Magnesium in PDB 8dba: Crystal Structure of Dodecameric Kaic
Protein crystallography data
The structure of Crystal Structure of Dodecameric Kaic, PDB code: 8dba
was solved by
R.A.P.Padua,
T.Grant,
W.Pitsawong,
M.S.Hoemberger,
R.Otten,
N.Bradshaw,
N.Grigorieff,
D.Kern,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.10 /
3.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.11,
136.09,
146.2,
93.13,
94.43,
108.09
|
R / Rfree (%)
|
23.6 /
27.9
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
23;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Dodecameric Kaic
(pdb code 8dba). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 23 binding sites of Magnesium where determined in the
Crystal Structure of Dodecameric Kaic, PDB code: 8dba:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 1 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:76.0
occ:1.00
|
O
|
A:HOH701
|
2.1
|
48.6
|
1.0
|
OE2
|
A:GLU302
|
2.8
|
97.3
|
1.0
|
OG
|
C:SER414
|
2.9
|
82.6
|
1.0
|
HZ1
|
A:LYS278
|
2.9
|
80.7
|
1.0
|
O2B
|
A:ADP604
|
2.9
|
93.1
|
1.0
|
HG
|
C:SER414
|
2.9
|
100.0
|
1.0
|
O3B
|
A:ADP604
|
3.0
|
77.4
|
1.0
|
HE2
|
A:LYS278
|
3.1
|
69.7
|
1.0
|
O
|
C:HOH703
|
3.2
|
49.6
|
1.0
|
PB
|
A:ADP604
|
3.2
|
84.0
|
1.0
|
HH21
|
C:ARG441
|
3.2
|
92.9
|
1.0
|
HH22
|
C:ARG441
|
3.3
|
92.9
|
1.0
|
NZ
|
A:LYS278
|
3.5
|
66.5
|
1.0
|
O1B
|
A:ADP604
|
3.6
|
69.1
|
1.0
|
NH2
|
C:ARG441
|
3.6
|
76.7
|
1.0
|
HD13
|
A:LEU399
|
3.6
|
75.2
|
1.0
|
CE
|
A:LYS278
|
3.6
|
58.6
|
1.0
|
HZ3
|
A:LYS278
|
3.7
|
80.7
|
1.0
|
HE3
|
A:LYS278
|
3.8
|
69.7
|
1.0
|
CD
|
A:GLU302
|
3.8
|
91.9
|
1.0
|
HG
|
A:SER279
|
4.0
|
70.8
|
1.0
|
OG
|
A:SER279
|
4.1
|
61.1
|
1.0
|
OE1
|
A:GLU302
|
4.2
|
82.5
|
1.0
|
CB
|
C:SER414
|
4.2
|
82.0
|
1.0
|
HA
|
C:SER414
|
4.2
|
111.6
|
1.0
|
CD1
|
A:LEU399
|
4.2
|
62.7
|
1.0
|
HD12
|
A:LEU399
|
4.2
|
75.2
|
1.0
|
HZ2
|
A:LYS278
|
4.3
|
80.7
|
1.0
|
HD11
|
A:LEU399
|
4.3
|
75.2
|
1.0
|
HB2
|
A:LYS278
|
4.3
|
80.2
|
1.0
|
CG
|
A:PRO363
|
4.4
|
61.8
|
1.0
|
HB2
|
C:SER414
|
4.5
|
99.3
|
1.0
|
HA
|
A:ALA274
|
4.6
|
73.7
|
1.0
|
H
|
A:SER279
|
4.7
|
81.9
|
1.0
|
CA
|
C:SER414
|
4.7
|
92.3
|
1.0
|
O3A
|
A:ADP604
|
4.8
|
76.2
|
1.0
|
HB3
|
C:SER414
|
4.8
|
99.3
|
1.0
|
OD2
|
A:ASP362
|
4.8
|
73.4
|
1.0
|
CZ
|
C:ARG441
|
4.9
|
85.8
|
1.0
|
O
|
C:SER414
|
4.9
|
89.2
|
1.0
|
HG1
|
A:THR397
|
4.9
|
80.5
|
1.0
|
|
Magnesium binding site 2 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 2 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:98.8
occ:1.00
|
O
|
A:HOH704
|
2.4
|
96.4
|
1.0
|
O
|
A:HOH702
|
2.5
|
88.2
|
1.0
|
OG1
|
A:THR38
|
2.6
|
90.7
|
1.0
|
O2A
|
A:ADP601
|
3.0
|
115.9
|
1.0
|
HB
|
A:THR38
|
3.0
|
124.1
|
1.0
|
HG21
|
A:THR38
|
3.2
|
147.7
|
1.0
|
HG1
|
A:THR38
|
3.2
|
109.7
|
1.0
|
O2B
|
A:ADP601
|
3.2
|
95.2
|
1.0
|
CB
|
A:THR38
|
3.3
|
102.7
|
1.0
|
O3A
|
A:ADP601
|
3.3
|
122.5
|
1.0
|
PA
|
A:ADP601
|
3.6
|
122.6
|
1.0
|
O
|
A:HOH705
|
3.7
|
91.2
|
1.0
|
CG2
|
A:THR38
|
3.8
|
122.3
|
1.0
|
OE2
|
A:GLU63
|
3.9
|
134.5
|
1.0
|
PB
|
A:ADP601
|
3.9
|
112.3
|
1.0
|
NH2
|
C:ARG209
|
3.9
|
126.2
|
1.0
|
HH22
|
C:ARG209
|
3.9
|
152.3
|
1.0
|
HH21
|
C:ARG209
|
4.0
|
152.3
|
1.0
|
O1A
|
A:ADP601
|
4.1
|
108.8
|
1.0
|
O
|
A:HOH703
|
4.1
|
93.7
|
1.0
|
CZ
|
C:ARG209
|
4.2
|
140.3
|
1.0
|
H
|
A:THR38
|
4.3
|
111.4
|
1.0
|
HG22
|
A:THR38
|
4.3
|
147.7
|
1.0
|
O1B
|
A:ADP601
|
4.4
|
104.8
|
1.0
|
HG23
|
A:THR38
|
4.4
|
147.7
|
1.0
|
NH1
|
C:ARG209
|
4.5
|
144.7
|
1.0
|
HH12
|
C:ARG209
|
4.5
|
174.6
|
1.0
|
CA
|
A:THR38
|
4.7
|
93.5
|
1.0
|
NE
|
C:ARG209
|
4.7
|
144.1
|
1.0
|
HE
|
C:ARG209
|
4.8
|
173.8
|
1.0
|
CD
|
A:GLU63
|
4.9
|
144.7
|
1.0
|
OD2
|
A:ASP130
|
4.9
|
102.5
|
1.0
|
N
|
A:THR38
|
4.9
|
92.1
|
1.0
|
HH11
|
C:ARG209
|
5.0
|
174.6
|
1.0
|
|
Magnesium binding site 3 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 3 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:36.8
occ:1.00
|
O
|
B:HOH703
|
2.1
|
42.5
|
1.0
|
O
|
B:HOH701
|
2.7
|
38.7
|
1.0
|
O3B
|
B:ADP604
|
2.8
|
86.9
|
1.0
|
OG
|
B:SER279
|
2.8
|
52.7
|
1.0
|
O1B
|
B:ADP604
|
3.1
|
69.3
|
1.0
|
OE2
|
B:GLU302
|
3.1
|
87.6
|
1.0
|
OD1
|
B:ASP362
|
3.2
|
52.0
|
1.0
|
PB
|
B:ADP604
|
3.3
|
78.7
|
1.0
|
HE2
|
B:LYS278
|
3.4
|
91.0
|
1.0
|
OD2
|
B:ASP362
|
3.7
|
81.2
|
1.0
|
CG
|
B:ASP362
|
3.8
|
67.5
|
1.0
|
HZ3
|
B:LYS278
|
3.9
|
103.8
|
1.0
|
O2B
|
B:ADP604
|
3.9
|
61.0
|
1.0
|
H
|
B:SER279
|
4.0
|
59.2
|
1.0
|
HB2
|
B:LYS278
|
4.1
|
68.5
|
1.0
|
HG1
|
B:THR397
|
4.1
|
81.3
|
1.0
|
HB3
|
B:PRO363
|
4.1
|
76.9
|
1.0
|
HZ2
|
B:LYS278
|
4.2
|
103.8
|
1.0
|
HD21
|
B:LEU399
|
4.2
|
89.4
|
1.0
|
HG3
|
B:PRO363
|
4.2
|
76.4
|
1.0
|
CE
|
B:LYS278
|
4.2
|
75.1
|
1.0
|
CD
|
B:GLU302
|
4.2
|
80.9
|
1.0
|
CB
|
B:SER279
|
4.2
|
58.8
|
1.0
|
NZ
|
B:LYS278
|
4.3
|
85.7
|
1.0
|
HB2
|
A:SER414
|
4.5
|
117.8
|
1.0
|
HB2
|
B:SER279
|
4.5
|
71.5
|
1.0
|
HE3
|
B:LYS278
|
4.6
|
91.0
|
1.0
|
N
|
B:SER279
|
4.6
|
51.3
|
1.0
|
O3A
|
B:ADP604
|
4.7
|
59.4
|
1.0
|
HB3
|
B:SER279
|
4.7
|
71.5
|
1.0
|
HH11
|
A:ARG441
|
4.8
|
101.1
|
1.0
|
OG1
|
B:THR397
|
4.8
|
67.0
|
1.0
|
OE1
|
B:GLU302
|
4.8
|
88.9
|
1.0
|
HG
|
B:LEU399
|
4.8
|
94.7
|
1.0
|
HB
|
B:THR397
|
4.9
|
62.1
|
1.0
|
HD3
|
B:PRO363
|
4.9
|
79.7
|
1.0
|
CG
|
B:PRO363
|
4.9
|
63.0
|
1.0
|
CB
|
B:PRO363
|
4.9
|
63.4
|
1.0
|
CA
|
B:SER279
|
5.0
|
59.4
|
1.0
|
HH12
|
A:ARG441
|
5.0
|
101.1
|
1.0
|
|
Magnesium binding site 4 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 4 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:65.3
occ:1.00
|
OG1
|
B:THR38
|
2.7
|
88.3
|
1.0
|
O
|
B:HOH702
|
2.7
|
65.7
|
1.0
|
HG1
|
B:THR38
|
2.8
|
106.8
|
1.0
|
O2B
|
B:ADP601
|
2.9
|
113.7
|
1.0
|
OE1
|
B:GLU63
|
3.3
|
108.4
|
1.0
|
HB
|
B:THR38
|
3.3
|
109.2
|
1.0
|
HG22
|
B:THR38
|
3.4
|
107.8
|
1.0
|
OE2
|
B:GLU63
|
3.5
|
133.1
|
1.0
|
CB
|
B:THR38
|
3.5
|
90.2
|
1.0
|
CD
|
B:GLU63
|
3.6
|
120.7
|
1.0
|
O3A
|
B:ADP601
|
3.6
|
118.0
|
1.0
|
PB
|
B:ADP601
|
3.7
|
111.6
|
1.0
|
O
|
B:HOH704
|
3.8
|
82.2
|
1.0
|
O2A
|
B:ADP601
|
3.9
|
123.9
|
1.0
|
O3B
|
B:ADP601
|
4.0
|
106.1
|
1.0
|
CG2
|
B:THR38
|
4.0
|
89.1
|
1.0
|
PA
|
B:ADP601
|
4.3
|
126.1
|
1.0
|
NH2
|
A:ARG209
|
4.4
|
125.1
|
1.0
|
OD1
|
B:ASP130
|
4.4
|
100.6
|
1.0
|
HG3
|
B:GLU63
|
4.5
|
143.5
|
1.0
|
H
|
B:THR38
|
4.5
|
110.6
|
1.0
|
OD2
|
B:ASP130
|
4.6
|
119.8
|
1.0
|
NE
|
A:ARG209
|
4.6
|
117.3
|
1.0
|
HG23
|
B:THR38
|
4.6
|
107.8
|
1.0
|
HG21
|
B:THR38
|
4.6
|
107.8
|
1.0
|
CZ
|
A:ARG209
|
4.6
|
130.7
|
1.0
|
CG
|
B:GLU63
|
4.7
|
118.8
|
1.0
|
O1A
|
B:ADP601
|
4.8
|
90.2
|
1.0
|
CA
|
B:THR38
|
4.8
|
90.4
|
1.0
|
HG21
|
B:THR166
|
4.9
|
115.6
|
1.0
|
HD2
|
A:LYS207
|
4.9
|
131.6
|
1.0
|
CG
|
B:ASP130
|
4.9
|
118.2
|
1.0
|
HZ3
|
A:LYS207
|
5.0
|
139.9
|
1.0
|
|
Magnesium binding site 5 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 5 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:84.0
occ:1.00
|
O
|
F:HOH705
|
2.5
|
89.1
|
1.0
|
OG1
|
F:THR38
|
2.8
|
91.0
|
1.0
|
HG21
|
F:THR38
|
3.0
|
112.2
|
1.0
|
HB
|
F:THR38
|
3.0
|
106.3
|
1.0
|
NH1
|
B:ARG209
|
3.2
|
124.2
|
1.0
|
CB
|
F:THR38
|
3.3
|
87.8
|
1.0
|
CD
|
B:ARG209
|
3.3
|
119.1
|
1.0
|
HG2
|
F:GLU63
|
3.4
|
141.8
|
1.0
|
O
|
F:HOH706
|
3.4
|
60.2
|
1.0
|
O2A
|
F:ADP601
|
3.5
|
117.5
|
1.0
|
CZ
|
B:ARG209
|
3.6
|
123.3
|
1.0
|
NE
|
B:ARG209
|
3.6
|
126.1
|
1.0
|
CG2
|
F:THR38
|
3.6
|
92.8
|
1.0
|
O1B
|
F:ADP601
|
3.6
|
99.4
|
1.0
|
O3A
|
F:ADP601
|
3.7
|
101.3
|
1.0
|
OE2
|
F:GLU63
|
3.7
|
130.7
|
1.0
|
O
|
F:HOH703
|
3.9
|
107.3
|
1.0
|
PA
|
F:ADP601
|
4.0
|
116.3
|
1.0
|
CD
|
F:GLU63
|
4.0
|
124.7
|
1.0
|
PB
|
F:ADP601
|
4.1
|
110.9
|
1.0
|
OD2
|
F:ASP130
|
4.1
|
96.5
|
1.0
|
O
|
F:HOH704
|
4.2
|
65.1
|
1.0
|
CG
|
F:GLU63
|
4.2
|
117.5
|
1.0
|
O2B
|
F:ADP601
|
4.2
|
104.9
|
1.0
|
HG22
|
F:THR38
|
4.2
|
112.2
|
1.0
|
HG23
|
F:THR38
|
4.3
|
112.2
|
1.0
|
O1A
|
F:ADP601
|
4.3
|
112.8
|
1.0
|
NH2
|
B:ARG209
|
4.5
|
114.9
|
1.0
|
H
|
F:THR38
|
4.6
|
105.9
|
1.0
|
OE1
|
F:GLU63
|
4.7
|
120.7
|
1.0
|
HG3
|
F:GLU63
|
4.7
|
141.8
|
1.0
|
CG
|
B:ARG209
|
4.8
|
115.4
|
1.0
|
CA
|
F:THR38
|
4.8
|
83.1
|
1.0
|
HD2
|
B:LYS207
|
4.8
|
132.9
|
1.0
|
HZ2
|
B:LYS207
|
4.9
|
125.0
|
1.0
|
|
Magnesium binding site 6 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 6 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:63.1
occ:1.00
|
O
|
C:HOH701
|
2.0
|
54.9
|
1.0
|
O2B
|
C:ADP604
|
2.5
|
97.3
|
1.0
|
PB
|
C:ADP604
|
3.2
|
106.5
|
1.0
|
OG
|
C:SER279
|
3.2
|
67.2
|
1.0
|
HH12
|
E:ARG441
|
3.3
|
112.2
|
1.0
|
O3B
|
C:ADP604
|
3.4
|
81.0
|
1.0
|
HG
|
C:SER279
|
3.5
|
81.6
|
1.0
|
HB2
|
E:SER414
|
3.6
|
119.8
|
1.0
|
O1B
|
C:ADP604
|
3.6
|
101.4
|
1.0
|
OD1
|
C:ASP362
|
3.6
|
86.7
|
1.0
|
NH1
|
E:ARG441
|
4.1
|
92.8
|
1.0
|
HH22
|
E:ARG441
|
4.2
|
93.6
|
1.0
|
HZ3
|
C:LYS278
|
4.2
|
107.5
|
1.0
|
OD2
|
C:ASP362
|
4.3
|
80.1
|
1.0
|
CB
|
E:SER414
|
4.4
|
99.1
|
1.0
|
HB3
|
E:SER414
|
4.4
|
119.8
|
1.0
|
CG
|
C:ASP362
|
4.4
|
78.8
|
1.0
|
HA
|
E:SER414
|
4.4
|
120.8
|
1.0
|
HG3
|
C:PRO363
|
4.4
|
88.6
|
1.0
|
HB3
|
C:PRO363
|
4.5
|
77.9
|
1.0
|
HH11
|
E:ARG441
|
4.5
|
112.2
|
1.0
|
HD3
|
C:PRO363
|
4.5
|
106.4
|
1.0
|
CB
|
C:SER279
|
4.5
|
67.9
|
1.0
|
HB2
|
C:SER279
|
4.6
|
82.4
|
1.0
|
HE2
|
C:LYS278
|
4.6
|
103.6
|
1.0
|
H
|
C:SER279
|
4.6
|
95.2
|
1.0
|
O
|
E:SER414
|
4.6
|
92.2
|
1.0
|
O3A
|
C:ADP604
|
4.7
|
74.2
|
1.0
|
HZ2
|
C:LYS278
|
4.7
|
107.5
|
1.0
|
OE1
|
C:GLU303
|
4.8
|
92.0
|
1.0
|
HB2
|
C:GLU302
|
4.8
|
126.0
|
1.0
|
NZ
|
C:LYS278
|
4.8
|
88.8
|
1.0
|
NH2
|
E:ARG441
|
4.9
|
77.3
|
1.0
|
CA
|
E:SER414
|
4.9
|
100.0
|
1.0
|
HZ1
|
E:LYS439
|
4.9
|
88.8
|
1.0
|
CZ
|
E:ARG441
|
4.9
|
88.6
|
1.0
|
O
|
C:HOH702
|
4.9
|
77.2
|
1.0
|
HB3
|
C:SER279
|
4.9
|
82.4
|
1.0
|
O1A
|
C:ADP604
|
5.0
|
98.8
|
1.0
|
OE1
|
C:GLU302
|
5.0
|
115.5
|
1.0
|
|
Magnesium binding site 7 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 7 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:98.3
occ:1.00
|
O
|
C:HOH707
|
2.0
|
97.3
|
1.0
|
O
|
C:HOH706
|
2.4
|
94.0
|
1.0
|
O1A
|
C:ADP601
|
2.7
|
112.4
|
1.0
|
HG1
|
C:THR38
|
2.8
|
112.1
|
1.0
|
O
|
C:HOH704
|
3.1
|
77.0
|
1.0
|
O3B
|
C:ADP601
|
3.5
|
104.5
|
1.0
|
O1B
|
C:ADP601
|
3.5
|
100.5
|
1.0
|
PA
|
C:ADP601
|
3.6
|
103.4
|
1.0
|
OG1
|
C:THR38
|
3.6
|
92.6
|
1.0
|
PB
|
C:ADP601
|
3.8
|
101.4
|
1.0
|
O3A
|
C:ADP601
|
3.8
|
104.0
|
1.0
|
HB
|
C:THR38
|
3.8
|
111.5
|
1.0
|
HG21
|
C:THR38
|
3.9
|
111.5
|
1.0
|
OE1
|
C:GLU63
|
3.9
|
116.6
|
1.0
|
O2A
|
C:ADP601
|
4.0
|
83.4
|
1.0
|
HZ3
|
E:LYS207
|
4.1
|
154.8
|
1.0
|
CB
|
C:THR38
|
4.2
|
92.2
|
1.0
|
HD2
|
E:LYS207
|
4.3
|
120.7
|
1.0
|
CG2
|
C:THR38
|
4.5
|
92.2
|
1.0
|
CD
|
C:GLU63
|
4.6
|
125.3
|
1.0
|
OE2
|
C:GLU63
|
4.6
|
120.6
|
1.0
|
OD2
|
C:ASP130
|
4.7
|
113.9
|
1.0
|
NZ
|
E:LYS207
|
5.0
|
128.3
|
1.0
|
HD22
|
C:ASN71
|
5.0
|
116.5
|
1.0
|
|
Magnesium binding site 8 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 8 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:85.8
occ:1.00
|
O2B
|
D:ADP604
|
1.9
|
92.5
|
1.0
|
O
|
D:ALA274
|
2.4
|
83.1
|
1.0
|
O3B
|
D:ADP604
|
2.5
|
75.9
|
1.0
|
PB
|
D:ADP604
|
2.5
|
106.7
|
1.0
|
HZ1
|
F:LYS439
|
2.5
|
88.3
|
1.0
|
HE3
|
F:LYS439
|
2.6
|
95.2
|
1.0
|
HE2
|
F:LYS439
|
2.9
|
95.2
|
1.0
|
CE
|
F:LYS439
|
3.0
|
78.6
|
1.0
|
O3A
|
D:ADP604
|
3.1
|
72.6
|
1.0
|
NZ
|
F:LYS439
|
3.1
|
72.8
|
1.0
|
C
|
D:ALA274
|
3.2
|
73.0
|
1.0
|
HZ1
|
D:LYS278
|
3.3
|
81.1
|
1.0
|
HA2
|
D:GLY275
|
3.5
|
70.4
|
1.0
|
HA
|
D:ALA274
|
3.6
|
72.2
|
1.0
|
HA
|
F:SER414
|
3.7
|
100.9
|
1.0
|
HZ2
|
F:LYS439
|
3.7
|
88.3
|
1.0
|
HZ3
|
F:LYS439
|
3.7
|
88.3
|
1.0
|
HB1
|
D:ALA274
|
3.7
|
74.1
|
1.0
|
HH22
|
F:ARG441
|
3.8
|
98.9
|
1.0
|
HZ3
|
D:LYS278
|
3.8
|
81.1
|
1.0
|
O
|
D:HOH702
|
3.9
|
44.1
|
1.0
|
CA
|
D:ALA274
|
3.9
|
63.9
|
1.0
|
O1B
|
D:ADP604
|
3.9
|
94.0
|
1.0
|
NZ
|
D:LYS278
|
4.0
|
66.8
|
1.0
|
N
|
D:GLY275
|
4.1
|
64.7
|
1.0
|
HH12
|
F:ARG441
|
4.1
|
117.8
|
1.0
|
NH2
|
F:ARG441
|
4.2
|
81.7
|
1.0
|
HZ2
|
D:LYS278
|
4.2
|
81.1
|
1.0
|
CA
|
D:GLY275
|
4.2
|
62.4
|
1.0
|
CB
|
D:ALA274
|
4.3
|
65.1
|
1.0
|
O2A
|
D:ADP604
|
4.3
|
88.9
|
1.0
|
PA
|
D:ADP604
|
4.4
|
64.4
|
1.0
|
OE2
|
D:GLU302
|
4.4
|
103.7
|
1.0
|
OG
|
F:SER414
|
4.5
|
80.1
|
1.0
|
CD
|
F:LYS439
|
4.5
|
73.3
|
1.0
|
NH1
|
F:ARG441
|
4.5
|
97.4
|
1.0
|
O
|
D:HOH701
|
4.5
|
44.6
|
1.0
|
HH21
|
F:ARG441
|
4.6
|
98.9
|
1.0
|
CZ
|
F:ARG441
|
4.6
|
89.7
|
1.0
|
CA
|
F:SER414
|
4.6
|
83.4
|
1.0
|
HD2
|
F:LYS439
|
4.7
|
88.9
|
1.0
|
H
|
D:ALA276
|
4.7
|
68.5
|
1.0
|
H
|
D:GLY275
|
4.8
|
78.5
|
1.0
|
HA3
|
D:GLY275
|
4.8
|
70.4
|
1.0
|
HB2
|
F:SER414
|
4.9
|
112.2
|
1.0
|
HD3
|
F:LYS439
|
4.9
|
88.9
|
1.0
|
HB2
|
F:LYS439
|
4.9
|
76.5
|
1.0
|
HB3
|
D:ALA274
|
4.9
|
74.1
|
1.0
|
CB
|
F:SER414
|
4.9
|
92.8
|
1.0
|
HB2
|
D:ALA274
|
5.0
|
74.1
|
1.0
|
O
|
F:SER414
|
5.0
|
100.1
|
1.0
|
|
Magnesium binding site 9 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 9 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg603
b:68.1
occ:1.00
|
O
|
D:HOH703
|
2.2
|
43.2
|
1.0
|
OG1
|
D:THR38
|
2.3
|
58.9
|
1.0
|
HH12
|
F:ARG209
|
2.4
|
122.8
|
1.0
|
HH22
|
F:ARG209
|
2.5
|
121.5
|
1.0
|
NH1
|
F:ARG209
|
2.8
|
101.6
|
1.0
|
NH2
|
F:ARG209
|
2.9
|
100.5
|
1.0
|
CZ
|
F:ARG209
|
3.1
|
105.2
|
1.0
|
HG21
|
D:THR38
|
3.1
|
105.8
|
1.0
|
O1B
|
D:ADP601
|
3.3
|
83.5
|
1.0
|
CB
|
D:THR38
|
3.3
|
69.5
|
1.0
|
HH11
|
F:ARG209
|
3.4
|
122.8
|
1.0
|
HB
|
D:THR38
|
3.4
|
84.3
|
1.0
|
OD1
|
D:ASP130
|
3.5
|
96.8
|
1.0
|
HH21
|
F:ARG209
|
3.5
|
121.5
|
1.0
|
CG2
|
D:THR38
|
3.7
|
87.4
|
1.0
|
O
|
D:HOH705
|
3.7
|
54.9
|
1.0
|
OD2
|
D:ASP130
|
3.9
|
82.2
|
1.0
|
O
|
D:HOH704
|
3.9
|
72.6
|
1.0
|
CG
|
D:ASP130
|
4.0
|
89.5
|
1.0
|
HG23
|
D:THR38
|
4.1
|
105.8
|
1.0
|
PB
|
D:ADP601
|
4.2
|
85.6
|
1.0
|
NE
|
F:ARG209
|
4.2
|
114.0
|
1.0
|
OE1
|
D:GLU63
|
4.3
|
100.7
|
1.0
|
O3B
|
D:ADP601
|
4.3
|
90.5
|
1.0
|
O3A
|
D:ADP601
|
4.3
|
87.2
|
1.0
|
HG22
|
D:THR38
|
4.4
|
105.8
|
1.0
|
H
|
D:THR38
|
4.5
|
91.5
|
1.0
|
HG3
|
D:GLU63
|
4.6
|
138.6
|
1.0
|
CD
|
D:GLU63
|
4.6
|
107.6
|
1.0
|
CA
|
D:THR38
|
4.6
|
74.5
|
1.0
|
HE
|
F:ARG209
|
4.6
|
137.6
|
1.0
|
O1A
|
D:ADP601
|
4.7
|
101.7
|
1.0
|
HG1
|
D:THR131
|
4.7
|
137.2
|
1.0
|
HD3
|
F:ARG209
|
4.7
|
128.3
|
1.0
|
O
|
D:HOH706
|
4.8
|
76.2
|
1.0
|
HA
|
D:THR38
|
4.8
|
90.3
|
1.0
|
HZ1
|
F:LYS207
|
4.9
|
117.8
|
1.0
|
OG1
|
D:THR131
|
4.9
|
113.6
|
1.0
|
N
|
D:THR38
|
5.0
|
75.5
|
1.0
|
PA
|
D:ADP601
|
5.0
|
90.0
|
1.0
|
|
Magnesium binding site 10 out
of 23 in 8dba
Go back to
Magnesium Binding Sites List in 8dba
Magnesium binding site 10 out
of 23 in the Crystal Structure of Dodecameric Kaic
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 Dodecameric Kaic within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg602
b:46.3
occ:1.00
|
O1B
|
E:ADP604
|
2.4
|
78.0
|
1.0
|
O
|
E:HOH705
|
2.4
|
41.9
|
1.0
|
OG
|
E:SER279
|
2.5
|
65.5
|
1.0
|
O2B
|
E:ADP604
|
2.9
|
75.6
|
1.0
|
HH11
|
D:ARG441
|
3.0
|
113.7
|
1.0
|
HG
|
E:SER279
|
3.0
|
79.5
|
1.0
|
PB
|
E:ADP604
|
3.1
|
74.8
|
1.0
|
HH12
|
D:ARG441
|
3.2
|
113.7
|
1.0
|
NH1
|
D:ARG441
|
3.2
|
94.0
|
1.0
|
OE1
|
E:GLU302
|
3.5
|
105.3
|
1.0
|
HB2
|
E:SER279
|
3.5
|
85.5
|
1.0
|
CB
|
E:SER279
|
3.6
|
70.5
|
1.0
|
O
|
E:HOH702
|
3.6
|
86.6
|
1.0
|
O1A
|
E:ADP604
|
3.6
|
96.5
|
1.0
|
OD2
|
E:ASP362
|
3.8
|
90.6
|
1.0
|
HD2
|
D:ARG441
|
3.9
|
104.4
|
1.0
|
HB3
|
E:SER279
|
4.0
|
85.5
|
1.0
|
H
|
E:SER279
|
4.0
|
79.6
|
1.0
|
O3A
|
E:ADP604
|
4.1
|
65.4
|
1.0
|
OD1
|
E:ASP362
|
4.1
|
80.2
|
1.0
|
OE1
|
E:GLU303
|
4.1
|
114.2
|
1.0
|
CZ
|
D:ARG441
|
4.1
|
100.1
|
1.0
|
PA
|
E:ADP604
|
4.2
|
82.3
|
1.0
|
O2A
|
E:ADP604
|
4.4
|
77.4
|
1.0
|
O3B
|
E:ADP604
|
4.4
|
61.6
|
1.0
|
CG
|
E:ASP362
|
4.4
|
86.8
|
1.0
|
CD
|
E:GLU302
|
4.5
|
103.3
|
1.0
|
N
|
E:SER279
|
4.7
|
65.6
|
1.0
|
CD
|
D:ARG441
|
4.7
|
86.2
|
1.0
|
HZ1
|
D:LYS439
|
4.7
|
93.0
|
1.0
|
NE
|
D:ARG441
|
4.7
|
99.1
|
1.0
|
CA
|
E:SER279
|
4.7
|
64.4
|
1.0
|
CD
|
E:GLU303
|
4.8
|
103.2
|
1.0
|
HH22
|
D:ARG441
|
4.8
|
102.0
|
1.0
|
HB3
|
E:GLU302
|
4.8
|
109.6
|
1.0
|
NH2
|
D:ARG441
|
4.9
|
84.3
|
1.0
|
HE3
|
D:LYS439
|
5.0
|
98.5
|
1.0
|
HG2
|
E:GLU303
|
5.0
|
118.0
|
1.0
|
HD3
|
D:ARG441
|
5.0
|
104.4
|
1.0
|
|
Reference:
W.Pitsawong,
R.A.P.Padua,
T.Grant,
M.S.Hoemberger,
R.Otten,
N.Bradshaw,
N.Grigorieff,
D.Kern.
From Primordial Clocks to Circadian Oscillators Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-05836-9
Page generated: Fri Oct 4 00:22:04 2024
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