
|
20.8
|
1.0
|
|
CX
|
D:KCX189
|
3.2
|
17.4
|
1.0
|
|
OE2
|
D:GLU192
|
3.3
|
19.2
|
1.0
|
|
OQ1
|
D:KCX189
|
3.5
|
17.6
|
1.0
|
|
NZ
|
D:LYS165
|
3.5
|
17.6
|
1.0
|
|
N
|
D:GLU192
|
3.7
|
18.1
|
1.0
|
|
ND2
|
J:ASN111
|
3.7
|
18.0
|
1.0
|
|
OD2
|
D:ASP191
|
3.7
|
20.0
|
1.0
|
|
O6
|
D:CAP600
|
3.9
|
21.3
|
1.0
|
|
NZ
|
D:LYS163
|
3.9
|
19.8
|
1.0
|
|
NE2
|
D:HIS281
|
4.0
|
16.0
|
1.0
|
|
CA
|
D:ASP191
|
4.1
|
18.4
|
1.0
|
|
CB
|
D:ASP191
|
4.1
|
18.4
|
1.0
|
|
C4
|
D:CAP600
|
4.1
|
20.5
|
1.0
|
|
CG
|
D:GLU192
|
4.3
|
18.2
|
1.0
|
|
C1
|
D:CAP600
|
4.3
|
21.0
|
1.0
|
|
NZ
|
D:KCX189
|
4.3
|
17.4
|
1.0
|
|
C
|
D:ASP191
|
4.4
|
18.3
|
1.0
|
|
CB
|
D:GLU192
|
4.5
|
18.1
|
1.0
|
|
CG1
|
D:VAL161
|
4.6
|
19.7
|
1.0
|
|
CA
|
D:GLU192
|
4.7
|
18.1
|
1.0
|
|
C5
|
D:CAP600
|
4.7
|
19.4
|
1.0
|
|
CE1
|
D:HIS281
|
4.8
|
16.4
|
1.0
|
|
O1
|
D:CAP600
|
4.8
|
21.2
|
1.0
|
|
CD2
|
D:HIS281
|
4.8
|
15.9
|
1.0
|
|
CE
|
D:LYS165
|
4.9
|
18.1
|
1.0
|
|
CG
|
J:ASN111
|
5.0
|
18.3
|
1.0
|
|
O
|
J:HOH451
|
5.0
|
15.9
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 5 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg500
b:26.4
occ:1.00
|
O6
|
E:CAP600
|
1.8
|
38.1
|
1.0
|
|
OD1
|
E:ASP191
|
2.1
|
25.1
|
1.0
|
|
OE1
|
E:GLU192
|
2.3
|
23.5
|
1.0
|
|
O3
|
E:CAP600
|
2.3
|
37.0
|
1.0
|
|
O2
|
E:CAP600
|
2.3
|
38.0
|
1.0
|
|
OQ2
|
E:KCX189
|
2.4
|
23.3
|
1.0
|
|
C
|
E:CAP600
|
2.4
|
38.1
|
1.0
|
|
C2
|
E:CAP600
|
2.7
|
38.1
|
1.0
|
|
C3
|
E:CAP600
|
3.0
|
37.3
|
1.0
|
|
CG
|
E:ASP191
|
3.2
|
24.5
|
1.0
|
|
CD
|
E:GLU192
|
3.2
|
23.5
|
1.0
|
|
CX
|
E:KCX189
|
3.4
|
23.2
|
1.0
|
|
O7
|
E:CAP600
|
3.5
|
38.4
|
1.0
|
|
OE2
|
E:GLU192
|
3.5
|
23.5
|
1.0
|
|
OQ1
|
E:KCX189
|
3.6
|
22.9
|
1.0
|
|
ND2
|
I:ASN111
|
3.7
|
23.6
|
1.0
|
|
OD2
|
E:ASP191
|
3.8
|
25.9
|
1.0
|
|
NZ
|
E:LYS163
|
3.8
|
27.3
|
1.0
|
|
NZ
|
E:LYS165
|
3.9
|
24.9
|
1.0
|
|
NE2
|
E:HIS281
|
4.0
|
19.9
|
1.0
|
|
C4
|
E:CAP600
|
4.0
|
35.9
|
1.0
|
|
C1
|
E:CAP600
|
4.1
|
38.5
|
1.0
|
|
N
|
E:GLU192
|
4.2
|
23.5
|
1.0
|
|
CA
|
E:ASP191
|
4.3
|
23.8
|
1.0
|
|
CB
|
E:ASP191
|
4.4
|
23.9
|
1.0
|
|
NZ
|
E:KCX189
|
4.6
|
23.1
|
1.0
|
|
O1
|
E:CAP600
|
4.6
|
39.9
|
1.0
|
|
C5
|
E:CAP600
|
4.6
|
34.6
|
1.0
|
|
CG
|
E:GLU192
|
4.6
|
23.2
|
1.0
|
|
CG1
|
E:VAL161
|
4.7
|
27.8
|
1.0
|
|
C
|
E:ASP191
|
4.8
|
23.6
|
1.0
|
|
CE1
|
E:HIS281
|
4.8
|
19.7
|
1.0
|
|
CD2
|
E:HIS281
|
4.9
|
19.5
|
1.0
|
|
CG
|
I:ASN111
|
4.9
|
23.1
|
1.0
|
|
CB
|
E:GLU192
|
4.9
|
23.4
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 6 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg500
b:25.5
occ:1.00
|
O7
|
F:CAP600
|
1.8
|
24.5
|
1.0
|
|
OE1
|
F:GLU192
|
2.0
|
21.6
|
1.0
|
|
OQ2
|
F:KCX189
|
2.0
|
22.7
|
1.0
|
|
O3
|
F:CAP600
|
2.1
|
24.3
|
1.0
|
|
OD1
|
F:ASP191
|
2.1
|
20.5
|
1.0
|
|
O2
|
F:CAP600
|
2.4
|
24.4
|
1.0
|
|
C
|
F:CAP600
|
2.5
|
24.5
|
1.0
|
|
C2
|
F:CAP600
|
2.7
|
24.4
|
1.0
|
|
C3
|
F:CAP600
|
2.9
|
24.3
|
1.0
|
|
CX
|
F:KCX189
|
3.0
|
22.8
|
1.0
|
|
CD
|
F:GLU192
|
3.1
|
21.1
|
1.0
|
|
OQ1
|
F:KCX189
|
3.2
|
22.9
|
1.0
|
|
CG
|
F:ASP191
|
3.3
|
20.7
|
1.0
|
|
OE2
|
F:GLU192
|
3.5
|
21.1
|
1.0
|
|
NZ
|
F:LYS165
|
3.6
|
26.1
|
1.0
|
|
O6
|
F:CAP600
|
3.7
|
24.6
|
1.0
|
|
ND2
|
C:ASN111
|
3.7
|
21.1
|
1.0
|
|
N
|
F:GLU192
|
3.9
|
20.5
|
1.0
|
|
OD2
|
F:ASP191
|
3.9
|
21.4
|
1.0
|
|
NZ
|
F:LYS163
|
3.9
|
25.3
|
1.0
|
|
NE2
|
F:HIS281
|
3.9
|
18.7
|
1.0
|
|
C4
|
F:CAP600
|
4.1
|
23.9
|
1.0
|
|
C1
|
F:CAP600
|
4.2
|
24.5
|
1.0
|
|
CA
|
F:ASP191
|
4.2
|
20.9
|
1.0
|
|
NZ
|
F:KCX189
|
4.2
|
22.4
|
1.0
|
|
CB
|
F:ASP191
|
4.3
|
20.8
|
1.0
|
|
CG
|
F:GLU192
|
4.4
|
20.6
|
1.0
|
|
CB
|
F:GLU192
|
4.6
|
20.4
|
1.0
|
|
C
|
F:ASP191
|
4.6
|
20.7
|
1.0
|
|
CG1
|
F:VAL161
|
4.6
|
25.4
|
1.0
|
|
CD2
|
F:HIS281
|
4.6
|
18.3
|
1.0
|
|
C5
|
F:CAP600
|
4.6
|
23.4
|
1.0
|
|
O1
|
F:CAP600
|
4.7
|
24.8
|
1.0
|
|
CE1
|
F:HIS281
|
4.8
|
18.5
|
1.0
|
|
CA
|
F:GLU192
|
4.8
|
20.5
|
1.0
|
|
CG2
|
F:VAL161
|
5.0
|
25.3
|
1.0
|
|
CG
|
C:ASN111
|
5.0
|
21.1
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 7 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 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 Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg500
b:20.4
occ:1.00
|
O7
|
G:CAP600
|
1.8
|
25.1
|
1.0
|
|
OQ2
|
G:KCX189
|
2.0
|
21.2
|
1.0
|
|
O3
|
G:CAP600
|
2.1
|
25.3
|
1.0
|
|
OE1
|
G:GLU192
|
2.1
|
18.8
|
1.0
|
|
OD1
|
G:ASP191
|
2.1
|
21.9
|
1.0
|
|
O2
|
G:CAP600
|
2.3
|
25.3
|
1.0
|
|
C
|
G:CAP600
|
2.5
|
25.3
|
1.0
|
|
C2
|
G:CAP600
|
2.6
|
25.4
|
1.0
|
|
C3
|
G:CAP600
|
2.8
|
25.1
|
1.0
|
|
CX
|
G:KCX189
|
3.0
|
21.2
|
1.0
|
|
CD
|
G:GLU192
|
3.1
|
19.3
|
1.0
|
|
OQ1
|
G:KCX189
|
3.3
|
21.3
|
1.0
|
|
CG
|
G:ASP191
|
3.3
|
21.9
|
1.0
|
|
OE2
|
G:GLU192
|
3.5
|
18.7
|
1.0
|
|
O6
|
G:CAP600
|
3.7
|
25.3
|
1.0
|
|
ND2
|
B:ASN111
|
3.8
|
20.8
|
1.0
|
|
N
|
G:GLU192
|
3.9
|
21.2
|
1.0
|
|
NE2
|
G:HIS281
|
3.9
|
20.0
|
1.0
|
|
NZ
|
G:LYS163
|
3.9
|
22.6
|
1.0
|
|
OD2
|
G:ASP191
|
3.9
|
22.6
|
1.0
|
|
C4
|
G:CAP600
|
4.0
|
24.8
|
1.0
|
|
NZ
|
G:LYS165
|
4.0
|
22.3
|
1.0
|
|
C1
|
G:CAP600
|
4.1
|
25.4
|
1.0
|
|
NZ
|
G:KCX189
|
4.2
|
21.3
|
1.0
|
|
CA
|
G:ASP191
|
4.2
|
21.6
|
1.0
|
|
CB
|
G:ASP191
|
4.3
|
21.5
|
1.0
|
|
CG
|
G:GLU192
|
4.4
|
20.1
|
1.0
|
|
CG1
|
G:VAL161
|
4.4
|
24.6
|
1.0
|
|
C
|
G:ASP191
|
4.6
|
21.4
|
1.0
|
|
O1
|
G:CAP600
|
4.6
|
26.2
|
1.0
|
|
CB
|
G:GLU192
|
4.6
|
20.9
|
1.0
|
|
C5
|
G:CAP600
|
4.6
|
24.3
|
1.0
|
|
CE1
|
G:HIS281
|
4.7
|
19.6
|
1.0
|
|
CD2
|
G:HIS281
|
4.7
|
19.7
|
1.0
|
|
CG2
|
G:VAL161
|
4.9
|
24.8
|
1.0
|
|
CA
|
G:GLU192
|
4.9
|
21.0
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 8 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg500
b:37.4
occ:1.00
|
OQ2
|
H:KCX189
|
1.9
|
35.4
|
1.0
|
|
O7
|
H:CAP600
|
2.0
|
42.4
|
1.0
|
|
O2
|
H:CAP600
|
2.2
|
42.3
|
1.0
|
|
OE1
|
H:GLU192
|
2.4
|
37.0
|
1.0
|
|
O3
|
H:CAP600
|
2.4
|
42.6
|
1.0
|
|
OD1
|
H:ASP191
|
2.6
|
38.2
|
1.0
|
|
C
|
H:CAP600
|
2.7
|
42.4
|
1.0
|
|
C2
|
H:CAP600
|
2.8
|
42.5
|
1.0
|
|
CX
|
H:KCX189
|
3.0
|
35.6
|
1.0
|
|
CG
|
H:ASP191
|
3.1
|
37.8
|
1.0
|
|
C3
|
H:CAP600
|
3.1
|
42.4
|
1.0
|
|
OQ1
|
H:KCX189
|
3.3
|
35.7
|
1.0
|
|
OD2
|
H:ASP191
|
3.3
|
38.2
|
1.0
|
|
CD
|
H:GLU192
|
3.6
|
37.2
|
1.0
|
|
N
|
H:GLU192
|
3.7
|
37.1
|
1.0
|
|
CA
|
H:ASP191
|
3.8
|
37.4
|
1.0
|
|
NZ
|
H:LYS163
|
3.8
|
41.0
|
1.0
|
|
NZ
|
H:LYS165
|
3.9
|
39.9
|
1.0
|
|
O6
|
H:CAP600
|
4.0
|
42.4
|
1.0
|
|
CB
|
H:ASP191
|
4.0
|
37.5
|
1.0
|
|
NE2
|
H:HIS281
|
4.1
|
33.3
|
1.0
|
|
NZ
|
H:KCX189
|
4.1
|
35.7
|
1.0
|
|
OE2
|
H:GLU192
|
4.2
|
37.4
|
1.0
|
|
C1
|
H:CAP600
|
4.2
|
42.4
|
1.0
|
|
CG1
|
H:VAL161
|
4.2
|
40.8
|
1.0
|
|
C
|
H:ASP191
|
4.3
|
37.3
|
1.0
|
|
ND2
|
A:ASN111
|
4.3
|
38.7
|
1.0
|
|
C4
|
H:CAP600
|
4.4
|
42.4
|
1.0
|
|
CB
|
H:GLU192
|
4.6
|
36.9
|
1.0
|
|
O
|
H:HOH1277
|
4.6
|
34.6
|
1.0
|
|
O1
|
H:CAP600
|
4.7
|
42.7
|
1.0
|
|
CG
|
H:GLU192
|
4.7
|
36.9
|
1.0
|
|
CA
|
H:GLU192
|
4.8
|
36.9
|
1.0
|
|
CE1
|
H:HIS281
|
4.8
|
33.5
|
1.0
|
|
C5
|
H:CAP600
|
4.9
|
42.2
|
1.0
|
|
CD2
|
H:HIS281
|
4.9
|
33.4
|
1.0
|
|
CG2
|
H:VAL161
|
4.9
|
40.9
|
1.0
|
|
CE
|
H:LYS163
|
5.0
|
41.0
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 9 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg500
b:20.4
occ:1.00
|
O7
|
I:CAP600
|
1.9
|
21.0
|
1.0
|
|
OQ2
|
I:KCX189
|
2.0
|
24.2
|
1.0
|
|
OD1
|
I:ASP191
|
2.0
|
24.7
|
1.0
|
|
OE1
|
I:GLU192
|
2.0
|
23.3
|
1.0
|
|
O3
|
I:CAP600
|
2.0
|
21.2
|
1.0
|
|
O2
|
I:CAP600
|
2.3
|
21.1
|
1.0
|
|
C
|
I:CAP600
|
2.6
|
21.1
|
1.0
|
|
C2
|
I:CAP600
|
2.7
|
21.2
|
1.0
|
|
C3
|
I:CAP600
|
2.8
|
20.9
|
1.0
|
|
CX
|
I:KCX189
|
3.0
|
24.4
|
1.0
|
|
CD
|
I:GLU192
|
3.1
|
23.6
|
1.0
|
|
CG
|
I:ASP191
|
3.2
|
24.8
|
1.0
|
|
OQ1
|
I:KCX189
|
3.3
|
24.1
|
1.0
|
|
OE2
|
I:GLU192
|
3.5
|
23.7
|
1.0
|
|
ND2
|
E:ASN111
|
3.6
|
22.2
|
1.0
|
|
NZ
|
I:LYS165
|
3.8
|
23.7
|
1.0
|
|
O6
|
I:CAP600
|
3.8
|
21.1
|
1.0
|
|
OD2
|
I:ASP191
|
3.8
|
25.1
|
1.0
|
|
N
|
I:GLU192
|
3.9
|
24.3
|
1.0
|
|
NZ
|
I:LYS163
|
3.9
|
26.6
|
1.0
|
|
NE2
|
I:HIS281
|
4.0
|
19.8
|
1.0
|
|
C4
|
I:CAP600
|
4.1
|
20.6
|
1.0
|
|
C1
|
I:CAP600
|
4.2
|
21.1
|
1.0
|
|
NZ
|
I:KCX189
|
4.2
|
24.5
|
1.0
|
|
CA
|
I:ASP191
|
4.2
|
24.6
|
1.0
|
|
CB
|
I:ASP191
|
4.3
|
24.6
|
1.0
|
|
CG
|
I:GLU192
|
4.4
|
23.9
|
1.0
|
|
C
|
I:ASP191
|
4.6
|
24.4
|
1.0
|
|
CB
|
I:GLU192
|
4.6
|
24.2
|
1.0
|
|
C5
|
I:CAP600
|
4.6
|
19.9
|
1.0
|
|
O1
|
I:CAP600
|
4.7
|
21.8
|
1.0
|
|
CG1
|
I:VAL161
|
4.7
|
28.1
|
1.0
|
|
CE1
|
I:HIS281
|
4.7
|
20.0
|
1.0
|
|
CD2
|
I:HIS281
|
4.8
|
19.4
|
1.0
|
|
CA
|
I:GLU192
|
4.9
|
24.3
|
1.0
|
|
CG
|
E:ASN111
|
4.9
|
22.1
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 3kdo
Go back to
Magnesium Binding Sites List in 3kdo
Magnesium binding site 10 out
of 10 in the Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Type III Rubisco SP6 Mutant Complexed with 2-Cabp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg500
b:19.0
occ:1.00
|
O7
|
J:CAP600
|
1.7
|
36.2
|
1.0
|
|
OQ2
|
J:KCX189
|
2.1
|
23.1
|
1.0
|
|
OE1
|
J:GLU192
|
2.2
|
22.3
|
1.0
|
|
O3
|
J:CAP600
|
2.2
|
35.7
|
1.0
|
|
OD2
|
J:ASP191
|
2.2
|
24.8
|
1.0
|
|
O2
|
J:CAP600
|
2.3
|
36.4
|
1.0
|
|
C
|
J:CAP600
|
2.4
|
36.3
|
1.0
|
|
C2
|
J:CAP600
|
2.6
|
36.4
|
1.0
|
|
C3
|
J:CAP600
|
3.0
|
35.9
|
1.0
|
|
CX
|
J:KCX189
|
3.1
|
23.1
|
1.0
|
|
CD
|
J:GLU192
|
3.2
|
22.3
|
1.0
|
|
CG
|
J:ASP191
|
3.3
|
24.1
|
1.0
|
|
OQ1
|
J:KCX189
|
3.5
|
23.3
|
1.0
|
|
OE2
|
J:GLU192
|
3.6
|
22.2
|
1.0
|
|
O6
|
J:CAP600
|
3.6
|
36.4
|
1.0
|
|
ND2
|
D:ASN111
|
3.8
|
24.4
|
1.0
|
|
OD1
|
J:ASP191
|
3.9
|
25.7
|
1.0
|
|
NZ
|
J:LYS163
|
3.9
|
28.1
|
1.0
|
|
NZ
|
J:LYS165
|
4.0
|
27.1
|
1.0
|
|
N
|
J:GLU192
|
4.0
|
22.6
|
1.0
|
|
NE2
|
J:HIS281
|
4.0
|
19.4
|
1.0
|
|
C4
|
J:CAP600
|
4.1
|
35.2
|
1.0
|
|
C1
|
J:CAP600
|
4.1
|
36.6
|
1.0
|
|
CA
|
J:ASP191
|
4.3
|
23.1
|
1.0
|
|
NZ
|
J:KCX189
|
4.3
|
22.8
|
1.0
|
|
CB
|
J:ASP191
|
4.4
|
23.2
|
1.0
|
|
O1
|
J:CAP600
|
4.5
|
37.3
|
1.0
|
|
CG1
|
J:VAL161
|
4.5
|
27.1
|
1.0
|
|
CG
|
J:GLU192
|
4.6
|
22.4
|
1.0
|
|
C
|
J:ASP191
|
4.7
|
22.8
|
1.0
|
|
C5
|
J:CAP600
|
4.8
|
34.4
|
1.0
|
|
CB
|
J:GLU192
|
4.8
|
22.4
|
1.0
|
|
CE1
|
J:HIS281
|
4.8
|
19.0
|
1.0
|
|
CD2
|
J:HIS281
|
4.9
|
19.0
|
1.0
|
|
OE2
|
D:GLU49
|
5.0
|
30.7
|
1.0
|
|
Reference:
Y.Nishitani,
S.Yoshida,
M.Fujihashi,
K.Kitagawa,
T.Doi,
H.Atomi,
T.Imanaka,
K.Miki.
Structure-Based Catalytic Optimization of A Type III Rubisco From A Hyperthermophile J.Biol.Chem. V. 285 39339 2010.
ISSN: ISSN 0021-9258
PubMed: 20926376
DOI: 10.1074/JBC.M110.147587
Page generated: Wed Aug 14 18:02:59 2024
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