Magnesium in PDB 5exc: Photoconverted Red Fluorescent Protein Dendrfp
Protein crystallography data
The structure of Photoconverted Red Fluorescent Protein Dendrfp, PDB code: 5exc
was solved by
V.Z.Pletnev,
N.V.Pletneva,
S.V.Pletnev,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.87 /
2.14
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.423,
69.521,
124.481,
89.88,
89.94,
65.57
|
|
R / Rfree (%)
|
19.5 /
27.9
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the Photoconverted Red Fluorescent Protein Dendrfp
(pdb code 5exc). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
Photoconverted Red Fluorescent Protein Dendrfp, PDB code: 5exc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 1 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:22.3
occ:1.00
|
CB
|
E:ASP55
|
2.3
|
17.3
|
1.0
|
|
OG
|
E:SER53
|
2.4
|
22.8
|
1.0
|
|
N
|
E:ILE56
|
2.5
|
21.6
|
1.0
|
|
CA
|
E:ASP55
|
2.5
|
18.5
|
1.0
|
|
N
|
E:ASP55
|
2.6
|
19.6
|
1.0
|
|
C
|
E:ASP55
|
2.7
|
20.3
|
1.0
|
|
CB
|
E:SER53
|
3.1
|
22.7
|
1.0
|
|
O
|
E:SER53
|
3.2
|
19.8
|
1.0
|
|
CG
|
E:ASP55
|
3.3
|
14.5
|
1.0
|
|
C
|
E:SER53
|
3.5
|
19.0
|
1.0
|
|
OD2
|
E:ASP55
|
3.6
|
13.1
|
1.0
|
|
CG2
|
E:ILE56
|
3.6
|
16.8
|
1.0
|
|
CA
|
E:ILE56
|
3.7
|
17.5
|
1.0
|
|
OG1
|
M:THR136
|
3.7
|
11.8
|
1.0
|
|
C
|
E:TYR54
|
3.7
|
20.4
|
1.0
|
|
O
|
E:ASP55
|
3.8
|
21.9
|
1.0
|
|
CA
|
E:SER53
|
4.0
|
19.9
|
1.0
|
|
CG2
|
M:THR136
|
4.0
|
14.9
|
1.0
|
|
CB
|
E:ILE56
|
4.2
|
17.4
|
1.0
|
|
N
|
E:TYR54
|
4.2
|
20.2
|
1.0
|
|
CB
|
M:THR136
|
4.3
|
14.2
|
1.0
|
|
OD1
|
E:ASP55
|
4.3
|
12.7
|
1.0
|
|
O
|
E:TYR54
|
4.4
|
21.9
|
1.0
|
|
CD2
|
M:LEU161
|
4.5
|
21.6
|
1.0
|
|
CD1
|
M:LEU161
|
4.5
|
26.5
|
1.0
|
|
CA
|
E:TYR54
|
4.6
|
18.8
|
1.0
|
|
CG1
|
E:ILE56
|
4.8
|
18.8
|
1.0
|
|
C
|
E:ILE56
|
4.9
|
15.0
|
1.0
|
|
NE1
|
M:TRP139
|
5.0
|
9.4
|
1.0
|
|
N
|
E:LEU57
|
5.0
|
13.4
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 2 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg303
b:28.9
occ:1.00
|
O
|
E:LEU42
|
1.9
|
18.4
|
1.0
|
|
C
|
E:LEU42
|
2.4
|
20.0
|
1.0
|
|
O
|
M:ASN205
|
2.6
|
23.4
|
0.3
|
|
O
|
M:ASN205
|
2.6
|
23.7
|
0.7
|
|
OH
|
E:TYR54
|
2.8
|
12.6
|
1.0
|
|
N
|
E:THR43
|
2.9
|
20.2
|
1.0
|
|
CA
|
E:THR43
|
3.1
|
22.0
|
1.0
|
|
N
|
M:VAL207
|
3.2
|
22.6
|
1.0
|
|
CB
|
E:LEU42
|
3.2
|
18.7
|
1.0
|
|
C
|
E:THR43
|
3.4
|
21.9
|
1.0
|
|
CA
|
E:LEU42
|
3.5
|
19.1
|
1.0
|
|
C
|
M:ASN205
|
3.5
|
23.4
|
0.7
|
|
C
|
M:ASN205
|
3.5
|
22.9
|
0.3
|
|
N
|
E:VAL44
|
3.6
|
22.6
|
1.0
|
|
CA
|
M:LYS206
|
3.7
|
22.8
|
1.0
|
|
O
|
M:TYR204
|
3.7
|
22.8
|
1.0
|
|
CZ
|
E:TYR54
|
3.8
|
12.7
|
1.0
|
|
CB
|
M:VAL207
|
3.8
|
21.3
|
1.0
|
|
C
|
M:LYS206
|
3.8
|
23.5
|
1.0
|
|
N
|
M:LYS206
|
4.0
|
23.7
|
1.0
|
|
CA
|
M:VAL207
|
4.0
|
22.6
|
1.0
|
|
CG2
|
M:VAL207
|
4.0
|
20.2
|
1.0
|
|
O
|
E:THR43
|
4.1
|
21.8
|
1.0
|
|
CE2
|
E:TYR54
|
4.1
|
12.4
|
1.0
|
|
CG2
|
E:VAL44
|
4.3
|
24.0
|
1.0
|
|
O
|
M:VAL207
|
4.4
|
20.4
|
1.0
|
|
N
|
E:LEU42
|
4.4
|
20.8
|
1.0
|
|
CB
|
E:THR43
|
4.5
|
22.5
|
1.0
|
|
CG
|
E:LEU42
|
4.6
|
18.5
|
1.0
|
|
CA
|
M:ASN205
|
4.6
|
23.2
|
0.7
|
|
CG2
|
E:ILE25
|
4.6
|
25.1
|
1.0
|
|
CD1
|
E:LEU42
|
4.7
|
18.7
|
1.0
|
|
C
|
M:VAL207
|
4.7
|
22.6
|
1.0
|
|
CA
|
M:ASN205
|
4.7
|
22.2
|
0.3
|
|
CA
|
E:VAL44
|
4.8
|
24.9
|
1.0
|
|
C
|
M:TYR204
|
4.8
|
23.4
|
1.0
|
|
CE1
|
E:TYR54
|
4.8
|
12.3
|
1.0
|
|
O
|
M:LYS206
|
4.9
|
24.9
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 3 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg101
b:19.2
occ:1.00
|
O
|
F:ILE56
|
2.3
|
21.7
|
1.0
|
|
OG1
|
F:THR59
|
2.4
|
27.5
|
1.0
|
|
N
|
F:THR59
|
2.9
|
21.9
|
1.0
|
|
O
|
F:ASP55
|
3.0
|
25.4
|
1.0
|
|
C
|
F:ILE56
|
3.1
|
18.3
|
1.0
|
|
CB
|
F:THR59
|
3.3
|
25.8
|
1.0
|
|
CZ2
|
N:TRP139
|
3.3
|
20.7
|
1.0
|
|
NE1
|
N:TRP139
|
3.4
|
22.7
|
1.0
|
|
N
|
F:THR58
|
3.4
|
14.2
|
1.0
|
|
CG2
|
F:THR59
|
3.4
|
25.9
|
1.0
|
|
CA
|
F:THR59
|
3.6
|
26.4
|
1.0
|
|
OG1
|
F:THR58
|
3.6
|
15.8
|
1.0
|
|
CE2
|
N:TRP139
|
3.7
|
20.9
|
1.0
|
|
CA
|
F:ILE56
|
3.8
|
18.5
|
1.0
|
|
O
|
F:HOH202
|
3.8
|
13.5
|
1.0
|
|
C
|
F:LEU57
|
3.8
|
13.0
|
1.0
|
|
C
|
F:THR58
|
3.9
|
19.4
|
1.0
|
|
CA
|
F:THR58
|
4.0
|
15.5
|
1.0
|
|
N
|
F:LEU57
|
4.0
|
15.9
|
1.0
|
|
C
|
F:ASP55
|
4.1
|
20.2
|
1.0
|
|
O
|
F:LEU57
|
4.3
|
12.5
|
1.0
|
|
N
|
F:ALA60
|
4.3
|
27.3
|
1.0
|
|
C
|
F:THR59
|
4.3
|
26.5
|
1.0
|
|
CA
|
F:LEU57
|
4.3
|
14.0
|
1.0
|
|
N
|
F:ILE56
|
4.4
|
20.1
|
1.0
|
|
CB
|
F:THR58
|
4.4
|
16.0
|
1.0
|
|
CH2
|
N:TRP139
|
4.5
|
18.6
|
1.0
|
|
CE
|
N:MET93
|
4.6
|
27.5
|
1.0
|
|
SD
|
N:MET93
|
4.6
|
29.6
|
1.0
|
|
CZ
|
N:PHE173
|
4.6
|
24.6
|
1.0
|
|
CD1
|
N:TRP139
|
4.7
|
20.1
|
1.0
|
|
CD2
|
N:TRP139
|
5.0
|
20.0
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 4 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg301
b:19.6
occ:1.00
|
O
|
N:GLY99
|
2.2
|
18.7
|
1.0
|
|
O
|
N:MET93
|
2.3
|
13.4
|
1.0
|
|
N
|
N:TYR95
|
2.6
|
17.3
|
1.0
|
|
CA
|
N:ILE100
|
2.6
|
19.0
|
1.0
|
|
CA
|
N:THR94
|
2.7
|
15.9
|
1.0
|
|
CD1
|
N:TYR95
|
2.8
|
17.9
|
1.0
|
|
C
|
N:THR94
|
3.0
|
16.7
|
1.0
|
|
C
|
N:GLY99
|
3.0
|
20.7
|
1.0
|
|
C
|
N:MET93
|
3.0
|
16.2
|
1.0
|
|
N
|
N:ILE100
|
3.2
|
19.1
|
1.0
|
|
N
|
N:THR94
|
3.2
|
16.6
|
1.0
|
|
CB
|
N:ILE100
|
3.4
|
19.4
|
1.0
|
|
C
|
N:ILE100
|
3.5
|
17.4
|
1.0
|
|
CE1
|
N:TYR95
|
3.6
|
19.5
|
1.0
|
|
CD1
|
N:ILE100
|
3.6
|
20.9
|
1.0
|
|
O
|
N:HOH442
|
3.7
|
29.7
|
1.0
|
|
CG
|
N:TYR95
|
3.7
|
17.9
|
1.0
|
|
N
|
N:CYS101
|
3.7
|
17.4
|
1.0
|
|
CA
|
N:TYR95
|
3.7
|
17.9
|
1.0
|
|
CB
|
N:TYR95
|
3.8
|
18.0
|
1.0
|
|
CG1
|
N:ILE100
|
4.0
|
19.3
|
1.0
|
|
CB
|
N:THR94
|
4.0
|
16.1
|
1.0
|
|
O
|
N:THR94
|
4.2
|
15.5
|
1.0
|
|
CG2
|
N:THR94
|
4.3
|
15.8
|
1.0
|
|
CA
|
N:MET93
|
4.4
|
18.7
|
1.0
|
|
CA
|
N:GLY99
|
4.5
|
20.4
|
1.0
|
|
O
|
N:TYR95
|
4.5
|
20.6
|
1.0
|
|
O
|
N:ILE100
|
4.5
|
16.8
|
1.0
|
|
OG1
|
N:THR94
|
4.6
|
13.7
|
1.0
|
|
C
|
N:TYR95
|
4.7
|
17.5
|
1.0
|
|
N
|
N:GLY99
|
4.7
|
21.1
|
1.0
|
|
CB
|
N:MET93
|
4.7
|
20.6
|
1.0
|
|
CG2
|
N:ILE100
|
4.8
|
19.4
|
1.0
|
|
CZ
|
N:TYR95
|
4.9
|
20.6
|
1.0
|
|
SG
|
N:CYS171
|
4.9
|
24.8
|
1.0
|
|
CD2
|
N:TYR95
|
4.9
|
17.3
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 5 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg302
b:21.9
occ:1.00
|
C
|
G:LEU57
|
1.9
|
16.3
|
1.0
|
|
O
|
G:ILE56
|
1.9
|
17.9
|
1.0
|
|
O
|
G:LEU57
|
2.3
|
16.5
|
1.0
|
|
N
|
G:THR58
|
2.3
|
17.9
|
1.0
|
|
CA
|
G:LEU57
|
2.3
|
16.1
|
1.0
|
|
C
|
G:ILE56
|
2.4
|
18.3
|
1.0
|
|
O
|
G:HOH402
|
2.4
|
20.4
|
1.0
|
|
N
|
G:LEU57
|
2.6
|
16.6
|
1.0
|
|
N
|
G:THR59
|
2.9
|
25.8
|
1.0
|
|
O
|
G:ASP55
|
3.2
|
24.2
|
1.0
|
|
CA
|
G:THR58
|
3.3
|
19.4
|
1.0
|
|
C
|
G:THR58
|
3.4
|
21.6
|
1.0
|
|
OG1
|
G:THR59
|
3.4
|
30.1
|
1.0
|
|
N
|
G:ALA60
|
3.7
|
26.3
|
1.0
|
|
CA
|
G:ILE56
|
3.7
|
19.7
|
1.0
|
|
CB
|
G:LEU57
|
3.8
|
16.6
|
1.0
|
|
CA
|
G:THR59
|
3.8
|
26.3
|
1.0
|
|
C
|
G:ASP55
|
4.1
|
20.2
|
1.0
|
|
C
|
G:THR59
|
4.1
|
26.1
|
1.0
|
|
CB
|
G:THR59
|
4.2
|
27.6
|
1.0
|
|
CB
|
G:ALA60
|
4.4
|
23.9
|
1.0
|
|
CE2
|
O:PHE120
|
4.4
|
19.3
|
1.0
|
|
N
|
G:ILE56
|
4.4
|
21.8
|
1.0
|
|
CB
|
G:THR58
|
4.4
|
19.9
|
1.0
|
|
OG1
|
G:THR58
|
4.5
|
19.7
|
1.0
|
|
O
|
G:THR58
|
4.5
|
20.6
|
1.0
|
|
CA
|
G:ALA60
|
4.6
|
25.7
|
1.0
|
|
O
|
G:TYR54
|
4.7
|
17.6
|
1.0
|
|
CG
|
G:LEU57
|
4.8
|
17.0
|
1.0
|
|
CB
|
G:ILE56
|
4.9
|
20.3
|
1.0
|
|
CG2
|
G:THR59
|
4.9
|
28.9
|
1.0
|
|
CG2
|
G:THR58
|
4.9
|
20.1
|
1.0
|
|
SD
|
O:MET93
|
5.0
|
26.3
|
1.0
|
|
CE
|
O:MET93
|
5.0
|
25.8
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 6 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Mg301
b:15.0
occ:1.00
|
O
|
O:MET93
|
1.9
|
15.0
|
1.0
|
|
CA
|
O:THR94
|
2.3
|
16.0
|
1.0
|
|
O
|
O:GLY99
|
2.3
|
15.8
|
1.0
|
|
N
|
O:TYR95
|
2.4
|
19.4
|
1.0
|
|
C
|
O:MET93
|
2.6
|
18.1
|
1.0
|
|
C
|
O:THR94
|
2.7
|
17.2
|
1.0
|
|
CA
|
O:ILE100
|
2.7
|
17.4
|
1.0
|
|
N
|
O:THR94
|
2.8
|
17.0
|
1.0
|
|
O
|
O:HOH417
|
3.0
|
12.2
|
1.0
|
|
C
|
O:GLY99
|
3.1
|
18.3
|
1.0
|
|
N
|
O:ILE100
|
3.3
|
17.0
|
1.0
|
|
C
|
O:ILE100
|
3.5
|
16.9
|
1.0
|
|
CB
|
O:THR94
|
3.5
|
14.2
|
1.0
|
|
CA
|
O:TYR95
|
3.6
|
21.7
|
1.0
|
|
CB
|
O:ILE100
|
3.6
|
19.4
|
1.0
|
|
CD1
|
O:ILE100
|
3.6
|
19.7
|
1.0
|
|
N
|
O:CYS101
|
3.7
|
17.1
|
1.0
|
|
CB
|
O:TYR95
|
3.8
|
22.9
|
1.0
|
|
O
|
O:THR94
|
3.8
|
17.5
|
1.0
|
|
CG2
|
O:THR94
|
3.9
|
13.8
|
1.0
|
|
CG
|
O:TYR95
|
3.9
|
24.4
|
1.0
|
|
OG1
|
O:THR94
|
4.1
|
12.8
|
1.0
|
|
CD2
|
O:TYR95
|
4.1
|
24.0
|
1.0
|
|
CA
|
O:MET93
|
4.1
|
20.7
|
1.0
|
|
CG1
|
O:ILE100
|
4.1
|
19.0
|
1.0
|
|
O
|
O:ILE100
|
4.5
|
16.5
|
1.0
|
|
CA
|
O:GLY99
|
4.6
|
18.8
|
1.0
|
|
CB
|
O:MET93
|
4.6
|
21.8
|
1.0
|
|
CD1
|
O:TYR95
|
4.6
|
23.8
|
1.0
|
|
N
|
O:MET93
|
4.6
|
20.4
|
1.0
|
|
C
|
O:TYR95
|
4.7
|
22.3
|
1.0
|
|
O
|
O:TYR95
|
4.7
|
21.4
|
1.0
|
|
CE2
|
O:TYR95
|
4.8
|
23.6
|
1.0
|
|
N
|
O:GLY99
|
5.0
|
21.5
|
1.0
|
|
CG2
|
O:ILE100
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 7 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg301
b:21.0
occ:1.00
|
O
|
H:HIS21
|
2.1
|
27.3
|
1.0
|
|
O
|
H:GLY16
|
2.1
|
21.6
|
1.0
|
|
CA
|
H:ASN17
|
2.2
|
23.7
|
1.0
|
|
CA
|
H:ALA22
|
2.6
|
20.6
|
1.0
|
|
C
|
H:GLY16
|
2.6
|
22.5
|
1.0
|
|
N
|
H:ASN17
|
2.8
|
23.6
|
1.0
|
|
C
|
H:HIS21
|
2.9
|
25.3
|
1.0
|
|
C
|
H:ALA22
|
3.0
|
22.1
|
1.0
|
|
C
|
H:ASN17
|
3.1
|
24.6
|
1.0
|
|
N
|
H:VAL18
|
3.1
|
26.3
|
1.0
|
|
N
|
H:ALA22
|
3.2
|
22.2
|
1.0
|
|
N
|
H:PHE23
|
3.2
|
23.8
|
1.0
|
|
CB
|
H:ASN17
|
3.3
|
21.9
|
1.0
|
|
CG
|
H:ASN17
|
3.4
|
21.3
|
1.0
|
|
CD2
|
H:PHE23
|
3.5
|
22.9
|
1.0
|
|
ND2
|
H:ASN17
|
3.5
|
19.9
|
1.0
|
|
CB
|
H:ALA22
|
3.8
|
21.2
|
1.0
|
|
O
|
H:ALA22
|
3.9
|
19.6
|
1.0
|
|
CE2
|
H:PHE23
|
3.9
|
22.8
|
1.0
|
|
CA
|
H:GLY16
|
3.9
|
23.3
|
1.0
|
|
OD1
|
H:ASN17
|
4.1
|
18.4
|
1.0
|
|
O
|
H:ASN17
|
4.1
|
23.4
|
1.0
|
|
CG
|
H:PHE23
|
4.2
|
25.5
|
1.0
|
|
CA
|
H:HIS21
|
4.4
|
28.8
|
1.0
|
|
CA
|
H:PHE23
|
4.4
|
23.7
|
1.0
|
|
CA
|
H:VAL18
|
4.4
|
23.7
|
1.0
|
|
CB
|
H:PHE23
|
4.6
|
25.7
|
1.0
|
|
O
|
H:VAL18
|
4.6
|
24.9
|
1.0
|
|
O
|
H:GLY20
|
4.6
|
27.6
|
1.0
|
|
O
|
H:PHE23
|
4.7
|
27.0
|
1.0
|
|
CB
|
H:VAL18
|
4.8
|
25.0
|
1.0
|
|
N
|
H:GLY16
|
4.9
|
22.4
|
1.0
|
|
N
|
H:HIS21
|
4.9
|
31.6
|
1.0
|
|
C
|
H:VAL18
|
4.9
|
26.8
|
1.0
|
|
CG2
|
H:VAL18
|
5.0
|
23.9
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 8 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg302
b:19.6
occ:1.00
|
O
|
P:GLY122
|
1.8
|
14.7
|
1.0
|
|
C
|
P:GLY122
|
2.1
|
18.4
|
1.0
|
|
N
|
P:MET123
|
2.4
|
22.6
|
1.0
|
|
N
|
H:ASN19
|
2.5
|
28.6
|
1.0
|
|
OD1
|
H:ASN19
|
2.6
|
30.0
|
1.0
|
|
CA
|
P:MET123
|
2.8
|
24.0
|
1.0
|
|
CA
|
H:VAL18
|
3.2
|
23.7
|
1.0
|
|
C
|
H:VAL18
|
3.2
|
26.8
|
1.0
|
|
CA
|
P:GLY122
|
3.3
|
18.7
|
1.0
|
|
CA
|
H:ASN19
|
3.4
|
28.7
|
1.0
|
|
C
|
P:MET123
|
3.5
|
26.8
|
1.0
|
|
CG
|
H:ASN19
|
3.5
|
30.7
|
1.0
|
|
CG1
|
H:VAL18
|
3.5
|
23.5
|
1.0
|
|
CD1
|
P:PHE125
|
3.8
|
23.0
|
1.0
|
|
CB
|
H:ASN19
|
3.8
|
29.3
|
1.0
|
|
N
|
P:ASN124
|
3.8
|
30.3
|
1.0
|
|
CB
|
H:VAL18
|
3.9
|
25.0
|
1.0
|
|
NH1
|
M:ARG104
|
3.9
|
21.5
|
1.0
|
|
CE1
|
P:PHE125
|
3.9
|
22.6
|
1.0
|
|
CB
|
P:MET123
|
4.1
|
25.1
|
1.0
|
|
N
|
P:GLY122
|
4.2
|
19.5
|
1.0
|
|
O
|
P:MET123
|
4.2
|
22.8
|
1.0
|
|
N
|
H:VAL18
|
4.4
|
26.3
|
1.0
|
|
O
|
H:VAL18
|
4.4
|
24.9
|
1.0
|
|
O
|
H:HOH406
|
4.4
|
7.0
|
1.0
|
|
CG
|
P:MET123
|
4.4
|
26.5
|
1.0
|
|
O
|
H:ASN17
|
4.7
|
23.4
|
1.0
|
|
CG2
|
H:VAL18
|
4.7
|
23.9
|
1.0
|
|
ND2
|
H:ASN19
|
4.8
|
29.8
|
1.0
|
|
C
|
H:ASN19
|
4.8
|
29.2
|
1.0
|
|
N
|
P:PHE125
|
4.9
|
31.7
|
1.0
|
|
O
|
P:ILE100
|
4.9
|
15.9
|
1.0
|
|
C
|
H:ASN17
|
4.9
|
24.6
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 9 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg303
b:19.5
occ:1.00
|
O
|
P:VAL118
|
1.9
|
25.0
|
1.0
|
|
O
|
H:GLU15
|
2.0
|
20.4
|
1.0
|
|
N
|
H:GLU15
|
2.3
|
30.5
|
1.0
|
|
CA
|
P:ARG119
|
2.7
|
27.8
|
1.0
|
|
C
|
H:GLU15
|
2.8
|
23.9
|
1.0
|
|
C
|
P:VAL118
|
2.8
|
27.6
|
1.0
|
|
CA
|
H:GLU15
|
2.9
|
27.7
|
1.0
|
|
N
|
P:ARG119
|
3.1
|
29.4
|
1.0
|
|
N
|
P:PHE120
|
3.1
|
22.4
|
1.0
|
|
C
|
H:MET14
|
3.2
|
28.8
|
1.0
|
|
C
|
P:ARG119
|
3.3
|
24.9
|
1.0
|
|
CB
|
H:GLU15
|
3.4
|
30.2
|
1.0
|
|
CA
|
H:MET14
|
3.4
|
30.4
|
1.0
|
|
CG
|
H:MET14
|
3.5
|
29.8
|
1.0
|
|
CB
|
P:ARG119
|
3.9
|
28.2
|
1.0
|
|
CG
|
H:GLU15
|
3.9
|
33.8
|
1.0
|
|
CB
|
H:MET14
|
4.0
|
30.9
|
1.0
|
|
N
|
H:GLY16
|
4.0
|
22.4
|
1.0
|
|
CA
|
P:VAL118
|
4.1
|
31.0
|
1.0
|
|
O
|
H:MET14
|
4.2
|
30.9
|
1.0
|
|
CD
|
P:ARG119
|
4.2
|
30.5
|
1.0
|
|
CA
|
P:PHE120
|
4.3
|
21.6
|
1.0
|
|
CG1
|
P:VAL118
|
4.4
|
20.0
|
1.0
|
|
CG
|
P:ARG119
|
4.4
|
29.4
|
0.6
|
|
O
|
P:ARG119
|
4.4
|
21.8
|
1.0
|
|
CB
|
P:VAL118
|
4.5
|
20.0
|
1.0
|
|
CB
|
P:PHE120
|
4.5
|
21.7
|
1.0
|
|
N
|
H:MET14
|
4.7
|
32.1
|
1.0
|
|
CA
|
H:GLY16
|
4.7
|
23.3
|
1.0
|
|
O
|
P:PHE120
|
4.8
|
19.2
|
1.0
|
|
O
|
H:HIS13
|
4.9
|
36.0
|
1.0
|
|
SD
|
H:MET14
|
4.9
|
28.5
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 5exc
Go back to
Magnesium Binding Sites List in 5exc
Magnesium binding site 10 out
of 11 in the Photoconverted Red Fluorescent Protein Dendrfp
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Photoconverted Red Fluorescent Protein Dendrfp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg301
b:18.4
occ:1.00
|
N
|
P:GLY99
|
2.1
|
15.5
|
1.0
|
|
O
|
P:ASN124
|
2.2
|
30.3
|
1.0
|
|
O
|
P:ASP97
|
2.4
|
26.5
|
1.0
|
|
CA
|
P:GLY99
|
2.5
|
13.9
|
1.0
|
|
C
|
P:LYS98
|
2.6
|
18.4
|
1.0
|
|
O
|
P:LYS98
|
3.0
|
17.4
|
1.0
|
|
C
|
P:ASP97
|
3.2
|
23.7
|
1.0
|
|
C
|
P:ASN124
|
3.4
|
35.0
|
1.0
|
|
CD
|
P:PRO126
|
3.5
|
28.3
|
1.0
|
|
CA
|
P:LYS98
|
3.5
|
22.1
|
1.0
|
|
N
|
P:LYS98
|
3.6
|
21.6
|
1.0
|
|
CA
|
P:PHE125
|
3.9
|
28.9
|
1.0
|
|
OD1
|
P:ASP97
|
3.9
|
16.6
|
1.0
|
|
C
|
P:GLY99
|
3.9
|
13.7
|
1.0
|
|
N
|
P:PHE125
|
4.0
|
31.7
|
1.0
|
|
CG
|
P:ASP97
|
4.0
|
21.0
|
1.0
|
|
N
|
P:PRO126
|
4.3
|
28.8
|
1.0
|
|
CB
|
P:LYS98
|
4.4
|
24.2
|
1.0
|
|
CB
|
P:ASP97
|
4.4
|
21.4
|
1.0
|
|
CA
|
P:ASP97
|
4.4
|
22.8
|
1.0
|
|
O
|
P:GLY99
|
4.5
|
11.9
|
1.0
|
|
C
|
P:PHE125
|
4.5
|
30.7
|
1.0
|
|
O
|
P:MET123
|
4.5
|
22.8
|
1.0
|
|
CG
|
P:PRO126
|
4.5
|
27.2
|
1.0
|
|
OD2
|
P:ASP97
|
4.6
|
22.6
|
1.0
|
|
CA
|
P:ASN124
|
4.6
|
33.0
|
1.0
|
|
CG
|
P:ASN124
|
4.6
|
41.8
|
1.0
|
|
CB
|
P:ASN124
|
4.7
|
37.7
|
1.0
|
|
OD1
|
P:ASN124
|
4.8
|
46.4
|
1.0
|
|
N
|
P:ILE100
|
4.8
|
13.5
|
1.0
|
|
ND2
|
P:ASN124
|
4.9
|
37.8
|
1.0
|
|
Reference:
N.V.Pletneva,
S.Pletnev,
A.A.Pakhomov,
R.V.Chertkova,
V.I.Martynov,
L.Muslinkina,
Z.Dauter,
V.Z.Pletnev.
Crystal Structure of the Fluorescent Protein From Dendronephthya Sp. in Both Green and Photoconverted Red Forms. Acta Crystallogr D Struct V. 72 922 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27487823
DOI: 10.1107/S205979831601038X
Page generated: Mon Dec 14 20:16:47 2020
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