Chlorine in PDB 5ltp: Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Protein crystallography data
The structure of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5, PDB code: 5ltp
was solved by
D.Clavel,
G.Gotthard,
A.Royant,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.34 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.870,
127.600,
146.840,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
21.1
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
(pdb code 5ltp). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5, PDB code: 5ltp:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 5ltp
Go back to
Chlorine Binding Sites List in 5ltp
Chlorine binding site 1 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:18.5
occ:0.70
|
O
|
A:HOH495
|
0.7
|
21.9
|
0.3
|
O
|
A:HOH412
|
2.0
|
13.1
|
0.3
|
OH
|
A:TYR175
|
2.9
|
19.7
|
1.0
|
OG
|
A:SER153
|
3.2
|
22.2
|
1.0
|
NH2
|
A:ARG88
|
3.3
|
17.4
|
1.0
|
NE2
|
A:HIS62
|
3.4
|
18.9
|
1.0
|
CB
|
A:SER153
|
3.6
|
22.0
|
1.0
|
OG1
|
A:THR173
|
3.6
|
18.4
|
1.0
|
CB
|
A:THR173
|
3.8
|
18.7
|
1.0
|
CZ
|
A:TYR175
|
3.9
|
19.5
|
1.0
|
CE2
|
A:PHE155
|
3.9
|
19.9
|
1.0
|
CE1
|
A:TYR175
|
4.0
|
19.7
|
1.0
|
CG2
|
A:THR173
|
4.0
|
18.4
|
1.0
|
CD2
|
A:CR259
|
4.2
|
17.9
|
1.0
|
CZ
|
A:ARG88
|
4.3
|
17.4
|
1.0
|
NE
|
A:ARG88
|
4.3
|
17.4
|
1.0
|
CD2
|
A:HIS62
|
4.3
|
18.6
|
1.0
|
CE1
|
A:HIS62
|
4.4
|
18.8
|
1.0
|
O
|
A:HOH411
|
4.4
|
24.5
|
1.0
|
NZ
|
A:LYS143
|
4.5
|
27.2
|
1.0
|
CB2
|
A:CR259
|
4.5
|
17.5
|
1.0
|
CD2
|
A:PHE155
|
4.6
|
20.5
|
1.0
|
NH1
|
A:ARG195
|
4.8
|
21.1
|
1.0
|
OG
|
A:SER141
|
4.9
|
23.1
|
0.7
|
CG2
|
A:CR259
|
4.9
|
17.7
|
1.0
|
CZ
|
A:PHE155
|
4.9
|
19.7
|
1.0
|
CA
|
A:SER153
|
5.0
|
22.1
|
1.0
|
O
|
A:HOH414
|
5.0
|
17.1
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 5ltp
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Chlorine Binding Sites List in 5ltp
Chlorine binding site 2 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:22.1
occ:0.70
|
O
|
B:HOH409
|
0.8
|
13.5
|
0.3
|
O
|
B:HOH446
|
2.1
|
20.6
|
0.3
|
OH
|
B:TYR175
|
3.0
|
20.7
|
1.0
|
OG
|
B:SER153
|
3.3
|
24.6
|
1.0
|
NH2
|
B:ARG88
|
3.4
|
20.8
|
1.0
|
NE2
|
B:HIS62
|
3.4
|
17.9
|
1.0
|
CB
|
B:SER153
|
3.7
|
24.1
|
1.0
|
OG1
|
B:THR173
|
3.7
|
24.0
|
1.0
|
CE1
|
B:PHE155
|
3.8
|
24.8
|
1.0
|
CB
|
B:THR173
|
4.0
|
23.9
|
1.0
|
CZ
|
B:TYR175
|
4.0
|
20.6
|
1.0
|
CD2
|
B:CR259
|
4.0
|
20.4
|
1.0
|
CE1
|
B:TYR175
|
4.1
|
21.5
|
1.0
|
CG2
|
B:THR173
|
4.2
|
22.9
|
1.0
|
CZ
|
B:ARG88
|
4.2
|
21.4
|
1.0
|
NE
|
B:ARG88
|
4.2
|
22.1
|
1.0
|
CE1
|
B:HIS62
|
4.3
|
17.4
|
1.0
|
CB2
|
B:CR259
|
4.4
|
18.5
|
1.0
|
CD2
|
B:HIS62
|
4.4
|
17.5
|
1.0
|
O
|
B:HOH412
|
4.4
|
31.6
|
1.0
|
NZ
|
B:LYS143
|
4.4
|
24.6
|
1.0
|
CD1
|
B:PHE155
|
4.5
|
25.7
|
1.0
|
NH1
|
B:ARG195
|
4.7
|
20.9
|
1.0
|
CG2
|
B:CR259
|
4.7
|
19.3
|
1.0
|
CZ
|
B:PHE155
|
4.8
|
24.8
|
1.0
|
CE2
|
B:CR259
|
5.0
|
21.2
|
1.0
|
O
|
B:HOH428
|
5.0
|
17.7
|
1.0
|
O2
|
B:CR259
|
5.0
|
17.5
|
1.0
|
OG
|
B:SER141
|
5.0
|
25.4
|
0.7
|
|
Chlorine binding site 3 out
of 6 in 5ltp
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Chlorine Binding Sites List in 5ltp
Chlorine binding site 3 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl301
b:18.3
occ:0.70
|
O
|
C:HOH463
|
0.9
|
11.8
|
0.3
|
O
|
C:HOH407
|
2.1
|
9.6
|
0.3
|
OH
|
C:TYR175
|
2.9
|
20.5
|
1.0
|
NH2
|
C:ARG88
|
3.3
|
16.9
|
1.0
|
OG
|
C:SER153
|
3.3
|
18.9
|
1.0
|
NE2
|
C:HIS62
|
3.4
|
20.1
|
1.0
|
CB
|
C:SER153
|
3.7
|
18.5
|
1.0
|
OG1
|
C:THR173
|
3.7
|
17.8
|
1.0
|
CE2
|
C:PHE155
|
3.9
|
16.1
|
1.0
|
CZ
|
C:TYR175
|
3.9
|
20.2
|
1.0
|
CB
|
C:THR173
|
3.9
|
17.9
|
1.0
|
CE1
|
C:TYR175
|
4.1
|
20.4
|
1.0
|
CD2
|
C:CR259
|
4.1
|
16.2
|
1.0
|
CG2
|
C:THR173
|
4.2
|
17.9
|
1.0
|
CZ
|
C:ARG88
|
4.2
|
16.5
|
1.0
|
CD2
|
C:HIS62
|
4.3
|
19.9
|
1.0
|
CE1
|
C:HIS62
|
4.3
|
19.9
|
1.0
|
NE
|
C:ARG88
|
4.3
|
16.7
|
1.0
|
CB2
|
C:CR259
|
4.4
|
16.4
|
1.0
|
NZ
|
C:LYS143
|
4.4
|
21.9
|
1.0
|
O
|
C:HOH405
|
4.4
|
25.6
|
1.0
|
CD2
|
C:PHE155
|
4.6
|
16.3
|
1.0
|
NH1
|
C:ARG195
|
4.7
|
17.3
|
1.0
|
CG2
|
C:CR259
|
4.8
|
16.2
|
1.0
|
CZ
|
C:PHE155
|
4.9
|
15.9
|
1.0
|
O2
|
C:CR259
|
4.9
|
17.3
|
1.0
|
O
|
C:HOH420
|
5.0
|
18.9
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 5ltp
Go back to
Chlorine Binding Sites List in 5ltp
Chlorine binding site 4 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl301
b:17.3
occ:0.70
|
O
|
D:HOH440
|
0.9
|
17.6
|
0.3
|
O
|
D:HOH418
|
2.0
|
10.8
|
0.3
|
OH
|
D:TYR175
|
2.9
|
17.8
|
1.0
|
OG
|
D:SER153
|
3.3
|
19.6
|
1.0
|
NH2
|
D:ARG88
|
3.3
|
16.7
|
1.0
|
NE2
|
D:HIS62
|
3.4
|
18.8
|
1.0
|
OG1
|
D:THR173
|
3.6
|
17.6
|
1.0
|
CB
|
D:SER153
|
3.7
|
18.4
|
1.0
|
CE2
|
D:PHE155
|
3.9
|
17.5
|
1.0
|
CB
|
D:THR173
|
3.9
|
17.2
|
1.0
|
CZ
|
D:TYR175
|
3.9
|
17.1
|
1.0
|
CD2
|
D:CR259
|
4.0
|
16.2
|
1.0
|
CE1
|
D:TYR175
|
4.1
|
17.1
|
1.0
|
CG2
|
D:THR173
|
4.2
|
17.0
|
1.0
|
CZ
|
D:ARG88
|
4.2
|
16.6
|
1.0
|
CD2
|
D:HIS62
|
4.3
|
18.6
|
1.0
|
NE
|
D:ARG88
|
4.3
|
16.5
|
1.0
|
CE1
|
D:HIS62
|
4.3
|
18.8
|
1.0
|
CB2
|
D:CR259
|
4.3
|
16.2
|
1.0
|
NZ
|
D:LYS143
|
4.4
|
22.8
|
1.0
|
O
|
D:HOH401
|
4.4
|
27.1
|
1.0
|
CD2
|
D:PHE155
|
4.5
|
17.6
|
1.0
|
NH1
|
D:ARG195
|
4.7
|
17.1
|
1.0
|
CG2
|
D:CR259
|
4.7
|
16.2
|
1.0
|
CZ
|
D:PHE155
|
4.9
|
17.4
|
1.0
|
CE2
|
D:CR259
|
4.9
|
16.8
|
1.0
|
O
|
D:HOH406
|
5.0
|
18.0
|
1.0
|
O2
|
D:CR259
|
5.0
|
16.3
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 5ltp
Go back to
Chlorine Binding Sites List in 5ltp
Chlorine binding site 5 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl301
b:22.1
occ:0.70
|
O
|
E:HOH490
|
0.8
|
30.9
|
0.3
|
O
|
E:HOH404
|
2.2
|
18.5
|
0.3
|
OH
|
E:TYR175
|
3.0
|
25.0
|
1.0
|
NH2
|
E:ARG88
|
3.3
|
20.5
|
1.0
|
OG
|
E:SER153
|
3.3
|
26.9
|
1.0
|
NE2
|
E:HIS62
|
3.4
|
24.9
|
1.0
|
OG1
|
E:THR173
|
3.7
|
22.1
|
1.0
|
CB
|
E:SER153
|
3.7
|
26.2
|
1.0
|
CE1
|
E:PHE155
|
3.8
|
23.1
|
1.0
|
CB
|
E:THR173
|
4.0
|
22.0
|
1.0
|
CD2
|
E:CR259
|
4.0
|
23.0
|
1.0
|
CZ
|
E:TYR175
|
4.0
|
24.2
|
1.0
|
CZ
|
E:ARG88
|
4.2
|
20.2
|
1.0
|
NZ
|
E:LYS143
|
4.2
|
32.2
|
1.0
|
CE1
|
E:TYR175
|
4.2
|
24.0
|
1.0
|
CG2
|
E:THR173
|
4.2
|
21.7
|
1.0
|
NE
|
E:ARG88
|
4.2
|
19.6
|
1.0
|
CB2
|
E:CR259
|
4.3
|
22.8
|
1.0
|
CE1
|
E:HIS62
|
4.3
|
25.0
|
1.0
|
CD2
|
E:HIS62
|
4.4
|
25.0
|
1.0
|
O
|
E:HOH405
|
4.4
|
31.2
|
1.0
|
CD1
|
E:PHE155
|
4.5
|
23.5
|
1.0
|
CG2
|
E:CR259
|
4.7
|
23.1
|
1.0
|
CZ
|
E:PHE155
|
4.7
|
23.1
|
1.0
|
NH1
|
E:ARG195
|
4.8
|
25.2
|
1.0
|
O2
|
E:CR259
|
4.9
|
22.5
|
1.0
|
CE2
|
E:CR259
|
5.0
|
23.3
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 5ltp
Go back to
Chlorine Binding Sites List in 5ltp
Chlorine binding site 6 out
of 6 in the Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Structure of the Yellow-Green Fluorescent Protein Mneongreen From Branchiostoma Lanceolatum at the Acidic pH 4.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl301
b:21.0
occ:0.70
|
O
|
F:HOH441
|
0.8
|
26.6
|
0.3
|
O
|
F:HOH463
|
2.1
|
16.4
|
0.3
|
OH
|
F:TYR175
|
2.9
|
22.6
|
1.0
|
NH2
|
F:ARG88
|
3.2
|
23.8
|
1.0
|
OG
|
F:SER153
|
3.3
|
25.5
|
1.0
|
NE2
|
F:HIS62
|
3.5
|
22.5
|
1.0
|
OG1
|
F:THR173
|
3.6
|
23.8
|
1.0
|
CB
|
F:SER153
|
3.6
|
24.1
|
1.0
|
CE1
|
F:PHE155
|
3.9
|
23.3
|
1.0
|
CB
|
F:THR173
|
3.9
|
23.6
|
1.0
|
CZ
|
F:TYR175
|
3.9
|
22.4
|
1.0
|
CE1
|
F:TYR175
|
4.1
|
22.2
|
1.0
|
CG2
|
F:THR173
|
4.1
|
23.5
|
1.0
|
CD2
|
F:CR259
|
4.1
|
22.1
|
1.0
|
CZ
|
F:ARG88
|
4.2
|
23.9
|
1.0
|
NE
|
F:ARG88
|
4.3
|
23.6
|
1.0
|
NZ
|
F:LYS143
|
4.3
|
24.4
|
1.0
|
CE1
|
F:HIS62
|
4.3
|
22.4
|
1.0
|
CB2
|
F:CR259
|
4.4
|
21.9
|
1.0
|
CD2
|
F:HIS62
|
4.4
|
22.1
|
1.0
|
O
|
F:HOH412
|
4.4
|
30.2
|
1.0
|
CD1
|
F:PHE155
|
4.6
|
23.3
|
1.0
|
CZ
|
F:PHE155
|
4.8
|
23.8
|
1.0
|
NH1
|
F:ARG195
|
4.8
|
20.6
|
1.0
|
CG2
|
F:CR259
|
4.8
|
22.3
|
1.0
|
O2
|
F:CR259
|
5.0
|
22.1
|
1.0
|
O
|
F:HOH437
|
5.0
|
20.6
|
1.0
|
|
Reference:
D.Clavel,
G.Gotthard,
D.Von Stetten,
D.De Sanctis,
H.Pasquier,
G.G.Lambert,
N.C.Shaner,
A.Royant.
Structural Analysis of the Bright Monomeric Yellow-Green Fluorescent Protein Mneongreen Obtained By Directed Evolution. Acta Crystallogr D Struct V. 72 1298 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27917830
DOI: 10.1107/S2059798316018623
Page generated: Fri Jul 26 12:10:35 2024
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