Magnesium in PDB 7e1h: Crystal Structure of Rd-Bef
Protein crystallography data
The structure of Crystal Structure of Rd-Bef, PDB code: 7e1h
was solved by
S.Hong,
X.Zhang,
P.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.47 /
2.81
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.858,
130.858,
271.355,
90,
90,
120
|
R / Rfree (%)
|
22.6 /
25.3
|
Other elements in 7e1h:
The structure of Crystal Structure of Rd-Bef also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Rd-Bef
(pdb code 7e1h). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Crystal Structure of Rd-Bef, PDB code: 7e1h:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7e1h
Go back to
Magnesium Binding Sites List in 7e1h
Magnesium binding site 1 out
of 3 in the Crystal Structure of Rd-Bef
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 Rd-Bef within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:13.8
occ:1.00
|
F1
|
A:BEF201
|
1.9
|
35.1
|
1.0
|
OD1
|
A:ASP10
|
2.0
|
30.2
|
1.0
|
OD2
|
A:ASP51
|
2.2
|
19.8
|
1.0
|
BE
|
A:BEF201
|
2.7
|
28.4
|
1.0
|
CG
|
A:ASP10
|
2.7
|
31.8
|
1.0
|
O
|
A:GLN53
|
2.8
|
49.7
|
1.0
|
OD2
|
A:ASP10
|
2.8
|
29.8
|
1.0
|
CG
|
A:ASP51
|
2.9
|
25.4
|
1.0
|
OD1
|
A:ASP51
|
3.1
|
36.3
|
1.0
|
OE2
|
A:GLU9
|
3.5
|
34.7
|
1.0
|
F2
|
A:BEF201
|
3.6
|
18.8
|
1.0
|
C
|
A:GLN53
|
3.8
|
44.7
|
1.0
|
F3
|
A:BEF201
|
3.8
|
23.7
|
1.0
|
OD1
|
I:ASP96
|
3.9
|
32.4
|
1.0
|
OD2
|
I:ASP96
|
3.9
|
28.8
|
1.0
|
CB
|
A:ASP10
|
4.1
|
30.8
|
1.0
|
CB
|
A:ASP51
|
4.3
|
20.1
|
1.0
|
CG
|
I:ASP96
|
4.3
|
32.0
|
1.0
|
N
|
A:ASP10
|
4.4
|
25.9
|
1.0
|
N
|
A:GLN53
|
4.5
|
24.6
|
1.0
|
CA
|
A:GLN53
|
4.6
|
28.0
|
1.0
|
N
|
A:LEU54
|
4.6
|
36.7
|
1.0
|
N
|
A:ASP11
|
4.7
|
32.4
|
1.0
|
NZ
|
A:LYS100
|
4.7
|
22.1
|
1.0
|
CD
|
A:GLU9
|
4.7
|
35.2
|
1.0
|
CA
|
A:ASP10
|
4.7
|
21.5
|
1.0
|
CB
|
A:GLN53
|
4.8
|
33.6
|
1.0
|
O
|
I:HOH223
|
4.8
|
39.2
|
1.0
|
CA
|
A:LEU54
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 7e1h
Go back to
Magnesium Binding Sites List in 7e1h
Magnesium binding site 2 out
of 3 in the Crystal Structure of Rd-Bef
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 Rd-Bef within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:14.7
occ:1.00
|
F1
|
B:BEF201
|
2.0
|
26.4
|
1.0
|
O
|
B:GLN53
|
2.1
|
18.8
|
1.0
|
OD2
|
B:ASP10
|
2.2
|
23.3
|
1.0
|
OE1
|
B:GLU9
|
2.2
|
22.5
|
1.0
|
O
|
B:HOH319
|
2.4
|
30.5
|
1.0
|
CD2
|
B:LEU54
|
2.8
|
22.9
|
1.0
|
CD
|
B:GLU9
|
3.0
|
27.7
|
1.0
|
OE2
|
B:GLU9
|
3.1
|
27.2
|
1.0
|
CG
|
B:ASP10
|
3.2
|
24.6
|
1.0
|
C
|
B:GLN53
|
3.2
|
14.0
|
1.0
|
BE
|
B:BEF201
|
3.3
|
18.5
|
1.0
|
OD1
|
B:ASP10
|
3.5
|
30.8
|
1.0
|
CG
|
B:ASP51
|
3.7
|
25.6
|
1.0
|
OD1
|
B:ASP51
|
3.8
|
26.3
|
1.0
|
OD2
|
B:ASP51
|
3.9
|
22.1
|
1.0
|
CA
|
B:LEU54
|
4.0
|
22.8
|
1.0
|
N
|
B:LEU54
|
4.0
|
18.6
|
1.0
|
CB
|
B:ASP51
|
4.1
|
20.4
|
1.0
|
CG
|
B:LEU54
|
4.2
|
23.9
|
1.0
|
N
|
B:ASP10
|
4.2
|
22.4
|
1.0
|
F2
|
B:BEF201
|
4.2
|
13.1
|
1.0
|
CA
|
B:GLN53
|
4.3
|
14.3
|
1.0
|
F3
|
B:BEF201
|
4.3
|
26.0
|
1.0
|
N
|
B:GLN53
|
4.4
|
9.7
|
1.0
|
CG
|
B:GLU9
|
4.5
|
30.3
|
1.0
|
CB
|
B:ASP10
|
4.6
|
22.1
|
1.0
|
CB
|
B:LEU54
|
4.6
|
24.7
|
1.0
|
CB
|
B:GLN53
|
4.7
|
12.9
|
1.0
|
O
|
J:HOH214
|
4.7
|
26.0
|
1.0
|
CA
|
B:GLU9
|
4.8
|
20.3
|
1.0
|
CE1
|
J:TYR97
|
4.9
|
16.8
|
1.0
|
O
|
J:HOH227
|
4.9
|
13.7
|
1.0
|
CB
|
B:GLU9
|
5.0
|
20.0
|
1.0
|
CA
|
B:ASP10
|
5.0
|
20.0
|
1.0
|
OE1
|
B:GLN53
|
5.0
|
16.4
|
1.0
|
OH
|
J:TYR97
|
5.0
|
31.3
|
1.0
|
N
|
B:ARG52
|
5.0
|
9.7
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 7e1h
Go back to
Magnesium Binding Sites List in 7e1h
Magnesium binding site 3 out
of 3 in the Crystal Structure of Rd-Bef
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 Rd-Bef within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg202
b:30.7
occ:1.00
|
O
|
E:GLN53
|
1.9
|
23.5
|
1.0
|
OD1
|
E:ASP10
|
2.0
|
34.5
|
1.0
|
OD2
|
E:ASP10
|
2.1
|
34.3
|
1.0
|
CG
|
E:ASP10
|
2.2
|
36.9
|
1.0
|
F1
|
E:BEF201
|
2.3
|
31.5
|
1.0
|
OD2
|
E:ASP51
|
2.8
|
42.2
|
1.0
|
C
|
E:GLN53
|
3.1
|
28.1
|
1.0
|
BE
|
E:BEF201
|
3.4
|
30.1
|
1.0
|
CB
|
E:ASP10
|
3.6
|
35.7
|
1.0
|
CA
|
E:LEU54
|
3.8
|
36.8
|
1.0
|
N
|
E:LEU54
|
3.8
|
26.8
|
1.0
|
CG
|
E:ASP51
|
4.0
|
47.1
|
1.0
|
OE1
|
E:GLN53
|
4.1
|
28.1
|
1.0
|
OE2
|
E:GLU9
|
4.1
|
38.6
|
1.0
|
F2
|
E:BEF201
|
4.2
|
18.2
|
1.0
|
CA
|
E:GLN53
|
4.2
|
37.8
|
1.0
|
N
|
E:ASP10
|
4.4
|
46.1
|
1.0
|
CB
|
E:GLN53
|
4.4
|
31.4
|
1.0
|
CG
|
E:LEU54
|
4.4
|
36.5
|
1.0
|
CA
|
E:ASP10
|
4.6
|
36.3
|
1.0
|
F3
|
E:BEF201
|
4.7
|
29.5
|
1.0
|
OD1
|
E:ASP51
|
4.7
|
46.9
|
1.0
|
N
|
E:GLN53
|
4.7
|
44.4
|
1.0
|
CB
|
E:LEU54
|
4.7
|
38.6
|
1.0
|
N
|
E:ASP11
|
4.8
|
37.0
|
1.0
|
C
|
E:LEU54
|
4.9
|
37.8
|
1.0
|
CD
|
E:GLU9
|
4.9
|
43.0
|
1.0
|
CD1
|
E:LEU54
|
5.0
|
35.7
|
1.0
|
CD
|
E:GLN53
|
5.0
|
37.6
|
1.0
|
|
Reference:
S.Hong,
P.Zhang.
Structural Basis of Phosphorylation-Induced Activation of the Response Regulator Vbrr To Be Published.
Page generated: Wed Oct 2 17:46:19 2024
|