Magnesium in PDB 4ijm: Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
Enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
All present enzymatic activity of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of Circadian Clock Protein Kaic A422V Mutant, PDB code: 4ijm
was solved by
M.Egli,
R.Pattanayek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.96 /
3.35
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.362,
134.468,
203.936,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
26.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
(pdb code 4ijm). 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 Circadian Clock Protein Kaic A422V Mutant, PDB code: 4ijm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 1 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg801
b:82.3
occ:1.00
|
OE2
|
A:GLU319
|
2.1
|
84.5
|
1.0
|
O
|
A:HOH950
|
2.1
|
0.8
|
1.0
|
O
|
A:HOH902
|
2.1
|
58.6
|
1.0
|
OG1
|
A:THR295
|
2.2
|
62.7
|
1.0
|
O3G
|
A:ATP802
|
2.4
|
86.0
|
1.0
|
CD
|
A:GLU319
|
3.1
|
94.6
|
1.0
|
O3A
|
A:ATP802
|
3.1
|
82.5
|
1.0
|
CB
|
A:THR295
|
3.2
|
57.8
|
1.0
|
O3B
|
A:ATP802
|
3.2
|
60.1
|
1.0
|
MG
|
B:MG606
|
3.4
|
69.9
|
1.0
|
PG
|
A:ATP802
|
3.4
|
68.7
|
1.0
|
CG2
|
A:THR295
|
3.5
|
67.4
|
1.0
|
CG
|
A:GLU319
|
3.8
|
93.7
|
1.0
|
PB
|
A:ATP802
|
3.9
|
59.5
|
1.0
|
O2G
|
A:ATP802
|
3.9
|
90.1
|
1.0
|
NE
|
B:ARG459
|
4.1
|
73.4
|
1.0
|
OE1
|
A:GLU319
|
4.1
|
92.8
|
1.0
|
OD2
|
A:ASP378
|
4.1
|
99.5
|
1.0
|
OE1
|
A:GLU318
|
4.2
|
0.2
|
1.0
|
O1A
|
A:ATP802
|
4.2
|
82.0
|
1.0
|
PA
|
A:ATP802
|
4.3
|
73.3
|
1.0
|
CA
|
A:THR295
|
4.5
|
67.2
|
1.0
|
NH2
|
B:ARG459
|
4.5
|
72.0
|
1.0
|
CZ
|
B:ARG459
|
4.6
|
79.1
|
1.0
|
O1G
|
A:ATP802
|
4.7
|
79.0
|
1.0
|
O2B
|
A:ATP802
|
4.7
|
58.2
|
1.0
|
CD
|
B:ARG459
|
4.7
|
78.4
|
1.0
|
OD1
|
A:ASP378
|
4.8
|
72.2
|
1.0
|
CG
|
B:ARG459
|
4.8
|
97.7
|
1.0
|
N
|
A:THR295
|
4.9
|
74.4
|
1.0
|
CG
|
A:ASP378
|
4.9
|
89.8
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 2 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:63.1
occ:1.00
|
O
|
B:HOH720
|
2.1
|
73.6
|
1.0
|
OE1
|
B:GLU318
|
2.1
|
95.4
|
1.0
|
OG1
|
B:THR295
|
2.2
|
65.7
|
1.0
|
O3B
|
B:ATP602
|
2.4
|
87.5
|
1.0
|
O2G
|
B:ATP602
|
2.9
|
86.4
|
1.0
|
PG
|
B:ATP602
|
3.1
|
93.0
|
1.0
|
CD
|
B:GLU318
|
3.2
|
78.8
|
1.0
|
PB
|
B:ATP602
|
3.4
|
65.4
|
1.0
|
O2B
|
B:ATP602
|
3.5
|
52.8
|
1.0
|
O3G
|
B:ATP602
|
3.5
|
58.6
|
1.0
|
OE2
|
B:GLU318
|
3.6
|
57.4
|
1.0
|
CB
|
B:THR295
|
3.6
|
60.5
|
1.0
|
O3A
|
B:ATP602
|
3.7
|
76.8
|
1.0
|
OD1
|
B:ASP378
|
3.7
|
66.6
|
1.0
|
OE2
|
B:GLU319
|
4.2
|
95.3
|
1.0
|
OD2
|
B:ASP378
|
4.3
|
66.9
|
1.0
|
N
|
B:THR295
|
4.3
|
56.8
|
1.0
|
CG
|
B:ASP378
|
4.4
|
70.2
|
1.0
|
CG2
|
B:THR295
|
4.4
|
62.4
|
1.0
|
CA
|
B:THR295
|
4.4
|
56.6
|
1.0
|
O1G
|
B:ATP602
|
4.5
|
74.6
|
1.0
|
CG
|
B:GLU318
|
4.5
|
59.7
|
1.0
|
O1B
|
B:ATP602
|
4.8
|
70.2
|
1.0
|
CB
|
B:GLU318
|
4.8
|
60.9
|
1.0
|
CE
|
B:LYS294
|
4.9
|
64.5
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 3 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:69.9
occ:1.00
|
CG
|
B:ARG459
|
2.2
|
97.7
|
1.0
|
O3G
|
A:ATP802
|
2.5
|
86.0
|
1.0
|
O1A
|
A:ATP802
|
2.5
|
82.0
|
1.0
|
O3A
|
A:ATP802
|
3.0
|
82.5
|
1.0
|
CD
|
B:ARG459
|
3.1
|
78.4
|
1.0
|
NE
|
B:ARG459
|
3.2
|
73.4
|
1.0
|
CB
|
B:ARG459
|
3.2
|
0.9
|
1.0
|
PA
|
A:ATP802
|
3.3
|
73.3
|
1.0
|
MG
|
A:MG801
|
3.4
|
82.3
|
1.0
|
C5'
|
A:ATP802
|
3.5
|
91.4
|
1.0
|
PG
|
A:ATP802
|
3.6
|
68.7
|
1.0
|
CA
|
B:ARG459
|
3.7
|
91.4
|
1.0
|
O5'
|
A:ATP802
|
3.8
|
79.0
|
1.0
|
O1G
|
A:ATP802
|
3.9
|
79.0
|
1.0
|
PB
|
A:ATP802
|
4.0
|
59.5
|
1.0
|
OE2
|
A:GLU319
|
4.0
|
84.5
|
1.0
|
O3B
|
A:ATP802
|
4.0
|
60.1
|
1.0
|
O1B
|
A:ATP802
|
4.0
|
94.1
|
1.0
|
CZ
|
B:ARG459
|
4.4
|
79.1
|
1.0
|
CD
|
A:GLU319
|
4.5
|
94.6
|
1.0
|
OE1
|
A:GLU319
|
4.6
|
92.8
|
1.0
|
N
|
B:ARG459
|
4.6
|
80.5
|
1.0
|
OG1
|
A:THR295
|
4.7
|
62.7
|
1.0
|
O
|
B:ARG459
|
4.7
|
0.9
|
1.0
|
O2A
|
A:ATP802
|
4.7
|
75.5
|
1.0
|
C
|
B:ARG459
|
4.7
|
93.4
|
1.0
|
C4'
|
A:ATP802
|
4.9
|
83.7
|
1.0
|
NZ
|
B:LYS457
|
4.9
|
69.6
|
1.0
|
O2G
|
A:ATP802
|
4.9
|
90.1
|
1.0
|
NH2
|
B:ARG459
|
5.0
|
72.0
|
1.0
|
CB
|
A:THR295
|
5.0
|
57.8
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 4ijm
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Magnesium Binding Sites List in 4ijm
Magnesium binding site 4 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:44.0
occ:1.00
|
OG1
|
C:THR295
|
2.1
|
56.3
|
1.0
|
OE1
|
C:GLU318
|
2.1
|
0.9
|
1.0
|
O2G
|
C:ATP602
|
2.2
|
82.5
|
1.0
|
O3B
|
C:ATP602
|
2.5
|
63.7
|
1.0
|
PG
|
C:ATP602
|
2.7
|
74.2
|
1.0
|
CD
|
C:GLU318
|
3.1
|
66.4
|
1.0
|
O1G
|
C:ATP602
|
3.2
|
74.9
|
1.0
|
CB
|
C:THR295
|
3.5
|
47.6
|
1.0
|
OE2
|
C:GLU318
|
3.5
|
53.9
|
1.0
|
OE2
|
C:GLU319
|
3.6
|
84.1
|
1.0
|
OD1
|
C:ASP378
|
3.6
|
35.1
|
1.0
|
OD2
|
C:ASP378
|
3.9
|
49.6
|
1.0
|
PB
|
C:ATP602
|
4.0
|
51.8
|
1.0
|
NH1
|
D:ARG459
|
4.0
|
82.2
|
1.0
|
CG2
|
C:THR295
|
4.1
|
35.1
|
1.0
|
CG
|
C:ASP378
|
4.1
|
53.2
|
1.0
|
O3G
|
C:ATP602
|
4.2
|
35.9
|
1.0
|
O3A
|
C:ATP602
|
4.3
|
43.2
|
1.0
|
CA
|
C:THR295
|
4.4
|
35.4
|
1.0
|
N
|
C:THR295
|
4.4
|
41.0
|
1.0
|
CG
|
C:GLU318
|
4.4
|
25.0
|
1.0
|
CB
|
C:GLU318
|
4.7
|
49.2
|
1.0
|
CD
|
C:GLU319
|
4.7
|
75.4
|
1.0
|
O2B
|
C:ATP602
|
4.7
|
26.8
|
1.0
|
O2A
|
C:ATP602
|
4.8
|
46.4
|
1.0
|
NH2
|
D:ARG459
|
4.8
|
41.4
|
1.0
|
O1B
|
C:ATP602
|
4.9
|
67.1
|
1.0
|
CZ
|
D:ARG459
|
4.9
|
61.2
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 5 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:55.5
occ:1.00
|
O
|
D:HOH739
|
2.1
|
38.3
|
1.0
|
O3B
|
D:ATP602
|
2.1
|
53.6
|
1.0
|
OG1
|
D:THR295
|
2.1
|
53.1
|
1.0
|
OE2
|
D:GLU319
|
2.3
|
84.0
|
1.0
|
O3G
|
D:ATP602
|
2.5
|
45.4
|
1.0
|
PG
|
D:ATP602
|
2.7
|
60.4
|
1.0
|
O2G
|
D:ATP602
|
3.1
|
66.5
|
1.0
|
CB
|
D:THR295
|
3.3
|
64.2
|
1.0
|
PB
|
D:ATP602
|
3.5
|
43.0
|
1.0
|
CD
|
D:GLU319
|
3.5
|
64.8
|
1.0
|
O3A
|
D:ATP602
|
3.6
|
50.3
|
1.0
|
O2A
|
D:ATP602
|
3.8
|
52.2
|
1.0
|
CG2
|
D:THR295
|
4.1
|
61.0
|
1.0
|
O1G
|
D:ATP602
|
4.1
|
34.8
|
1.0
|
OE1
|
D:GLU318
|
4.1
|
70.8
|
1.0
|
O2B
|
D:ATP602
|
4.1
|
66.9
|
1.0
|
CG
|
D:GLU319
|
4.2
|
52.9
|
1.0
|
NE
|
E:ARG459
|
4.3
|
58.2
|
1.0
|
NH2
|
E:ARG459
|
4.3
|
52.6
|
1.0
|
PA
|
D:ATP602
|
4.4
|
48.5
|
1.0
|
OE1
|
D:GLU319
|
4.4
|
66.7
|
1.0
|
CA
|
D:THR295
|
4.5
|
49.3
|
1.0
|
O1B
|
D:ATP602
|
4.5
|
32.6
|
1.0
|
CZ
|
E:ARG459
|
4.5
|
47.9
|
1.0
|
N
|
D:THR295
|
4.5
|
48.4
|
1.0
|
OD2
|
D:ASP378
|
4.9
|
56.0
|
1.0
|
OD1
|
D:ASP378
|
4.9
|
37.6
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 6 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg601
b:59.5
occ:1.00
|
O
|
E:HOH725
|
2.1
|
62.6
|
1.0
|
OE1
|
E:GLU318
|
2.1
|
0.8
|
1.0
|
OG1
|
E:THR295
|
2.2
|
56.0
|
1.0
|
O3B
|
E:ATP602
|
2.2
|
86.2
|
1.0
|
O2G
|
E:ATP602
|
2.6
|
82.0
|
1.0
|
PG
|
E:ATP602
|
3.0
|
75.1
|
1.0
|
O
|
F:HOH708
|
3.1
|
73.4
|
1.0
|
CD
|
E:GLU318
|
3.3
|
82.9
|
1.0
|
PB
|
E:ATP602
|
3.5
|
75.8
|
1.0
|
CB
|
E:THR295
|
3.6
|
58.0
|
1.0
|
OE2
|
E:GLU319
|
3.7
|
77.3
|
1.0
|
O3A
|
E:ATP602
|
3.8
|
94.5
|
1.0
|
O2B
|
E:ATP602
|
3.8
|
39.0
|
1.0
|
OE2
|
E:GLU318
|
3.9
|
75.3
|
1.0
|
OD1
|
E:ASP378
|
3.9
|
49.0
|
1.0
|
OD2
|
E:ASP378
|
4.0
|
73.8
|
1.0
|
O1G
|
E:ATP602
|
4.0
|
64.2
|
1.0
|
O3G
|
E:ATP602
|
4.0
|
70.7
|
1.0
|
NH2
|
F:ARG459
|
4.2
|
67.7
|
1.0
|
CG
|
E:ASP378
|
4.3
|
79.7
|
1.0
|
CG2
|
E:THR295
|
4.3
|
64.7
|
1.0
|
CG
|
E:GLU318
|
4.5
|
52.1
|
1.0
|
CA
|
E:THR295
|
4.5
|
68.3
|
1.0
|
N
|
E:THR295
|
4.6
|
74.9
|
1.0
|
CB
|
E:GLU318
|
4.6
|
62.4
|
1.0
|
O1B
|
E:ATP602
|
4.7
|
55.9
|
1.0
|
CD
|
E:GLU319
|
4.8
|
73.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 4ijm
Go back to
Magnesium Binding Sites List in 4ijm
Magnesium binding site 7 out
of 7 in the Crystal Structure of Circadian Clock Protein Kaic A422V Mutant
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 Circadian Clock Protein Kaic A422V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg601
b:85.6
occ:1.00
|
OE1
|
F:GLU318
|
2.1
|
95.1
|
1.0
|
OG1
|
F:THR295
|
2.1
|
84.5
|
1.0
|
O2G
|
F:ATP602
|
2.9
|
0.5
|
1.0
|
O3B
|
F:ATP602
|
3.1
|
91.2
|
1.0
|
OE2
|
F:GLU319
|
3.2
|
0.3
|
1.0
|
CD
|
F:GLU318
|
3.4
|
96.9
|
1.0
|
OD2
|
F:ASP378
|
3.5
|
77.5
|
1.0
|
CB
|
F:THR295
|
3.5
|
67.8
|
1.0
|
O
|
F:HOH740
|
3.7
|
60.4
|
1.0
|
PG
|
F:ATP602
|
3.7
|
94.1
|
1.0
|
OD1
|
F:ASP378
|
3.9
|
75.3
|
1.0
|
CG2
|
F:THR295
|
3.9
|
75.3
|
1.0
|
CG
|
F:ASP378
|
4.0
|
82.5
|
1.0
|
CB
|
F:GLU318
|
4.1
|
91.3
|
1.0
|
CD
|
F:GLU319
|
4.2
|
89.8
|
1.0
|
OE2
|
F:GLU318
|
4.2
|
94.2
|
1.0
|
O3G
|
F:ATP602
|
4.3
|
0.4
|
1.0
|
CG
|
F:GLU318
|
4.3
|
90.0
|
1.0
|
CG
|
F:GLU319
|
4.3
|
83.8
|
1.0
|
NH2
|
A:ARG459
|
4.4
|
79.5
|
1.0
|
PB
|
F:ATP602
|
4.5
|
82.7
|
1.0
|
CA
|
F:THR295
|
4.6
|
74.2
|
1.0
|
O3A
|
F:ATP602
|
4.7
|
90.3
|
1.0
|
NE
|
A:ARG459
|
4.7
|
87.8
|
1.0
|
CZ
|
A:ARG459
|
4.8
|
87.2
|
1.0
|
N
|
F:THR295
|
4.8
|
81.7
|
1.0
|
O2B
|
F:ATP602
|
4.9
|
66.2
|
1.0
|
O1G
|
F:ATP602
|
4.9
|
70.3
|
1.0
|
|
Reference:
M.Egli,
R.Pattanayek,
J.H.Sheehan,
Y.Xu,
T.Mori,
J.A.Smith,
C.H.Johnson.
Loop-Loop Interactions Regulate Kaia-Stimulated Kaic Phosphorylation in the Cyanobacterial Kaiabc Circadian Clock. Biochemistry V. 52 1208 2013.
ISSN: ISSN 0006-2960
PubMed: 23351065
DOI: 10.1021/BI301691A
Page generated: Fri Aug 16 16:45:37 2024
|