Chlorine in PDB 6yec: E.Coli'S Putrescine Receptor Potf Complexed with Spermine
Protein crystallography data
The structure of E.Coli'S Putrescine Receptor Potf Complexed with Spermine, PDB code: 6yec
was solved by
S.Shanmugaratnam,
P.Kroeger,
B.Hocker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.58 /
2.09
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.401,
70.401,
273.497,
90,
90,
120
|
R / Rfree (%)
|
21.5 /
24
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
(pdb code 6yec). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
E.Coli'S Putrescine Receptor Potf Complexed with Spermine, PDB code: 6yec:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 6yec
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Chlorine Binding Sites List in 6yec
Chlorine binding site 1 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl512
b:120.2
occ:1.00
|
OE2
|
B:GLU108
|
4.0
|
97.2
|
1.0
|
OE1
|
B:GLU108
|
4.2
|
96.3
|
1.0
|
CD
|
B:GLU108
|
4.5
|
92.3
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 6yec
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Chlorine Binding Sites List in 6yec
Chlorine binding site 2 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl513
b:95.4
occ:1.00
|
CD
|
B:LYS171
|
4.7
|
88.6
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 6yec
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Chlorine Binding Sites List in 6yec
Chlorine binding site 3 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl514
b:84.9
occ:1.00
|
O
|
B:HOH607
|
3.4
|
50.8
|
1.0
|
O2
|
B:EDO503
|
3.6
|
87.8
|
1.0
|
N
|
B:ASP39
|
3.6
|
55.6
|
1.0
|
CG2
|
B:VAL61
|
4.1
|
65.2
|
1.0
|
OD1
|
B:ASP39
|
4.2
|
79.4
|
1.0
|
CA
|
B:ASP39
|
4.2
|
60.5
|
1.0
|
CE2
|
B:TYR59
|
4.6
|
64.9
|
1.0
|
C2
|
B:EDO503
|
4.6
|
89.0
|
1.0
|
C
|
B:SER38
|
4.6
|
50.8
|
1.0
|
CA
|
B:SER38
|
4.7
|
54.7
|
1.0
|
CG
|
B:ASP39
|
5.0
|
75.7
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 6yec
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Chlorine Binding Sites List in 6yec
Chlorine binding site 4 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl515
b:66.8
occ:1.00
|
O
|
B:HOH652
|
3.1
|
69.0
|
1.0
|
ND2
|
B:ASN65
|
3.2
|
68.7
|
1.0
|
N
|
B:ASN65
|
3.5
|
55.2
|
1.0
|
CB
|
B:ASN65
|
3.5
|
57.2
|
1.0
|
O
|
B:HOH617
|
3.7
|
64.6
|
1.0
|
CG
|
B:ASN65
|
3.8
|
64.2
|
1.0
|
CH2
|
B:TRP37
|
4.0
|
54.4
|
1.0
|
CA
|
B:ASN65
|
4.1
|
58.7
|
1.0
|
C13
|
B:SPM501
|
4.2
|
69.7
|
1.0
|
CH2
|
B:TRP244
|
4.2
|
55.5
|
1.0
|
CZ2
|
B:TRP244
|
4.3
|
52.9
|
1.0
|
C
|
B:SER64
|
4.5
|
58.5
|
1.0
|
CA
|
B:SER64
|
4.6
|
64.2
|
1.0
|
C11
|
B:SPM501
|
4.6
|
61.4
|
1.0
|
OE2
|
B:GLU185
|
4.6
|
64.5
|
1.0
|
CZ3
|
B:TRP37
|
4.6
|
50.8
|
1.0
|
OG
|
B:SER64
|
4.7
|
66.2
|
1.0
|
OE1
|
B:GLU184
|
4.9
|
77.9
|
1.0
|
OD1
|
B:ASN65
|
4.9
|
61.3
|
1.0
|
N10
|
B:SPM501
|
5.0
|
60.4
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 6yec
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Chlorine Binding Sites List in 6yec
Chlorine binding site 5 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl410
b:98.8
occ:1.00
|
N
|
A:LYS289
|
3.5
|
60.9
|
1.0
|
OD2
|
A:ASP290
|
3.6
|
100.7
|
1.0
|
O
|
A:LYS287
|
3.7
|
72.1
|
1.0
|
N
|
A:ASP290
|
3.8
|
69.5
|
1.0
|
CG
|
A:ASP290
|
4.1
|
94.2
|
1.0
|
CA
|
A:ASN288
|
4.2
|
65.5
|
1.0
|
CB
|
A:LYS289
|
4.2
|
69.7
|
1.0
|
C
|
A:ASN288
|
4.3
|
62.4
|
1.0
|
CA
|
A:LYS289
|
4.3
|
66.6
|
1.0
|
CB
|
A:ASP290
|
4.4
|
82.3
|
1.0
|
CG
|
A:LYS289
|
4.6
|
74.5
|
1.0
|
C
|
A:LYS289
|
4.6
|
60.1
|
1.0
|
C
|
A:LYS287
|
4.7
|
67.3
|
1.0
|
OD1
|
A:ASP290
|
4.7
|
96.5
|
1.0
|
CA
|
A:ASP290
|
4.8
|
71.5
|
1.0
|
OE1
|
A:GLU291
|
4.9
|
75.8
|
1.0
|
N
|
A:ASN288
|
4.9
|
65.2
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 6yec
Go back to
Chlorine Binding Sites List in 6yec
Chlorine binding site 6 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl411
b:137.5
occ:1.00
|
NZ
|
A:LYS289
|
3.0
|
93.2
|
1.0
|
CE
|
A:LYS289
|
3.6
|
89.0
|
1.0
|
CD
|
A:LYS289
|
4.0
|
80.5
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 6yec
Go back to
Chlorine Binding Sites List in 6yec
Chlorine binding site 7 out
of 7 in the E.Coli'S Putrescine Receptor Potf Complexed with Spermine
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of E.Coli'S Putrescine Receptor Potf Complexed with Spermine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl412
b:71.9
occ:1.00
|
N
|
A:SER87
|
3.2
|
49.1
|
1.0
|
N
|
A:PHE277
|
3.2
|
50.4
|
1.0
|
N
|
A:ALA86
|
3.4
|
52.3
|
1.0
|
O
|
A:HOH514
|
3.7
|
52.7
|
1.0
|
O
|
A:PHE277
|
3.7
|
56.2
|
1.0
|
CA
|
A:PHE276
|
3.7
|
51.4
|
1.0
|
OG
|
A:SER87
|
3.7
|
59.0
|
1.0
|
CB
|
A:SER87
|
3.8
|
52.7
|
1.0
|
CB
|
A:ALA86
|
3.8
|
48.8
|
1.0
|
CB
|
A:PHE276
|
3.8
|
49.4
|
1.0
|
CA
|
A:ALA86
|
3.9
|
51.3
|
1.0
|
C
|
A:PHE276
|
4.0
|
50.0
|
1.0
|
C
|
A:ALA86
|
4.0
|
52.1
|
1.0
|
CB
|
A:SER85
|
4.0
|
58.4
|
1.0
|
CA
|
A:SER87
|
4.1
|
52.6
|
1.0
|
CA
|
A:PHE277
|
4.2
|
53.5
|
1.0
|
C
|
A:SER85
|
4.2
|
49.7
|
1.0
|
C
|
A:PHE277
|
4.2
|
53.8
|
1.0
|
CD2
|
A:PHE277
|
4.4
|
62.4
|
1.0
|
CA
|
A:SER85
|
4.5
|
49.2
|
1.0
|
CB
|
A:PHE277
|
4.5
|
57.8
|
1.0
|
OG
|
A:SER85
|
4.7
|
62.7
|
1.0
|
NE2
|
A:HIS123
|
4.8
|
61.1
|
1.0
|
O
|
A:ALA275
|
4.9
|
52.5
|
1.0
|
CG
|
A:PHE277
|
5.0
|
60.2
|
1.0
|
|
Reference:
P.Kroger,
S.Shanmugaratnam,
N.Ferruz,
K.Schweimer,
B.Hocker.
A Comprehensive Binding Study Illustrates Ligand Recognition in the Periplasmic Binding Protein Potf. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 33406388
DOI: 10.1016/J.STR.2020.12.005
Page generated: Mon Jul 29 17:40:01 2024
|