Magnesium in PDB 5hk4: Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
Enzymatic activity of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
All present enzymatic activity of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant):
4.1.1.39;
Protein crystallography data
The structure of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant), PDB code: 5hk4
was solved by
M.A.Arbing,
A.Shin,
D.Cascio,
S.Satagopan,
J.A.North,
F.R.Tabita,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
81.96 /
2.15
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.090,
100.410,
100.320,
113.06,
88.86,
108.01
|
|
R / Rfree (%)
|
22.5 /
25.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
(pdb code 5hk4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant), PDB code: 5hk4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 1 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:32.5
occ:1.00
|
OE1
|
A:GLU195
|
2.0
|
40.0
|
1.0
|
|
OQ2
|
A:KCX192
|
2.1
|
34.6
|
1.0
|
|
OD1
|
A:ASP194
|
2.1
|
39.6
|
1.0
|
|
HO2
|
A:CAP500
|
2.1
|
47.1
|
1.0
|
|
O6
|
A:CAP500
|
2.1
|
34.4
|
1.0
|
|
O3
|
A:CAP500
|
2.2
|
35.8
|
1.0
|
|
O2
|
A:CAP500
|
2.3
|
39.2
|
1.0
|
|
C
|
A:CAP500
|
2.8
|
42.3
|
1.0
|
|
C2
|
A:CAP500
|
2.8
|
35.0
|
1.0
|
|
HO3
|
A:CAP500
|
2.8
|
43.0
|
1.0
|
|
H
|
A:GLU195
|
3.0
|
44.5
|
1.0
|
|
C3
|
A:CAP500
|
3.0
|
39.6
|
1.0
|
|
CD
|
A:GLU195
|
3.1
|
40.3
|
1.0
|
|
CX
|
A:KCX192
|
3.1
|
35.2
|
1.0
|
|
HD21
|
B:ASN112
|
3.1
|
45.2
|
1.0
|
|
HE2
|
A:HIS288
|
3.2
|
45.4
|
1.0
|
|
CG
|
A:ASP194
|
3.2
|
39.2
|
1.0
|
|
OQ1
|
A:KCX192
|
3.4
|
37.0
|
1.0
|
|
HZ1
|
A:LYS167
|
3.4
|
47.9
|
1.0
|
|
HG21
|
A:ILE165
|
3.4
|
39.5
|
1.0
|
|
HA
|
A:ASP194
|
3.5
|
43.0
|
1.0
|
|
HZ2
|
A:LYS169
|
3.5
|
47.1
|
1.0
|
|
HZ3
|
A:LYS169
|
3.5
|
47.1
|
1.0
|
|
OE2
|
A:GLU195
|
3.6
|
41.5
|
1.0
|
|
HZ1
|
A:LYS169
|
3.6
|
47.1
|
1.0
|
|
HZ3
|
A:LYS167
|
3.6
|
47.9
|
1.0
|
|
H3
|
A:CAP500
|
3.6
|
47.5
|
1.0
|
|
NZ
|
A:LYS169
|
3.7
|
39.2
|
1.0
|
|
HD22
|
B:ASN112
|
3.7
|
45.2
|
1.0
|
|
ND2
|
B:ASN112
|
3.8
|
37.7
|
1.0
|
|
N
|
A:GLU195
|
3.8
|
37.1
|
1.0
|
|
NE2
|
A:HIS288
|
3.9
|
37.9
|
1.0
|
|
OD2
|
A:ASP194
|
3.9
|
40.5
|
1.0
|
|
NZ
|
A:LYS167
|
3.9
|
39.9
|
1.0
|
|
HB3
|
A:GLU195
|
4.0
|
44.7
|
1.0
|
|
O7
|
A:CAP500
|
4.0
|
42.0
|
1.0
|
|
HG12
|
A:ILE165
|
4.1
|
43.9
|
1.0
|
|
CA
|
A:ASP194
|
4.2
|
35.8
|
1.0
|
|
C1
|
A:CAP500
|
4.3
|
42.1
|
1.0
|
|
CB
|
A:ASP194
|
4.3
|
37.1
|
1.0
|
|
C4
|
A:CAP500
|
4.3
|
39.9
|
1.0
|
|
NZ
|
A:KCX192
|
4.3
|
32.8
|
1.0
|
|
CG2
|
A:ILE165
|
4.3
|
32.9
|
1.0
|
|
CG
|
A:GLU195
|
4.4
|
38.6
|
1.0
|
|
H4
|
A:CAP500
|
4.4
|
47.8
|
1.0
|
|
HE1
|
A:HIS288
|
4.4
|
44.9
|
1.0
|
|
HZ2
|
A:LYS167
|
4.4
|
47.9
|
1.0
|
|
CE1
|
A:HIS288
|
4.5
|
37.4
|
1.0
|
|
C
|
A:ASP194
|
4.5
|
36.5
|
1.0
|
|
CB
|
A:GLU195
|
4.5
|
37.2
|
1.0
|
|
HD3
|
A:PRO196
|
4.6
|
48.2
|
1.0
|
|
HG23
|
A:ILE165
|
4.6
|
39.5
|
1.0
|
|
H51
|
A:CAP500
|
4.6
|
46.2
|
1.0
|
|
O1
|
A:CAP500
|
4.7
|
41.3
|
1.0
|
|
H11
|
A:CAP500
|
4.7
|
50.5
|
1.0
|
|
HB3
|
A:ASP194
|
4.8
|
44.6
|
1.0
|
|
CA
|
A:GLU195
|
4.8
|
36.5
|
1.0
|
|
HE2
|
A:LYS167
|
4.8
|
48.1
|
1.0
|
|
HG22
|
A:ILE165
|
4.8
|
39.5
|
1.0
|
|
CD2
|
A:HIS288
|
4.9
|
36.4
|
1.0
|
|
C5
|
A:CAP500
|
4.9
|
38.5
|
1.0
|
|
H12
|
A:CAP500
|
4.9
|
50.5
|
1.0
|
|
H52
|
A:CAP500
|
4.9
|
46.2
|
1.0
|
|
HG3
|
A:GLU195
|
4.9
|
46.3
|
1.0
|
|
HG2
|
A:GLU195
|
4.9
|
46.3
|
1.0
|
|
HB2
|
A:ASP194
|
4.9
|
44.6
|
1.0
|
|
CG
|
B:ASN112
|
5.0
|
37.2
|
1.0
|
|
HG3
|
A:LYS169
|
5.0
|
49.8
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 2 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:34.0
occ:1.00
|
OQ1
|
B:KCX192
|
1.9
|
38.7
|
1.0
|
|
HO2
|
B:CAP500
|
2.0
|
44.5
|
1.0
|
|
OD1
|
B:ASP194
|
2.0
|
38.9
|
1.0
|
|
OE1
|
B:GLU195
|
2.1
|
28.8
|
1.0
|
|
O3
|
B:CAP500
|
2.2
|
38.5
|
1.0
|
|
O2
|
B:CAP500
|
2.2
|
37.0
|
1.0
|
|
O6
|
B:CAP500
|
2.2
|
35.1
|
1.0
|
|
HO3
|
B:CAP500
|
2.8
|
46.2
|
1.0
|
|
C2
|
B:CAP500
|
2.8
|
38.0
|
1.0
|
|
C
|
B:CAP500
|
2.8
|
36.7
|
1.0
|
|
H
|
B:GLU195
|
3.0
|
41.3
|
1.0
|
|
C3
|
B:CAP500
|
3.0
|
38.6
|
1.0
|
|
CX
|
B:KCX192
|
3.1
|
38.1
|
1.0
|
|
HD21
|
A:ASN112
|
3.1
|
46.1
|
1.0
|
|
CD
|
B:GLU195
|
3.2
|
29.9
|
1.0
|
|
CG
|
B:ASP194
|
3.2
|
38.3
|
1.0
|
|
HE2
|
B:HIS288
|
3.3
|
38.1
|
1.0
|
|
HZ1
|
B:LYS167
|
3.3
|
50.5
|
1.0
|
|
HG21
|
B:ILE165
|
3.3
|
40.7
|
1.0
|
|
HZ2
|
B:LYS169
|
3.4
|
49.9
|
1.0
|
|
OQ2
|
B:KCX192
|
3.4
|
38.7
|
1.0
|
|
HZ1
|
B:LYS169
|
3.4
|
49.9
|
1.0
|
|
HZ3
|
B:LYS169
|
3.4
|
49.9
|
1.0
|
|
HA
|
B:ASP194
|
3.4
|
38.8
|
1.0
|
|
HZ3
|
B:LYS167
|
3.4
|
50.5
|
1.0
|
|
NZ
|
B:LYS169
|
3.6
|
41.6
|
1.0
|
|
H3
|
B:CAP500
|
3.6
|
46.3
|
1.0
|
|
OE2
|
B:GLU195
|
3.6
|
29.4
|
1.0
|
|
HD22
|
A:ASN112
|
3.7
|
46.1
|
1.0
|
|
ND2
|
A:ASN112
|
3.7
|
38.4
|
1.0
|
|
NZ
|
B:LYS167
|
3.8
|
42.1
|
1.0
|
|
N
|
B:GLU195
|
3.8
|
34.4
|
1.0
|
|
OD2
|
B:ASP194
|
3.9
|
39.9
|
1.0
|
|
NE2
|
B:HIS288
|
4.0
|
31.8
|
1.0
|
|
HB3
|
B:GLU195
|
4.0
|
39.8
|
1.0
|
|
HG12
|
B:ILE165
|
4.0
|
43.8
|
1.0
|
|
O7
|
B:CAP500
|
4.1
|
37.2
|
1.0
|
|
CA
|
B:ASP194
|
4.1
|
32.3
|
1.0
|
|
NZ
|
B:KCX192
|
4.2
|
36.1
|
1.0
|
|
C1
|
B:CAP500
|
4.2
|
38.1
|
1.0
|
|
HZ2
|
B:LYS167
|
4.2
|
50.5
|
1.0
|
|
CB
|
B:ASP194
|
4.3
|
35.2
|
1.0
|
|
C4
|
B:CAP500
|
4.3
|
40.8
|
1.0
|
|
CG2
|
B:ILE165
|
4.3
|
33.9
|
1.0
|
|
H4
|
B:CAP500
|
4.4
|
48.9
|
1.0
|
|
CG
|
B:GLU195
|
4.4
|
32.0
|
1.0
|
|
C
|
B:ASP194
|
4.5
|
33.4
|
1.0
|
|
HE1
|
B:HIS288
|
4.5
|
38.6
|
1.0
|
|
H51
|
B:CAP500
|
4.5
|
48.3
|
1.0
|
|
CB
|
B:GLU195
|
4.6
|
33.2
|
1.0
|
|
HG23
|
B:ILE165
|
4.6
|
40.7
|
1.0
|
|
HD3
|
B:PRO196
|
4.6
|
40.0
|
1.0
|
|
CE1
|
B:HIS288
|
4.6
|
32.1
|
1.0
|
|
O1
|
B:CAP500
|
4.6
|
38.3
|
1.0
|
|
H11
|
B:CAP500
|
4.7
|
45.7
|
1.0
|
|
HB3
|
B:ASP194
|
4.8
|
42.3
|
1.0
|
|
HG22
|
B:ILE165
|
4.8
|
40.7
|
1.0
|
|
CA
|
B:GLU195
|
4.8
|
34.0
|
1.0
|
|
HE2
|
B:LYS167
|
4.8
|
50.4
|
1.0
|
|
C5
|
B:CAP500
|
4.9
|
40.2
|
1.0
|
|
CG1
|
B:ILE165
|
4.9
|
36.5
|
1.0
|
|
O
|
A:HOH675
|
4.9
|
36.5
|
1.0
|
|
HB2
|
B:ASP194
|
4.9
|
42.3
|
1.0
|
|
H12
|
B:CAP500
|
4.9
|
45.7
|
1.0
|
|
HG3
|
B:LYS169
|
4.9
|
47.4
|
1.0
|
|
H52
|
B:CAP500
|
4.9
|
48.3
|
1.0
|
|
CD2
|
B:HIS288
|
5.0
|
30.8
|
1.0
|
|
HG3
|
B:GLU195
|
5.0
|
38.5
|
1.0
|
|
HG2
|
B:GLU195
|
5.0
|
38.5
|
1.0
|
|
CG
|
A:ASN112
|
5.0
|
39.2
|
1.0
|
|
CE
|
B:LYS167
|
5.0
|
42.0
|
1.0
|
|
HD13
|
B:ILE165
|
5.0
|
45.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 3 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:44.2
occ:1.00
|
OD1
|
C:ASP194
|
2.0
|
38.8
|
1.0
|
|
HO2
|
C:CAP500
|
2.0
|
50.5
|
1.0
|
|
OE1
|
C:GLU195
|
2.1
|
37.5
|
1.0
|
|
OQ1
|
C:KCX192
|
2.1
|
43.0
|
1.0
|
|
O3
|
C:CAP500
|
2.1
|
40.2
|
1.0
|
|
O6
|
C:CAP500
|
2.1
|
42.3
|
1.0
|
|
O2
|
C:CAP500
|
2.2
|
42.1
|
1.0
|
|
C
|
C:CAP500
|
2.7
|
43.4
|
1.0
|
|
HO3
|
C:CAP500
|
2.7
|
48.2
|
1.0
|
|
C2
|
C:CAP500
|
2.7
|
43.0
|
1.0
|
|
C3
|
C:CAP500
|
2.9
|
41.9
|
1.0
|
|
H
|
C:GLU195
|
3.0
|
45.0
|
1.0
|
|
HD21
|
D:ASN112
|
3.0
|
51.7
|
1.0
|
|
CX
|
C:KCX192
|
3.1
|
43.2
|
1.0
|
|
CD
|
C:GLU195
|
3.1
|
37.6
|
1.0
|
|
HE2
|
C:HIS288
|
3.2
|
44.9
|
1.0
|
|
CG
|
C:ASP194
|
3.2
|
38.8
|
1.0
|
|
OQ2
|
C:KCX192
|
3.3
|
44.6
|
1.0
|
|
HG21
|
C:ILE165
|
3.4
|
44.5
|
1.0
|
|
HA
|
C:ASP194
|
3.4
|
43.6
|
1.0
|
|
HZ2
|
C:LYS169
|
3.4
|
52.8
|
1.0
|
|
H3
|
C:CAP500
|
3.5
|
50.3
|
1.0
|
|
HZ3
|
C:LYS169
|
3.5
|
52.8
|
1.0
|
|
HZ1
|
C:LYS167
|
3.5
|
53.1
|
1.0
|
|
HZ1
|
C:LYS169
|
3.6
|
52.8
|
1.0
|
|
OE2
|
C:GLU195
|
3.6
|
38.8
|
1.0
|
|
HZ3
|
C:LYS167
|
3.7
|
53.1
|
1.0
|
|
ND2
|
D:ASN112
|
3.7
|
43.1
|
1.0
|
|
NZ
|
C:LYS169
|
3.7
|
44.0
|
1.0
|
|
HD22
|
D:ASN112
|
3.7
|
51.7
|
1.0
|
|
N
|
C:GLU195
|
3.8
|
37.5
|
1.0
|
|
NE2
|
C:HIS288
|
3.9
|
37.4
|
1.0
|
|
OD2
|
C:ASP194
|
3.9
|
40.1
|
1.0
|
|
O7
|
C:CAP500
|
3.9
|
44.7
|
1.0
|
|
HB3
|
C:GLU195
|
4.0
|
43.9
|
1.0
|
|
NZ
|
C:LYS167
|
4.0
|
44.3
|
1.0
|
|
HG12
|
C:ILE165
|
4.1
|
47.7
|
1.0
|
|
CA
|
C:ASP194
|
4.1
|
36.3
|
1.0
|
|
C1
|
C:CAP500
|
4.2
|
44.5
|
1.0
|
|
C4
|
C:CAP500
|
4.2
|
43.5
|
1.0
|
|
CB
|
C:ASP194
|
4.3
|
37.3
|
1.0
|
|
NZ
|
C:KCX192
|
4.3
|
42.1
|
1.0
|
|
CG2
|
C:ILE165
|
4.3
|
37.0
|
1.0
|
|
H4
|
C:CAP500
|
4.3
|
52.2
|
1.0
|
|
HE1
|
C:HIS288
|
4.4
|
44.8
|
1.0
|
|
CG
|
C:GLU195
|
4.4
|
37.0
|
1.0
|
|
CE1
|
C:HIS288
|
4.5
|
37.3
|
1.0
|
|
C
|
C:ASP194
|
4.5
|
37.2
|
1.0
|
|
HG23
|
C:ILE165
|
4.5
|
44.5
|
1.0
|
|
H51
|
C:CAP500
|
4.5
|
52.0
|
1.0
|
|
HZ2
|
C:LYS167
|
4.5
|
53.1
|
1.0
|
|
CB
|
C:GLU195
|
4.5
|
36.6
|
1.0
|
|
HD3
|
C:PRO196
|
4.6
|
43.6
|
1.0
|
|
H11
|
C:CAP500
|
4.7
|
53.4
|
1.0
|
|
O1
|
C:CAP500
|
4.7
|
45.2
|
1.0
|
|
C5
|
C:CAP500
|
4.8
|
43.3
|
1.0
|
|
HB3
|
C:ASP194
|
4.8
|
44.8
|
1.0
|
|
CA
|
C:GLU195
|
4.8
|
36.8
|
1.0
|
|
H52
|
C:CAP500
|
4.8
|
52.0
|
1.0
|
|
HG22
|
C:ILE165
|
4.8
|
44.5
|
1.0
|
|
CD2
|
C:HIS288
|
4.8
|
36.1
|
1.0
|
|
H12
|
C:CAP500
|
4.8
|
53.4
|
1.0
|
|
CG
|
D:ASN112
|
4.9
|
43.2
|
1.0
|
|
HB2
|
C:ASP194
|
4.9
|
44.8
|
1.0
|
|
HG3
|
C:GLU195
|
4.9
|
44.4
|
1.0
|
|
HG3
|
C:LYS169
|
5.0
|
52.0
|
1.0
|
|
HG2
|
C:GLU195
|
5.0
|
44.4
|
1.0
|
|
HE2
|
C:LYS167
|
5.0
|
53.6
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 4 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:38.5
occ:1.00
|
OD1
|
D:ASP194
|
2.0
|
32.7
|
1.0
|
|
OE1
|
D:GLU195
|
2.0
|
41.8
|
1.0
|
|
HO2
|
D:CAP500
|
2.0
|
45.9
|
1.0
|
|
OQ2
|
D:KCX192
|
2.1
|
39.1
|
1.0
|
|
O3
|
D:CAP500
|
2.1
|
40.1
|
1.0
|
|
O7
|
D:CAP500
|
2.2
|
39.4
|
1.0
|
|
O2
|
D:CAP500
|
2.3
|
38.2
|
1.0
|
|
HO3
|
D:CAP500
|
2.8
|
48.1
|
1.0
|
|
C2
|
D:CAP500
|
2.8
|
40.2
|
1.0
|
|
C
|
D:CAP500
|
2.8
|
40.1
|
1.0
|
|
H
|
D:GLU195
|
2.9
|
45.1
|
1.0
|
|
C3
|
D:CAP500
|
3.0
|
40.7
|
1.0
|
|
HD21
|
C:ASN112
|
3.1
|
50.0
|
1.0
|
|
CD
|
D:GLU195
|
3.1
|
41.6
|
1.0
|
|
HE2
|
D:HIS288
|
3.2
|
47.5
|
1.0
|
|
CX
|
D:KCX192
|
3.2
|
38.7
|
1.0
|
|
CG
|
D:ASP194
|
3.2
|
33.7
|
1.0
|
|
HZ1
|
D:LYS167
|
3.3
|
57.8
|
1.0
|
|
HZ2
|
D:LYS169
|
3.4
|
52.6
|
1.0
|
|
HG21
|
D:ILE165
|
3.4
|
39.6
|
1.0
|
|
HA
|
D:ASP194
|
3.4
|
41.9
|
1.0
|
|
HZ3
|
D:LYS169
|
3.4
|
52.6
|
1.0
|
|
OQ1
|
D:KCX192
|
3.5
|
39.1
|
1.0
|
|
H3
|
D:CAP500
|
3.5
|
48.9
|
1.0
|
|
HZ1
|
D:LYS169
|
3.5
|
52.6
|
1.0
|
|
HZ3
|
D:LYS167
|
3.6
|
57.8
|
1.0
|
|
OE2
|
D:GLU195
|
3.6
|
43.2
|
1.0
|
|
NZ
|
D:LYS169
|
3.7
|
43.9
|
1.0
|
|
HD22
|
C:ASN112
|
3.7
|
50.0
|
1.0
|
|
ND2
|
C:ASN112
|
3.7
|
41.6
|
1.0
|
|
N
|
D:GLU195
|
3.7
|
37.6
|
1.0
|
|
NE2
|
D:HIS288
|
3.9
|
39.6
|
1.0
|
|
NZ
|
D:LYS167
|
3.9
|
48.1
|
1.0
|
|
HB3
|
D:GLU195
|
3.9
|
46.3
|
1.0
|
|
OD2
|
D:ASP194
|
4.0
|
34.9
|
1.0
|
|
O6
|
D:CAP500
|
4.0
|
41.4
|
1.0
|
|
CA
|
D:ASP194
|
4.1
|
34.9
|
1.0
|
|
HG12
|
D:ILE165
|
4.2
|
42.0
|
1.0
|
|
C1
|
D:CAP500
|
4.3
|
39.3
|
1.0
|
|
C4
|
D:CAP500
|
4.3
|
43.9
|
1.0
|
|
CB
|
D:ASP194
|
4.3
|
34.0
|
1.0
|
|
CG2
|
D:ILE165
|
4.3
|
33.0
|
1.0
|
|
CG
|
D:GLU195
|
4.4
|
39.8
|
1.0
|
|
NZ
|
D:KCX192
|
4.4
|
37.5
|
1.0
|
|
HZ2
|
D:LYS167
|
4.4
|
57.8
|
1.0
|
|
HE1
|
D:HIS288
|
4.4
|
46.2
|
1.0
|
|
H4
|
D:CAP500
|
4.4
|
52.7
|
1.0
|
|
C
|
D:ASP194
|
4.4
|
36.1
|
1.0
|
|
CB
|
D:GLU195
|
4.5
|
38.6
|
1.0
|
|
CE1
|
D:HIS288
|
4.5
|
38.5
|
1.0
|
|
H51
|
D:CAP500
|
4.5
|
52.5
|
1.0
|
|
HG23
|
D:ILE165
|
4.5
|
39.6
|
1.0
|
|
HD3
|
D:PRO196
|
4.6
|
45.3
|
1.0
|
|
H11
|
D:CAP500
|
4.7
|
47.1
|
1.0
|
|
O1
|
D:CAP500
|
4.7
|
38.6
|
1.0
|
|
CA
|
D:GLU195
|
4.7
|
37.6
|
1.0
|
|
HB3
|
D:ASP194
|
4.8
|
40.9
|
1.0
|
|
HE2
|
D:LYS167
|
4.8
|
58.0
|
1.0
|
|
HG22
|
D:ILE165
|
4.8
|
39.6
|
1.0
|
|
C5
|
D:CAP500
|
4.8
|
43.7
|
1.0
|
|
CD2
|
D:HIS288
|
4.9
|
38.8
|
1.0
|
|
HG3
|
D:LYS169
|
4.9
|
50.4
|
1.0
|
|
H12
|
D:CAP500
|
4.9
|
47.1
|
1.0
|
|
HG2
|
D:GLU195
|
4.9
|
47.8
|
1.0
|
|
HG3
|
D:GLU195
|
4.9
|
47.8
|
1.0
|
|
CG
|
C:ASN112
|
4.9
|
41.1
|
1.0
|
|
H52
|
D:CAP500
|
4.9
|
52.5
|
1.0
|
|
HB2
|
D:ASP194
|
4.9
|
40.9
|
1.0
|
|
CE
|
D:LYS167
|
5.0
|
48.3
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 5 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg501
b:37.2
occ:1.00
|
HO2
|
E:CAP500
|
2.0
|
45.0
|
1.0
|
|
OD1
|
E:ASP194
|
2.1
|
40.6
|
1.0
|
|
OQ2
|
E:KCX192
|
2.1
|
39.9
|
1.0
|
|
O7
|
E:CAP500
|
2.1
|
38.8
|
1.0
|
|
OE1
|
E:GLU195
|
2.1
|
36.9
|
1.0
|
|
O2
|
E:CAP500
|
2.2
|
37.5
|
1.0
|
|
O3
|
E:CAP500
|
2.2
|
38.7
|
1.0
|
|
C2
|
E:CAP500
|
2.7
|
39.6
|
1.0
|
|
C
|
E:CAP500
|
2.7
|
40.4
|
1.0
|
|
HO3
|
E:CAP500
|
2.9
|
46.4
|
1.0
|
|
C3
|
E:CAP500
|
3.0
|
39.8
|
1.0
|
|
CX
|
E:KCX192
|
3.1
|
38.7
|
1.0
|
|
H
|
E:GLU195
|
3.1
|
44.5
|
1.0
|
|
CG
|
E:ASP194
|
3.2
|
39.8
|
1.0
|
|
CD
|
E:GLU195
|
3.2
|
38.1
|
1.0
|
|
HE2
|
E:HIS288
|
3.3
|
48.6
|
1.0
|
|
HD21
|
F:ASN112
|
3.3
|
52.6
|
1.0
|
|
OQ1
|
E:KCX192
|
3.3
|
39.3
|
1.0
|
|
HG21
|
E:ILE165
|
3.3
|
46.0
|
1.0
|
|
HZ1
|
E:LYS167
|
3.4
|
56.3
|
1.0
|
|
HZ3
|
E:LYS169
|
3.5
|
53.0
|
1.0
|
|
HA
|
E:ASP194
|
3.5
|
42.9
|
1.0
|
|
HZ2
|
E:LYS169
|
3.5
|
53.0
|
1.0
|
|
HZ1
|
E:LYS169
|
3.6
|
53.0
|
1.0
|
|
HZ3
|
E:LYS167
|
3.6
|
56.3
|
1.0
|
|
H3
|
E:CAP500
|
3.6
|
47.8
|
1.0
|
|
OE2
|
E:GLU195
|
3.6
|
39.0
|
1.0
|
|
NZ
|
E:LYS169
|
3.7
|
44.1
|
1.0
|
|
OD2
|
E:ASP194
|
3.8
|
40.7
|
1.0
|
|
HD22
|
F:ASN112
|
3.8
|
52.6
|
1.0
|
|
ND2
|
F:ASN112
|
3.8
|
43.9
|
1.0
|
|
NZ
|
E:LYS167
|
3.9
|
47.0
|
1.0
|
|
HG12
|
E:ILE165
|
4.0
|
49.7
|
1.0
|
|
N
|
E:GLU195
|
4.0
|
37.1
|
1.0
|
|
O6
|
E:CAP500
|
4.0
|
41.9
|
1.0
|
|
NE2
|
E:HIS288
|
4.0
|
40.5
|
1.0
|
|
HB3
|
E:GLU195
|
4.1
|
45.5
|
1.0
|
|
C1
|
E:CAP500
|
4.2
|
41.1
|
1.0
|
|
CA
|
E:ASP194
|
4.2
|
35.8
|
1.0
|
|
C4
|
E:CAP500
|
4.3
|
42.0
|
1.0
|
|
CB
|
E:ASP194
|
4.3
|
37.1
|
1.0
|
|
CG2
|
E:ILE165
|
4.3
|
38.3
|
1.0
|
|
NZ
|
E:KCX192
|
4.3
|
37.3
|
1.0
|
|
H4
|
E:CAP500
|
4.4
|
50.4
|
1.0
|
|
HZ2
|
E:LYS167
|
4.4
|
56.3
|
1.0
|
|
CG
|
E:GLU195
|
4.5
|
38.4
|
1.0
|
|
HE1
|
E:HIS288
|
4.6
|
48.3
|
1.0
|
|
O1
|
E:CAP500
|
4.6
|
42.1
|
1.0
|
|
HG23
|
E:ILE165
|
4.6
|
46.0
|
1.0
|
|
H51
|
E:CAP500
|
4.6
|
50.8
|
1.0
|
|
C
|
E:ASP194
|
4.6
|
35.8
|
1.0
|
|
H11
|
E:CAP500
|
4.6
|
49.4
|
1.0
|
|
CB
|
E:GLU195
|
4.7
|
37.9
|
1.0
|
|
CE1
|
E:HIS288
|
4.7
|
40.2
|
1.0
|
|
HD3
|
E:PRO196
|
4.7
|
46.6
|
1.0
|
|
CG1
|
E:ILE165
|
4.8
|
41.4
|
1.0
|
|
HG22
|
E:ILE165
|
4.8
|
46.0
|
1.0
|
|
HD13
|
E:ILE165
|
4.8
|
52.5
|
1.0
|
|
HB3
|
E:ASP194
|
4.8
|
44.5
|
1.0
|
|
H12
|
E:CAP500
|
4.9
|
49.4
|
1.0
|
|
HE2
|
E:LYS167
|
4.9
|
55.9
|
1.0
|
|
HB2
|
E:ASP194
|
4.9
|
44.5
|
1.0
|
|
C5
|
E:CAP500
|
4.9
|
42.3
|
1.0
|
|
O
|
F:HOH609
|
4.9
|
34.0
|
1.0
|
|
HG3
|
E:LYS169
|
4.9
|
54.1
|
1.0
|
|
CD2
|
E:HIS288
|
4.9
|
38.9
|
1.0
|
|
H52
|
E:CAP500
|
5.0
|
50.8
|
1.0
|
|
CA
|
E:GLU195
|
5.0
|
37.3
|
1.0
|
|
O
|
F:HOH645
|
5.0
|
42.3
|
1.0
|
|
HG3
|
E:GLU195
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 5hk4
Go back to
Magnesium Binding Sites List in 5hk4
Magnesium binding site 6 out
of 6 in the Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure Function Studies of R. Palustris Rubisco (A47V-M331A Mutant) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg501
b:37.6
occ:1.00
|
HO2
|
F:CAP500
|
2.0
|
51.1
|
1.0
|
|
OQ1
|
F:KCX192
|
2.0
|
45.3
|
1.0
|
|
OD1
|
F:ASP194
|
2.1
|
48.8
|
1.0
|
|
OE1
|
F:GLU195
|
2.1
|
41.1
|
1.0
|
|
O3
|
F:CAP500
|
2.2
|
45.5
|
1.0
|
|
O7
|
F:CAP500
|
2.2
|
43.7
|
1.0
|
|
O2
|
F:CAP500
|
2.2
|
42.6
|
1.0
|
|
C2
|
F:CAP500
|
2.8
|
45.1
|
1.0
|
|
C
|
F:CAP500
|
2.8
|
45.1
|
1.0
|
|
HO3
|
F:CAP500
|
2.8
|
54.6
|
1.0
|
|
C3
|
F:CAP500
|
3.0
|
46.0
|
1.0
|
|
H
|
F:GLU195
|
3.0
|
50.0
|
1.0
|
|
CX
|
F:KCX192
|
3.0
|
44.8
|
1.0
|
|
HE2
|
F:HIS288
|
3.2
|
53.8
|
1.0
|
|
CG
|
F:ASP194
|
3.2
|
48.2
|
1.0
|
|
CD
|
F:GLU195
|
3.2
|
41.7
|
1.0
|
|
HD21
|
E:ASN112
|
3.2
|
51.7
|
1.0
|
|
OQ2
|
F:KCX192
|
3.3
|
46.5
|
1.0
|
|
HG21
|
F:ILE165
|
3.3
|
53.1
|
1.0
|
|
HA
|
F:ASP194
|
3.3
|
50.6
|
1.0
|
|
H3
|
F:CAP500
|
3.5
|
55.2
|
1.0
|
|
HZ2
|
F:LYS169
|
3.6
|
58.1
|
1.0
|
|
HZ1
|
F:LYS167
|
3.6
|
58.6
|
1.0
|
|
HZ3
|
F:LYS169
|
3.6
|
58.1
|
1.0
|
|
HZ1
|
F:LYS169
|
3.7
|
58.1
|
1.0
|
|
HZ3
|
F:LYS167
|
3.7
|
58.6
|
1.0
|
|
OE2
|
F:GLU195
|
3.7
|
43.0
|
1.0
|
|
N
|
F:GLU195
|
3.8
|
41.6
|
1.0
|
|
NZ
|
F:LYS169
|
3.8
|
48.4
|
1.0
|
|
OD2
|
F:ASP194
|
3.8
|
50.0
|
1.0
|
|
NE2
|
F:HIS288
|
3.9
|
44.9
|
1.0
|
|
ND2
|
E:ASN112
|
3.9
|
43.1
|
1.0
|
|
HG12
|
F:ILE165
|
3.9
|
56.5
|
1.0
|
|
HB3
|
F:GLU195
|
3.9
|
48.7
|
1.0
|
|
HD22
|
E:ASN112
|
3.9
|
51.7
|
1.0
|
|
O6
|
F:CAP500
|
4.0
|
45.9
|
1.0
|
|
CA
|
F:ASP194
|
4.1
|
42.1
|
1.0
|
|
NZ
|
F:LYS167
|
4.1
|
48.8
|
1.0
|
|
CG2
|
F:ILE165
|
4.2
|
44.2
|
1.0
|
|
CB
|
F:ASP194
|
4.2
|
45.0
|
1.0
|
|
C1
|
F:CAP500
|
4.2
|
46.9
|
1.0
|
|
NZ
|
F:KCX192
|
4.2
|
41.9
|
1.0
|
|
C4
|
F:CAP500
|
4.3
|
48.9
|
1.0
|
|
H4
|
F:CAP500
|
4.4
|
58.6
|
1.0
|
|
CG
|
F:GLU195
|
4.4
|
40.9
|
1.0
|
|
HG23
|
F:ILE165
|
4.5
|
53.1
|
1.0
|
|
C
|
F:ASP194
|
4.5
|
41.1
|
1.0
|
|
CB
|
F:GLU195
|
4.5
|
40.5
|
1.0
|
|
HE1
|
F:HIS288
|
4.5
|
53.5
|
1.0
|
|
CE1
|
F:HIS288
|
4.6
|
44.5
|
1.0
|
|
HZ2
|
F:LYS167
|
4.6
|
58.6
|
1.0
|
|
H51
|
F:CAP500
|
4.6
|
58.4
|
1.0
|
|
H11
|
F:CAP500
|
4.7
|
56.2
|
1.0
|
|
HD3
|
F:PRO196
|
4.7
|
54.3
|
1.0
|
|
O1
|
F:CAP500
|
4.7
|
48.5
|
1.0
|
|
HG22
|
F:ILE165
|
4.7
|
53.1
|
1.0
|
|
CG1
|
F:ILE165
|
4.8
|
47.1
|
1.0
|
|
CA
|
F:GLU195
|
4.8
|
41.1
|
1.0
|
|
HB3
|
F:ASP194
|
4.8
|
54.0
|
1.0
|
|
CD2
|
F:HIS288
|
4.8
|
43.3
|
1.0
|
|
HB2
|
F:ASP194
|
4.9
|
54.0
|
1.0
|
|
C5
|
F:CAP500
|
4.9
|
48.7
|
1.0
|
|
H52
|
F:CAP500
|
4.9
|
58.4
|
1.0
|
|
H12
|
F:CAP500
|
4.9
|
56.2
|
1.0
|
|
HE2
|
F:LYS167
|
4.9
|
58.9
|
1.0
|
|
HD2
|
F:HIS288
|
4.9
|
52.0
|
1.0
|
|
HD13
|
F:ILE165
|
5.0
|
59.5
|
1.0
|
|
HG3
|
F:GLU195
|
5.0
|
49.0
|
1.0
|
|
CB
|
F:ILE165
|
5.0
|
45.9
|
1.0
|
|
Reference:
M.A.Arbing,
S.Satagopan,
V.A.Varaljay,
F.R.Tabita.
Structure Function Studies of R. Palustris Rubisco. To Be Published.
Page generated: Tue Aug 12 10:50:57 2025
|
