Chlorine in PDB 6rk7: Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
All present enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum:
2.5.1.6;
Protein crystallography data
The structure of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rk7
was solved by
A.Shahar,
R.Zarivach,
S.Bershtein,
D.Kleiner,
F.Shmulevich,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.66 /
1.80
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.999,
106.139,
234.377,
90.00,
96.86,
90.00
|
R / Rfree (%)
|
16.9 /
19.4
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
(pdb code 6rk7). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rk7:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 6rk7
Go back to
Chlorine Binding Sites List in 6rk7
Chlorine binding site 1 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:34.1
occ:1.00
|
NZ
|
A:LYS160
|
3.1
|
28.9
|
1.0
|
NE2
|
A:HIS16
|
3.2
|
29.4
|
1.0
|
NZ
|
A:LYS238
|
3.2
|
32.1
|
1.0
|
CE
|
A:LYS238
|
3.6
|
31.1
|
1.0
|
OD2
|
B:ASP113
|
3.7
|
31.9
|
1.0
|
CE1
|
A:HIS16
|
3.7
|
29.2
|
1.0
|
C5'
|
A:SAM401
|
3.7
|
31.8
|
1.0
|
O
|
A:HOH546
|
3.9
|
60.0
|
1.0
|
C4'
|
A:SAM401
|
3.9
|
29.4
|
1.0
|
CE
|
A:LYS160
|
4.0
|
28.9
|
1.0
|
O
|
A:HOH518
|
4.1
|
44.0
|
1.0
|
OD2
|
A:ASP18
|
4.2
|
29.7
|
1.0
|
OD2
|
A:ASP231
|
4.2
|
34.7
|
1.0
|
O
|
A:HOH522
|
4.3
|
31.0
|
1.0
|
O3'
|
A:SAM401
|
4.4
|
31.4
|
1.0
|
CD2
|
A:HIS16
|
4.4
|
26.7
|
1.0
|
O
|
A:HOH775
|
4.4
|
58.1
|
1.0
|
CD
|
A:LYS160
|
4.5
|
27.6
|
1.0
|
C3'
|
A:SAM401
|
4.8
|
29.9
|
1.0
|
CG
|
B:ASP113
|
4.8
|
28.5
|
1.0
|
ND1
|
A:HIS16
|
5.0
|
26.8
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 6rk7
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Chlorine Binding Sites List in 6rk7
Chlorine binding site 2 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl403
b:34.5
occ:1.00
|
NE2
|
B:HIS16
|
3.1
|
24.7
|
1.0
|
NZ
|
B:LYS160
|
3.1
|
33.5
|
1.0
|
NZ
|
B:LYS238
|
3.3
|
32.0
|
1.0
|
CE
|
B:LYS238
|
3.6
|
31.0
|
1.0
|
CE1
|
B:HIS16
|
3.7
|
26.6
|
1.0
|
C5'
|
B:SAM401
|
3.7
|
36.1
|
1.0
|
O
|
A:HOH547
|
3.7
|
54.8
|
1.0
|
OD2
|
A:ASP113
|
3.8
|
35.4
|
1.0
|
O
|
A:HOH508
|
3.8
|
53.8
|
1.0
|
CE
|
B:LYS160
|
3.9
|
33.7
|
1.0
|
C4'
|
B:SAM401
|
3.9
|
32.4
|
1.0
|
O
|
B:HOH555
|
4.0
|
50.4
|
1.0
|
O
|
B:HOH518
|
4.1
|
44.5
|
1.0
|
OD2
|
B:ASP231
|
4.2
|
39.5
|
1.0
|
OD2
|
B:ASP18
|
4.3
|
31.4
|
1.0
|
CD2
|
B:HIS16
|
4.3
|
25.8
|
1.0
|
O
|
B:HOH513
|
4.3
|
34.4
|
1.0
|
O3'
|
B:SAM401
|
4.3
|
33.5
|
1.0
|
CD
|
B:LYS160
|
4.5
|
33.0
|
1.0
|
C3'
|
B:SAM401
|
4.8
|
31.6
|
1.0
|
CG
|
A:ASP113
|
4.8
|
34.3
|
1.0
|
O4'
|
B:SAM401
|
4.9
|
31.6
|
1.0
|
ND1
|
B:HIS16
|
4.9
|
27.4
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 6rk7
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Chlorine Binding Sites List in 6rk7
Chlorine binding site 3 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl403
b:33.9
occ:1.00
|
O
|
E:HOH720
|
3.1
|
52.7
|
1.0
|
NE2
|
E:HIS16
|
3.1
|
23.6
|
1.0
|
NZ
|
E:LYS160
|
3.2
|
30.5
|
1.0
|
NZ
|
E:LYS238
|
3.2
|
28.8
|
1.0
|
O
|
E:HOH735
|
3.4
|
56.8
|
1.0
|
CE1
|
E:HIS16
|
3.6
|
25.6
|
1.0
|
CE
|
E:LYS238
|
3.7
|
29.5
|
1.0
|
OD2
|
F:ASP113
|
3.7
|
31.8
|
1.0
|
C5'
|
E:SAM401
|
3.8
|
35.5
|
1.0
|
CE
|
E:LYS160
|
3.9
|
29.4
|
1.0
|
C4'
|
E:SAM401
|
4.0
|
32.4
|
1.0
|
O
|
E:HOH630
|
4.0
|
54.7
|
1.0
|
O
|
E:HOH551
|
4.0
|
44.5
|
1.0
|
OD2
|
E:ASP18
|
4.2
|
26.4
|
1.0
|
OD2
|
E:ASP231
|
4.2
|
36.0
|
1.0
|
CD2
|
E:HIS16
|
4.3
|
25.4
|
1.0
|
O3'
|
E:SAM401
|
4.3
|
31.0
|
1.0
|
O
|
E:HOH509
|
4.4
|
46.2
|
1.0
|
O
|
E:HOH510
|
4.4
|
36.6
|
1.0
|
CD
|
E:LYS160
|
4.6
|
28.0
|
1.0
|
CG
|
F:ASP113
|
4.8
|
33.5
|
1.0
|
C3'
|
E:SAM401
|
4.9
|
30.1
|
1.0
|
ND1
|
E:HIS16
|
4.9
|
24.1
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 6rk7
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Chlorine Binding Sites List in 6rk7
Chlorine binding site 4 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl403
b:31.6
occ:1.00
|
NE2
|
F:HIS16
|
3.1
|
26.4
|
1.0
|
NZ
|
F:LYS160
|
3.1
|
29.8
|
1.0
|
NZ
|
F:LYS238
|
3.2
|
30.8
|
1.0
|
CE
|
F:LYS238
|
3.6
|
27.9
|
1.0
|
CE1
|
F:HIS16
|
3.6
|
28.8
|
1.0
|
C5'
|
F:SAM401
|
3.7
|
30.0
|
1.0
|
OD2
|
E:ASP113
|
3.7
|
31.1
|
1.0
|
C4'
|
F:SAM401
|
3.8
|
27.3
|
1.0
|
CE
|
F:LYS160
|
3.9
|
29.1
|
1.0
|
O
|
F:HOH1122
|
4.0
|
54.8
|
1.0
|
O
|
F:HOH1118
|
4.1
|
37.6
|
1.0
|
O
|
E:HOH511
|
4.1
|
53.1
|
1.0
|
OD2
|
F:ASP231
|
4.2
|
34.8
|
1.0
|
OD2
|
F:ASP18
|
4.2
|
26.7
|
1.0
|
CD2
|
F:HIS16
|
4.3
|
24.8
|
1.0
|
O3'
|
F:SAM401
|
4.4
|
26.9
|
1.0
|
O
|
F:HOH1106
|
4.4
|
34.4
|
1.0
|
CD
|
F:LYS160
|
4.5
|
25.5
|
1.0
|
C3'
|
F:SAM401
|
4.8
|
26.9
|
1.0
|
CG
|
E:ASP113
|
4.8
|
30.6
|
1.0
|
O4'
|
F:SAM401
|
4.9
|
26.3
|
1.0
|
ND1
|
F:HIS16
|
4.9
|
26.9
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 6rk7
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Chlorine Binding Sites List in 6rk7
Chlorine binding site 5 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl403
b:38.1
occ:1.00
|
NE2
|
G:HIS16
|
3.1
|
32.9
|
1.0
|
NZ
|
G:LYS160
|
3.1
|
34.0
|
1.0
|
NZ
|
G:LYS238
|
3.2
|
37.5
|
1.0
|
CE
|
G:LYS238
|
3.6
|
37.7
|
1.0
|
O
|
H:HOH530
|
3.6
|
62.8
|
1.0
|
CE1
|
G:HIS16
|
3.6
|
33.2
|
1.0
|
OD2
|
H:ASP113
|
3.7
|
41.1
|
1.0
|
O
|
H:HOH506
|
3.7
|
51.4
|
1.0
|
C5'
|
G:SAM401
|
3.8
|
35.8
|
1.0
|
CE
|
G:LYS160
|
3.8
|
34.0
|
1.0
|
C4'
|
G:SAM401
|
4.0
|
34.4
|
1.0
|
O
|
G:HOH539
|
4.1
|
51.4
|
1.0
|
OD2
|
G:ASP231
|
4.2
|
40.5
|
1.0
|
O
|
G:HOH501
|
4.2
|
44.6
|
1.0
|
OD2
|
G:ASP18
|
4.2
|
35.6
|
1.0
|
CD2
|
G:HIS16
|
4.3
|
35.5
|
1.0
|
O
|
G:HOH510
|
4.3
|
38.2
|
1.0
|
O3'
|
G:SAM401
|
4.3
|
33.4
|
1.0
|
CD
|
G:LYS160
|
4.5
|
33.3
|
1.0
|
CG
|
H:ASP113
|
4.8
|
36.4
|
1.0
|
C3'
|
G:SAM401
|
4.9
|
35.8
|
1.0
|
ND1
|
G:HIS16
|
4.9
|
32.6
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 6rk7
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Chlorine Binding Sites List in 6rk7
Chlorine binding site 6 out
of 6 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl403
b:39.9
occ:1.00
|
NZ
|
H:LYS160
|
3.1
|
43.0
|
1.0
|
NE2
|
H:HIS16
|
3.1
|
34.5
|
1.0
|
NZ
|
H:LYS238
|
3.3
|
39.9
|
1.0
|
CE
|
H:LYS238
|
3.7
|
37.4
|
1.0
|
OD2
|
G:ASP113
|
3.7
|
45.7
|
1.0
|
CE1
|
H:HIS16
|
3.7
|
34.8
|
1.0
|
C5'
|
H:SAM401
|
3.7
|
43.2
|
1.0
|
CE
|
H:LYS160
|
3.9
|
41.3
|
1.0
|
C4'
|
H:SAM401
|
3.9
|
42.3
|
1.0
|
O
|
H:HOH544
|
4.0
|
47.5
|
1.0
|
OD2
|
H:ASP231
|
4.2
|
46.4
|
1.0
|
O3'
|
H:SAM401
|
4.2
|
37.2
|
1.0
|
OD2
|
H:ASP18
|
4.3
|
36.5
|
1.0
|
O
|
H:HOH507
|
4.3
|
39.7
|
1.0
|
CD2
|
H:HIS16
|
4.3
|
34.8
|
1.0
|
CD
|
H:LYS160
|
4.6
|
39.4
|
1.0
|
CG
|
G:ASP113
|
4.7
|
43.6
|
1.0
|
C3'
|
H:SAM401
|
4.7
|
39.1
|
1.0
|
ND1
|
H:HIS16
|
5.0
|
33.0
|
1.0
|
|
Reference:
D.Kleiner,
F.Shmulevich,
R.Zarivach,
A.Shahar,
M.Sharon,
G.Ben-Nissan,
S.Bershtein.
The Inter-Dimeric Interface Controls Function and Stability of Ureaplasma Urealiticum Methionine S-Adenosyltransferase. J.Mol.Biol. 2019.
ISSN: ESSN 1089-8638
PubMed: 31520601
DOI: 10.1016/J.JMB.2019.09.003
Page generated: Mon Jul 29 14:32:29 2024
|