Magnesium in PDB 8a0x: Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
Protein crystallography data
The structure of Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna, PDB code: 8a0x
was solved by
S.Hadzi,
R.Loris,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.34 /
3.30
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.62,
113.62,
121.05,
90,
90,
90
|
R / Rfree (%)
|
23.8 /
26.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
(pdb code 8a0x). 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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna, PDB code: 8a0x:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 1 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:30.0
occ:1.00
|
NE2
|
A:GLN92
|
3.6
|
62.9
|
1.0
|
OG
|
A:SER47
|
3.7
|
64.0
|
1.0
|
CG
|
A:GLN92
|
4.3
|
61.2
|
1.0
|
CD
|
A:GLN92
|
4.4
|
61.9
|
1.0
|
O
|
A:SER47
|
4.6
|
66.7
|
1.0
|
MG
|
A:MG203
|
4.6
|
30.0
|
1.0
|
CB
|
A:SER47
|
4.7
|
65.3
|
1.0
|
C
|
A:SER47
|
4.7
|
66.2
|
1.0
|
N
|
A:ILE48
|
4.7
|
65.6
|
1.0
|
CA
|
A:ILE48
|
4.8
|
64.7
|
1.0
|
CG1
|
A:ILE48
|
4.9
|
63.0
|
1.0
|
OE1
|
A:GLN51
|
4.9
|
78.6
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 2 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:30.0
occ:1.00
|
OD1
|
A:ASP43
|
2.8
|
72.7
|
1.0
|
CG
|
A:ASP43
|
3.8
|
73.5
|
1.0
|
OD2
|
A:ASP43
|
4.1
|
75.7
|
1.0
|
OE1
|
A:GLU50
|
4.1
|
78.3
|
1.0
|
O
|
A:ASP43
|
4.6
|
71.9
|
1.0
|
CG1
|
A:VAL46
|
4.6
|
68.5
|
1.0
|
CB
|
A:SER47
|
4.8
|
65.3
|
1.0
|
CD
|
A:GLU50
|
4.9
|
78.9
|
1.0
|
N
|
A:SER47
|
4.9
|
66.5
|
1.0
|
CA
|
A:SER47
|
4.9
|
65.9
|
1.0
|
CB
|
A:VAL46
|
5.0
|
68.7
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 3 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg203
b:30.0
occ:1.00
|
MG
|
A:MG201
|
4.6
|
30.0
|
1.0
|
O
|
A:GLN92
|
4.7
|
60.1
|
1.0
|
CG
|
A:GLN92
|
4.8
|
61.2
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 8a0x
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Magnesium Binding Sites List in 8a0x
Magnesium binding site 4 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:30.0
occ:1.00
|
OD1
|
B:ASP43
|
2.7
|
63.3
|
1.0
|
CG
|
B:ASP43
|
3.7
|
64.6
|
1.0
|
OD2
|
B:ASP43
|
3.9
|
67.6
|
1.0
|
OE1
|
B:GLU50
|
4.2
|
78.8
|
1.0
|
CB
|
B:SER47
|
4.4
|
61.8
|
1.0
|
O
|
B:ASP43
|
4.6
|
58.0
|
1.0
|
CA
|
B:SER47
|
4.9
|
60.6
|
1.0
|
N
|
B:SER47
|
5.0
|
59.7
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 8a0x
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Magnesium Binding Sites List in 8a0x
Magnesium binding site 5 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg201
b:30.0
occ:1.00
|
O
|
D:GLU12
|
3.5
|
74.1
|
1.0
|
NH1
|
D:ARG15
|
4.1
|
87.0
|
1.0
|
CG
|
D:GLU12
|
4.1
|
75.7
|
1.0
|
CZ
|
D:ARG15
|
4.4
|
86.3
|
1.0
|
C
|
D:GLU12
|
4.4
|
70.7
|
1.0
|
OE1
|
D:GLU7
|
4.5
|
71.8
|
1.0
|
CA
|
D:GLU12
|
4.5
|
67.5
|
1.0
|
CB
|
D:GLU12
|
4.8
|
69.6
|
1.0
|
OE2
|
D:GLU7
|
4.8
|
70.7
|
1.0
|
NH2
|
D:ARG15
|
4.8
|
89.3
|
1.0
|
NE
|
D:ARG15
|
4.8
|
81.7
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 6 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg101
b:30.0
occ:1.00
|
C2
|
F:DA17
|
2.9
|
74.9
|
1.0
|
N3
|
F:DA17
|
3.1
|
71.9
|
1.0
|
N3
|
E:DG17
|
3.2
|
84.2
|
1.0
|
O4'
|
E:DG18
|
3.4
|
74.0
|
1.0
|
N2
|
E:DG17
|
3.5
|
84.7
|
1.0
|
C2
|
E:DG17
|
3.8
|
85.5
|
1.0
|
O4'
|
F:DA18
|
3.8
|
63.1
|
1.0
|
N1
|
F:DA17
|
4.1
|
78.0
|
1.0
|
O2
|
E:DT16
|
4.1
|
89.9
|
1.0
|
C1'
|
E:DG17
|
4.2
|
83.5
|
1.0
|
C4
|
E:DG17
|
4.2
|
85.4
|
1.0
|
C4'
|
E:DG18
|
4.3
|
71.5
|
1.0
|
C4
|
F:DA17
|
4.3
|
72.4
|
1.0
|
C4'
|
F:DA18
|
4.5
|
60.5
|
1.0
|
C1'
|
E:DG18
|
4.5
|
74.7
|
1.0
|
N9
|
E:DG17
|
4.6
|
85.5
|
1.0
|
O4'
|
E:DG17
|
4.7
|
84.0
|
1.0
|
N9
|
E:DG18
|
4.7
|
78.2
|
1.0
|
C5'
|
E:DG18
|
4.7
|
72.1
|
1.0
|
C5'
|
F:DA18
|
4.8
|
59.3
|
1.0
|
C2
|
E:DT16
|
5.0
|
90.0
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 7 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg101
b:30.0
occ:1.00
|
O4'
|
F:DC20
|
3.8
|
71.8
|
1.0
|
O3'
|
F:DC20
|
3.9
|
75.2
|
1.0
|
N3
|
F:DG19
|
4.2
|
74.2
|
1.0
|
C1'
|
F:DC20
|
4.2
|
72.8
|
1.0
|
C4'
|
F:DC20
|
4.2
|
74.3
|
1.0
|
C1'
|
F:DG19
|
4.3
|
68.9
|
1.0
|
O3'
|
F:DG19
|
4.3
|
70.3
|
1.0
|
O4'
|
F:DG19
|
4.4
|
67.6
|
1.0
|
C4'
|
F:DG19
|
4.5
|
66.5
|
1.0
|
C3'
|
F:DC20
|
4.6
|
76.5
|
1.0
|
OP1
|
F:DG21
|
4.8
|
80.7
|
1.0
|
N2
|
F:DG19
|
4.8
|
76.5
|
1.0
|
C3'
|
F:DG19
|
5.0
|
68.5
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 8 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg102
b:30.0
occ:1.00
|
OP2
|
F:DG21
|
2.2
|
83.9
|
1.0
|
C5'
|
F:DG21
|
3.0
|
81.2
|
1.0
|
P
|
F:DG21
|
3.4
|
82.2
|
1.0
|
C3'
|
F:DC20
|
3.5
|
76.5
|
1.0
|
O5'
|
F:DG21
|
3.7
|
79.7
|
1.0
|
O3'
|
F:DC20
|
3.9
|
75.2
|
1.0
|
C2'
|
F:DC20
|
4.1
|
76.8
|
1.0
|
C4'
|
F:DG21
|
4.3
|
81.8
|
1.0
|
C8
|
F:DG21
|
4.5
|
81.6
|
1.0
|
C3'
|
F:DG21
|
4.5
|
84.7
|
1.0
|
C2'
|
F:DG21
|
4.6
|
85.1
|
1.0
|
C4'
|
F:DC20
|
4.6
|
74.3
|
1.0
|
OP1
|
F:DG21
|
4.7
|
80.7
|
1.0
|
C5'
|
F:DC20
|
4.7
|
76.2
|
1.0
|
C7
|
F:DT22
|
5.0
|
81.9
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 9 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg103
b:30.0
occ:1.00
|
C6
|
F:DT28
|
2.8
|
136.6
|
1.0
|
C2'
|
F:DA27
|
3.0
|
120.6
|
1.0
|
C7
|
F:DT28
|
3.0
|
139.8
|
1.0
|
C5'
|
F:DT28
|
3.2
|
128.1
|
1.0
|
C5
|
F:DT28
|
3.3
|
139.1
|
1.0
|
O4'
|
F:DT28
|
3.7
|
131.3
|
1.0
|
N1
|
F:DT28
|
3.9
|
135.7
|
1.0
|
C4'
|
F:DT28
|
4.0
|
128.6
|
1.0
|
C1'
|
F:DA27
|
4.0
|
122.0
|
1.0
|
C2'
|
F:DT28
|
4.1
|
131.6
|
1.0
|
C1'
|
F:DT28
|
4.1
|
133.0
|
1.0
|
OP2
|
F:DT28
|
4.2
|
130.3
|
1.0
|
C3'
|
F:DA27
|
4.2
|
118.0
|
1.0
|
N9
|
F:DA27
|
4.4
|
124.4
|
1.0
|
O5'
|
F:DT28
|
4.4
|
125.9
|
1.0
|
C8
|
F:DA27
|
4.5
|
125.6
|
1.0
|
C3'
|
F:DT28
|
4.5
|
128.3
|
1.0
|
O3'
|
F:DA27
|
4.6
|
115.7
|
1.0
|
P
|
F:DT28
|
4.7
|
129.7
|
1.0
|
C4
|
F:DT28
|
4.7
|
141.0
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 8a0x
Go back to
Magnesium Binding Sites List in 8a0x
Magnesium binding site 10 out
of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna
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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg104
b:30.0
occ:1.00
|
O3'
|
F:DG8
|
3.9
|
95.1
|
1.0
|
OP1
|
F:DT9
|
4.0
|
87.5
|
1.0
|
C5'
|
F:DG8
|
4.3
|
100.2
|
1.0
|
NH2
|
A:ARG49
|
4.4
|
76.4
|
1.0
|
C4'
|
F:DG8
|
4.5
|
99.7
|
1.0
|
CG1
|
A:VAL46
|
4.5
|
68.5
|
1.0
|
P
|
F:DT9
|
4.6
|
88.7
|
1.0
|
NH2
|
A:ARG56
|
4.7
|
75.0
|
1.0
|
C3'
|
F:DG8
|
4.8
|
97.3
|
1.0
|
OE2
|
A:GLU50
|
5.0
|
79.6
|
1.0
|
|
Reference:
S.Hadzi,
R.Loris.
Fuzzy Dna Recognition By A Prokaryotic Transcription Factor To Be Published.
Page generated: Thu Oct 3 17:10:26 2024
|