Chlorine in PDB 4e4j: Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
Protein crystallography data
The structure of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans, PDB code: 4e4j
was solved by
J.Benach,
P.Gallego,
R.Planell,
E.Querol,
J.A.Perez Pons,
D.Reverter,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.00 /
2.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.548,
128.875,
220.279,
90.00,
91.41,
90.00
|
|
R / Rfree (%)
|
21 /
23.8
|
Chlorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Chlorine atom in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
(pdb code 4e4j). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the
Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans, PDB code: 4e4j:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Chlorine binding site 1 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 1 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl501
b:19.6
occ:1.00
|
N
|
A:GLY428
|
3.1
|
15.7
|
1.0
|
|
NZ
|
B:LYS94
|
3.3
|
16.2
|
1.0
|
|
N
|
A:ARG408
|
3.4
|
15.7
|
1.0
|
|
CB
|
A:ARG408
|
3.5
|
14.1
|
1.0
|
|
C
|
A:GLY428
|
3.7
|
15.5
|
1.0
|
|
CG
|
A:GLU407
|
3.7
|
23.2
|
1.0
|
|
CG
|
A:ARG408
|
3.7
|
13.7
|
1.0
|
|
N
|
A:SER429
|
3.7
|
14.9
|
1.0
|
|
N
|
A:GLU407
|
3.8
|
16.0
|
1.0
|
|
CE
|
B:LYS94
|
3.8
|
18.8
|
1.0
|
|
CA
|
A:GLY428
|
3.8
|
14.7
|
1.0
|
|
CD
|
A:ARG408
|
3.9
|
15.1
|
1.0
|
|
CB
|
A:TYR406
|
4.0
|
13.9
|
1.0
|
|
CA
|
A:ARG408
|
4.0
|
16.5
|
1.0
|
|
O
|
A:PHE426
|
4.0
|
19.3
|
1.0
|
|
OD1
|
A:ASN427
|
4.1
|
20.0
|
1.0
|
|
O
|
A:GLY428
|
4.1
|
16.3
|
1.0
|
|
C
|
A:ASN427
|
4.2
|
15.8
|
1.0
|
|
CA
|
A:ASN427
|
4.2
|
17.4
|
1.0
|
|
CD
|
B:LYS94
|
4.3
|
18.7
|
1.0
|
|
C
|
A:GLU407
|
4.3
|
19.2
|
1.0
|
|
CA
|
A:SER429
|
4.3
|
17.0
|
1.0
|
|
C
|
A:TYR406
|
4.4
|
16.2
|
1.0
|
|
CA
|
A:TYR406
|
4.4
|
15.3
|
1.0
|
|
CD2
|
A:TYR406
|
4.4
|
13.5
|
1.0
|
|
CA
|
A:GLU407
|
4.4
|
18.3
|
1.0
|
|
CG
|
A:TYR406
|
4.5
|
14.6
|
1.0
|
|
CB
|
A:GLU407
|
4.6
|
19.8
|
1.0
|
|
OE2
|
A:GLU407
|
4.6
|
28.2
|
1.0
|
|
CD
|
A:GLU407
|
4.7
|
26.4
|
1.0
|
|
OG
|
A:SER432
|
4.9
|
19.3
|
1.0
|
|
NE
|
A:ARG408
|
4.9
|
18.0
|
1.0
|
|
C
|
A:PHE426
|
5.0
|
18.4
|
1.0
|
|
Chlorine binding site 2 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 2 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl501
b:21.0
occ:1.00
|
N
|
B:GLY428
|
3.2
|
17.3
|
1.0
|
|
NZ
|
A:LYS94
|
3.2
|
18.6
|
1.0
|
|
N
|
B:ARG408
|
3.3
|
19.3
|
1.0
|
|
CB
|
B:ARG408
|
3.4
|
20.6
|
1.0
|
|
CG
|
B:ARG408
|
3.6
|
20.8
|
1.0
|
|
CG
|
B:GLU407
|
3.6
|
21.3
|
1.0
|
|
C
|
B:GLY428
|
3.7
|
20.3
|
1.0
|
|
N
|
B:SER429
|
3.7
|
21.4
|
1.0
|
|
N
|
B:GLU407
|
3.8
|
19.6
|
1.0
|
|
CA
|
B:GLY428
|
3.8
|
16.9
|
1.0
|
|
CD
|
B:ARG408
|
3.8
|
20.1
|
1.0
|
|
CE
|
A:LYS94
|
3.8
|
17.8
|
1.0
|
|
CB
|
B:TYR406
|
3.9
|
18.3
|
1.0
|
|
CA
|
B:ARG408
|
4.0
|
20.9
|
1.0
|
|
O
|
B:PHE426
|
4.1
|
20.6
|
1.0
|
|
O
|
B:GLY428
|
4.2
|
22.0
|
1.0
|
|
C
|
B:ASN427
|
4.2
|
17.4
|
1.0
|
|
OD1
|
B:ASN427
|
4.3
|
20.4
|
1.0
|
|
CD
|
A:LYS94
|
4.3
|
16.9
|
1.0
|
|
CA
|
B:ASN427
|
4.3
|
18.7
|
1.0
|
|
C
|
B:GLU407
|
4.3
|
19.6
|
1.0
|
|
CA
|
B:SER429
|
4.3
|
22.8
|
1.0
|
|
C
|
B:TYR406
|
4.3
|
19.6
|
1.0
|
|
CA
|
B:TYR406
|
4.4
|
18.6
|
1.0
|
|
CA
|
B:GLU407
|
4.4
|
19.4
|
1.0
|
|
CG
|
B:TYR406
|
4.4
|
19.8
|
1.0
|
|
CD2
|
B:TYR406
|
4.5
|
19.7
|
1.0
|
|
OE2
|
B:GLU407
|
4.6
|
26.0
|
1.0
|
|
CB
|
B:GLU407
|
4.6
|
19.5
|
1.0
|
|
CD
|
B:GLU407
|
4.7
|
25.5
|
1.0
|
|
NE
|
B:ARG408
|
4.8
|
19.5
|
1.0
|
|
OG
|
B:SER432
|
4.9
|
25.5
|
1.0
|
|
Chlorine binding site 3 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 3 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl501
b:21.9
occ:1.00
|
N
|
C:GLY428
|
3.2
|
18.5
|
1.0
|
|
N
|
C:ARG408
|
3.3
|
19.1
|
1.0
|
|
CB
|
C:ARG408
|
3.4
|
14.6
|
1.0
|
|
NZ
|
D:LYS94
|
3.4
|
11.1
|
1.0
|
|
CG
|
C:ARG408
|
3.6
|
13.2
|
1.0
|
|
C
|
C:GLY428
|
3.6
|
18.6
|
1.0
|
|
CG
|
C:GLU407
|
3.7
|
22.2
|
1.0
|
|
N
|
C:SER429
|
3.7
|
18.6
|
1.0
|
|
CA
|
C:GLY428
|
3.8
|
18.7
|
1.0
|
|
N
|
C:GLU407
|
3.8
|
17.2
|
1.0
|
|
CD
|
C:ARG408
|
3.8
|
12.3
|
1.0
|
|
CB
|
C:TYR406
|
3.9
|
17.3
|
1.0
|
|
CE
|
D:LYS94
|
3.9
|
13.7
|
1.0
|
|
CA
|
C:ARG408
|
4.0
|
18.1
|
1.0
|
|
O
|
C:GLY428
|
4.1
|
19.8
|
1.0
|
|
O
|
C:PHE426
|
4.2
|
17.9
|
1.0
|
|
OD1
|
C:ASN427
|
4.2
|
18.7
|
1.0
|
|
C
|
C:ASN427
|
4.2
|
18.6
|
1.0
|
|
CD
|
D:LYS94
|
4.3
|
17.0
|
1.0
|
|
CD2
|
C:TYR406
|
4.3
|
17.6
|
1.0
|
|
C
|
C:GLU407
|
4.3
|
19.4
|
1.0
|
|
CA
|
C:SER429
|
4.4
|
19.4
|
1.0
|
|
CA
|
C:TYR406
|
4.4
|
16.3
|
1.0
|
|
C
|
C:TYR406
|
4.4
|
17.9
|
1.0
|
|
CA
|
C:ASN427
|
4.4
|
18.4
|
1.0
|
|
CG
|
C:TYR406
|
4.4
|
19.7
|
1.0
|
|
CA
|
C:GLU407
|
4.5
|
19.2
|
1.0
|
|
CB
|
C:GLU407
|
4.7
|
19.7
|
1.0
|
|
CD
|
C:GLU407
|
4.7
|
23.9
|
1.0
|
|
OE2
|
C:GLU407
|
4.8
|
22.1
|
1.0
|
|
OG
|
C:SER432
|
4.8
|
22.1
|
1.0
|
|
NE
|
C:ARG408
|
4.9
|
13.6
|
1.0
|
|
Chlorine binding site 4 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 4 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl501
b:21.8
occ:1.00
|
N
|
D:GLY428
|
3.1
|
21.2
|
1.0
|
|
NZ
|
C:LYS94
|
3.1
|
22.6
|
1.0
|
|
N
|
D:ARG408
|
3.5
|
19.5
|
1.0
|
|
CB
|
D:ARG408
|
3.5
|
16.7
|
1.0
|
|
C
|
D:GLY428
|
3.6
|
22.8
|
1.0
|
|
N
|
D:SER429
|
3.6
|
23.3
|
1.0
|
|
CA
|
D:GLY428
|
3.7
|
21.6
|
1.0
|
|
CG
|
D:ARG408
|
3.7
|
18.6
|
1.0
|
|
CG
|
D:GLU407
|
3.8
|
23.0
|
1.0
|
|
CE
|
C:LYS94
|
3.8
|
20.6
|
1.0
|
|
N
|
D:GLU407
|
3.9
|
18.6
|
1.0
|
|
CB
|
D:TYR406
|
3.9
|
15.6
|
1.0
|
|
CD
|
D:ARG408
|
4.0
|
21.0
|
1.0
|
|
O
|
D:GLY428
|
4.0
|
22.4
|
1.0
|
|
O
|
D:PHE426
|
4.0
|
20.7
|
1.0
|
|
CA
|
D:ARG408
|
4.1
|
18.3
|
1.0
|
|
C
|
D:ASN427
|
4.1
|
21.8
|
1.0
|
|
OD1
|
D:ASN427
|
4.1
|
25.8
|
1.0
|
|
CA
|
D:ASN427
|
4.2
|
21.9
|
1.0
|
|
CD
|
C:LYS94
|
4.3
|
20.3
|
1.0
|
|
CA
|
D:SER429
|
4.3
|
24.8
|
1.0
|
|
CD2
|
D:TYR406
|
4.4
|
18.3
|
1.0
|
|
CA
|
D:TYR406
|
4.4
|
17.6
|
1.0
|
|
CG
|
D:TYR406
|
4.4
|
18.3
|
1.0
|
|
C
|
D:TYR406
|
4.4
|
18.4
|
1.0
|
|
C
|
D:GLU407
|
4.4
|
19.5
|
1.0
|
|
CA
|
D:GLU407
|
4.6
|
19.5
|
1.0
|
|
OE2
|
D:GLU407
|
4.7
|
23.9
|
1.0
|
|
CB
|
D:GLU407
|
4.8
|
19.6
|
1.0
|
|
CD
|
D:GLU407
|
4.8
|
26.4
|
1.0
|
|
OG
|
D:SER432
|
4.8
|
22.2
|
1.0
|
|
NE
|
D:ARG408
|
5.0
|
22.2
|
1.0
|
|
C
|
D:PHE426
|
5.0
|
20.8
|
1.0
|
|
Chlorine binding site 5 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 5 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl501
b:20.8
occ:1.00
|
N
|
E:GLY428
|
3.2
|
20.0
|
1.0
|
|
NZ
|
F:LYS94
|
3.2
|
17.9
|
1.0
|
|
N
|
E:ARG408
|
3.4
|
17.3
|
1.0
|
|
CB
|
E:ARG408
|
3.4
|
16.8
|
1.0
|
|
CG
|
E:GLU407
|
3.6
|
23.4
|
1.0
|
|
CG
|
E:ARG408
|
3.6
|
18.6
|
1.0
|
|
C
|
E:GLY428
|
3.7
|
22.7
|
1.0
|
|
N
|
E:SER429
|
3.8
|
22.4
|
1.0
|
|
CE
|
F:LYS94
|
3.8
|
19.6
|
1.0
|
|
N
|
E:GLU407
|
3.8
|
15.4
|
1.0
|
|
CA
|
E:GLY428
|
3.9
|
20.8
|
1.0
|
|
CD
|
E:ARG408
|
3.9
|
17.5
|
1.0
|
|
CA
|
E:ARG408
|
4.0
|
18.4
|
1.0
|
|
CB
|
E:TYR406
|
4.0
|
16.1
|
1.0
|
|
OD1
|
E:ASN427
|
4.0
|
26.2
|
1.0
|
|
O
|
E:GLY428
|
4.1
|
23.1
|
1.0
|
|
O
|
E:PHE426
|
4.1
|
18.4
|
1.0
|
|
CD
|
F:LYS94
|
4.2
|
19.9
|
1.0
|
|
C
|
E:ASN427
|
4.2
|
21.0
|
1.0
|
|
CA
|
E:ASN427
|
4.3
|
19.8
|
1.0
|
|
CA
|
E:SER429
|
4.3
|
22.2
|
1.0
|
|
C
|
E:GLU407
|
4.3
|
18.3
|
1.0
|
|
C
|
E:TYR406
|
4.4
|
15.5
|
1.0
|
|
CA
|
E:TYR406
|
4.4
|
15.2
|
1.0
|
|
CD2
|
E:TYR406
|
4.4
|
14.9
|
1.0
|
|
CG
|
E:TYR406
|
4.4
|
16.6
|
1.0
|
|
CA
|
E:GLU407
|
4.5
|
16.0
|
1.0
|
|
OE2
|
E:GLU407
|
4.6
|
25.8
|
1.0
|
|
CD
|
E:GLU407
|
4.6
|
26.2
|
1.0
|
|
CB
|
E:GLU407
|
4.6
|
19.4
|
1.0
|
|
OG
|
E:SER432
|
4.9
|
21.5
|
1.0
|
|
NE
|
E:ARG408
|
4.9
|
19.0
|
1.0
|
|
CG
|
E:ASN427
|
5.0
|
24.9
|
1.0
|
|
Chlorine binding site 6 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 6 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl501
b:19.4
occ:1.00
|
N
|
F:GLY428
|
3.1
|
21.2
|
1.0
|
|
NZ
|
E:LYS94
|
3.3
|
21.6
|
1.0
|
|
N
|
F:ARG408
|
3.4
|
20.8
|
1.0
|
|
CB
|
F:ARG408
|
3.4
|
21.7
|
1.0
|
|
C
|
F:GLY428
|
3.6
|
24.1
|
1.0
|
|
CG
|
F:GLU407
|
3.7
|
22.8
|
1.0
|
|
N
|
F:SER429
|
3.7
|
24.1
|
1.0
|
|
CG
|
F:ARG408
|
3.7
|
21.0
|
1.0
|
|
CA
|
F:GLY428
|
3.8
|
24.1
|
1.0
|
|
N
|
F:GLU407
|
3.8
|
19.9
|
1.0
|
|
CE
|
E:LYS94
|
3.9
|
19.0
|
1.0
|
|
CB
|
F:TYR406
|
3.9
|
18.3
|
1.0
|
|
CA
|
F:ARG408
|
4.0
|
21.7
|
1.0
|
|
CD
|
F:ARG408
|
4.1
|
21.0
|
1.0
|
|
O
|
F:PHE426
|
4.1
|
22.2
|
1.0
|
|
O
|
F:GLY428
|
4.1
|
23.4
|
1.0
|
|
OD1
|
F:ASN427
|
4.1
|
22.9
|
1.0
|
|
C
|
F:ASN427
|
4.2
|
21.5
|
1.0
|
|
CA
|
F:ASN427
|
4.3
|
21.2
|
1.0
|
|
CD
|
E:LYS94
|
4.3
|
19.0
|
1.0
|
|
CA
|
F:SER429
|
4.3
|
26.5
|
1.0
|
|
C
|
F:GLU407
|
4.4
|
23.1
|
1.0
|
|
CA
|
F:TYR406
|
4.4
|
18.1
|
1.0
|
|
C
|
F:TYR406
|
4.4
|
18.6
|
1.0
|
|
CD2
|
F:TYR406
|
4.4
|
20.4
|
1.0
|
|
CG
|
F:TYR406
|
4.4
|
20.9
|
1.0
|
|
CA
|
F:GLU407
|
4.5
|
21.5
|
1.0
|
|
CB
|
F:GLU407
|
4.7
|
21.8
|
1.0
|
|
CD
|
F:GLU407
|
4.7
|
26.9
|
1.0
|
|
OE2
|
F:GLU407
|
4.7
|
27.6
|
1.0
|
|
OG
|
F:SER432
|
5.0
|
26.7
|
1.0
|
|
Chlorine binding site 7 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 7 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl501
b:24.8
occ:1.00
|
N
|
G:GLY428
|
3.1
|
26.3
|
1.0
|
|
NZ
|
H:LYS94
|
3.4
|
17.6
|
1.0
|
|
N
|
G:ARG408
|
3.4
|
22.9
|
1.0
|
|
CB
|
G:ARG408
|
3.5
|
21.1
|
1.0
|
|
CG
|
G:ARG408
|
3.6
|
23.0
|
1.0
|
|
C
|
G:GLY428
|
3.6
|
28.7
|
1.0
|
|
CG
|
G:GLU407
|
3.7
|
24.4
|
1.0
|
|
N
|
G:SER429
|
3.7
|
28.3
|
1.0
|
|
CA
|
G:GLY428
|
3.7
|
27.9
|
1.0
|
|
CD
|
G:ARG408
|
3.8
|
21.5
|
1.0
|
|
N
|
G:GLU407
|
3.8
|
21.0
|
1.0
|
|
CE
|
H:LYS94
|
3.9
|
19.0
|
1.0
|
|
CB
|
G:TYR406
|
4.0
|
22.3
|
1.0
|
|
CA
|
G:ARG408
|
4.0
|
23.8
|
1.0
|
|
O
|
G:GLY428
|
4.1
|
30.0
|
1.0
|
|
OD1
|
G:ASN427
|
4.1
|
26.3
|
1.0
|
|
O
|
G:PHE426
|
4.1
|
26.2
|
1.0
|
|
C
|
G:ASN427
|
4.1
|
25.0
|
1.0
|
|
CA
|
G:ASN427
|
4.2
|
25.2
|
1.0
|
|
CD
|
H:LYS94
|
4.3
|
20.4
|
1.0
|
|
CA
|
G:SER429
|
4.3
|
27.1
|
1.0
|
|
C
|
G:GLU407
|
4.4
|
23.3
|
1.0
|
|
CD2
|
G:TYR406
|
4.4
|
21.1
|
1.0
|
|
CA
|
G:TYR406
|
4.4
|
23.1
|
1.0
|
|
C
|
G:TYR406
|
4.4
|
21.2
|
1.0
|
|
CG
|
G:TYR406
|
4.5
|
20.5
|
1.0
|
|
CA
|
G:GLU407
|
4.5
|
22.0
|
1.0
|
|
OE2
|
G:GLU407
|
4.6
|
28.4
|
1.0
|
|
CD
|
G:GLU407
|
4.6
|
27.8
|
1.0
|
|
CB
|
G:GLU407
|
4.7
|
21.9
|
1.0
|
|
NE
|
G:ARG408
|
4.8
|
24.4
|
1.0
|
|
OG
|
G:SER432
|
4.9
|
28.5
|
1.0
|
|
Chlorine binding site 8 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 8 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl501
b:24.2
occ:1.00
|
N
|
H:GLY428
|
3.1
|
20.6
|
1.0
|
|
NZ
|
G:LYS94
|
3.2
|
25.6
|
1.0
|
|
N
|
H:ARG408
|
3.4
|
19.1
|
1.0
|
|
CB
|
H:ARG408
|
3.5
|
20.6
|
1.0
|
|
CG
|
H:GLU407
|
3.6
|
22.0
|
1.0
|
|
CG
|
H:ARG408
|
3.7
|
22.2
|
1.0
|
|
C
|
H:GLY428
|
3.7
|
24.3
|
1.0
|
|
N
|
H:SER429
|
3.7
|
25.0
|
1.0
|
|
N
|
H:GLU407
|
3.8
|
20.4
|
1.0
|
|
CE
|
G:LYS94
|
3.8
|
24.9
|
1.0
|
|
CA
|
H:GLY428
|
3.8
|
23.0
|
1.0
|
|
CB
|
H:TYR406
|
3.9
|
21.8
|
1.0
|
|
CD
|
H:ARG408
|
4.0
|
22.3
|
1.0
|
|
CA
|
H:ARG408
|
4.0
|
20.8
|
1.0
|
|
O
|
H:PHE426
|
4.0
|
19.9
|
1.0
|
|
OD1
|
H:ASN427
|
4.1
|
23.4
|
1.0
|
|
C
|
H:ASN427
|
4.1
|
20.6
|
1.0
|
|
CA
|
H:ASN427
|
4.2
|
21.8
|
1.0
|
|
O
|
H:GLY428
|
4.2
|
25.5
|
1.0
|
|
C
|
H:GLU407
|
4.3
|
20.5
|
1.0
|
|
C
|
H:TYR406
|
4.3
|
21.9
|
1.0
|
|
CA
|
H:TYR406
|
4.4
|
21.5
|
1.0
|
|
CA
|
H:SER429
|
4.4
|
26.4
|
1.0
|
|
CD
|
G:LYS94
|
4.4
|
24.1
|
1.0
|
|
CD2
|
H:TYR406
|
4.4
|
20.7
|
1.0
|
|
CA
|
H:GLU407
|
4.4
|
21.4
|
1.0
|
|
CG
|
H:TYR406
|
4.4
|
22.7
|
1.0
|
|
CD
|
H:GLU407
|
4.6
|
24.5
|
1.0
|
|
CB
|
H:GLU407
|
4.6
|
21.1
|
1.0
|
|
OE2
|
H:GLU407
|
4.6
|
23.8
|
1.0
|
|
OG
|
H:SER432
|
4.9
|
29.6
|
1.0
|
|
C
|
H:PHE426
|
5.0
|
21.7
|
1.0
|
|
Chlorine binding site 9 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 9 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Cl501
b:28.4
occ:1.00
|
NZ
|
J:LYS94
|
3.1
|
22.9
|
1.0
|
|
N
|
I:GLY428
|
3.2
|
25.1
|
1.0
|
|
N
|
I:ARG408
|
3.4
|
22.5
|
1.0
|
|
CB
|
I:ARG408
|
3.4
|
19.4
|
1.0
|
|
CG
|
I:GLU407
|
3.6
|
25.8
|
1.0
|
|
CG
|
I:ARG408
|
3.6
|
21.2
|
1.0
|
|
C
|
I:GLY428
|
3.7
|
25.2
|
1.0
|
|
N
|
I:SER429
|
3.7
|
23.6
|
1.0
|
|
CE
|
J:LYS94
|
3.8
|
23.6
|
1.0
|
|
CA
|
I:GLY428
|
3.8
|
23.6
|
1.0
|
|
N
|
I:GLU407
|
3.9
|
24.9
|
1.0
|
|
CD
|
I:ARG408
|
3.9
|
19.0
|
1.0
|
|
CA
|
I:ARG408
|
4.0
|
22.4
|
1.0
|
|
OD1
|
I:ASN427
|
4.0
|
22.0
|
1.0
|
|
CB
|
I:TYR406
|
4.1
|
24.4
|
1.0
|
|
O
|
I:GLY428
|
4.1
|
26.1
|
1.0
|
|
O
|
I:PHE426
|
4.1
|
24.5
|
1.0
|
|
CD
|
J:LYS94
|
4.2
|
24.7
|
1.0
|
|
C
|
I:ASN427
|
4.2
|
25.5
|
1.0
|
|
CA
|
I:ASN427
|
4.3
|
25.1
|
1.0
|
|
CA
|
I:SER429
|
4.3
|
25.0
|
1.0
|
|
C
|
I:GLU407
|
4.3
|
24.1
|
1.0
|
|
OE2
|
I:GLU407
|
4.5
|
28.1
|
1.0
|
|
C
|
I:TYR406
|
4.5
|
25.4
|
1.0
|
|
CA
|
I:GLU407
|
4.5
|
24.1
|
1.0
|
|
CD2
|
I:TYR406
|
4.5
|
24.2
|
1.0
|
|
CA
|
I:TYR406
|
4.5
|
24.4
|
1.0
|
|
CD
|
I:GLU407
|
4.5
|
26.0
|
1.0
|
|
CG
|
I:TYR406
|
4.6
|
24.6
|
1.0
|
|
CB
|
I:GLU407
|
4.6
|
25.3
|
1.0
|
|
OG
|
I:SER432
|
4.8
|
26.9
|
1.0
|
|
NE
|
I:ARG408
|
4.9
|
21.0
|
1.0
|
|
CB
|
I:SER429
|
5.0
|
25.0
|
1.0
|
|
CG
|
I:ASN427
|
5.0
|
24.6
|
1.0
|
|
Chlorine binding site 10 out
of 12 in 4e4j
Go back to
Chlorine Binding Sites List in 4e4j
Chlorine binding site 10 out
of 12 in the Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 10 of Crystal Structure of Arginine Deiminase From Mycoplasma Penetrans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Cl501
b:24.4
occ:1.00
|
NZ
|
I:LYS94
|
3.1
|
20.8
|
1.0
|
|
N
|
J:GLY428
|
3.1
|
25.4
|
1.0
|
|
N
|
J:ARG408
|
3.4
|
25.0
|
1.0
|
|
CB
|
J:ARG408
|
3.4
|
24.9
|
1.0
|
|
C
|
J:GLY428
|
3.6
|
27.4
|
1.0
|
|
CG
|
J:GLU407
|
3.6
|
28.4
|
1.0
|
|
N
|
J:SER429
|
3.7
|
28.5
|
1.0
|
|
CG
|
J:ARG408
|
3.7
|
23.8
|
1.0
|
|
CA
|
J:GLY428
|
3.8
|
26.0
|
1.0
|
|
CE
|
I:LYS94
|
3.8
|
23.9
|
1.0
|
|
N
|
J:GLU407
|
3.9
|
23.4
|
1.0
|
|
CD
|
J:ARG408
|
3.9
|
24.2
|
1.0
|
|
CA
|
J:ARG408
|
4.0
|
25.4
|
1.0
|
|
CB
|
J:TYR406
|
4.0
|
21.4
|
1.0
|
|
OD1
|
J:ASN427
|
4.0
|
26.0
|
1.0
|
|
O
|
J:GLY428
|
4.1
|
28.3
|
1.0
|
|
O
|
J:PHE426
|
4.2
|
22.4
|
1.0
|
|
C
|
J:ASN427
|
4.2
|
23.9
|
1.0
|
|
CA
|
J:SER429
|
4.3
|
28.5
|
1.0
|
|
CD
|
I:LYS94
|
4.3
|
24.7
|
1.0
|
|
CA
|
J:ASN427
|
4.3
|
23.6
|
1.0
|
|
C
|
J:GLU407
|
4.4
|
24.5
|
1.0
|
|
C
|
J:TYR406
|
4.4
|
23.7
|
1.0
|
|
CA
|
J:TYR406
|
4.4
|
22.8
|
1.0
|
|
CD2
|
J:TYR406
|
4.5
|
20.7
|
1.0
|
|
CA
|
J:GLU407
|
4.5
|
24.5
|
1.0
|
|
CG
|
J:TYR406
|
4.5
|
22.4
|
1.0
|
|
CD
|
J:GLU407
|
4.5
|
31.2
|
1.0
|
|
OE2
|
J:GLU407
|
4.6
|
31.2
|
1.0
|
|
CB
|
J:GLU407
|
4.6
|
25.4
|
1.0
|
|
NE
|
J:ARG408
|
4.9
|
25.9
|
1.0
|
|
Reference:
P.Gallego,
R.Planell,
J.Benach,
E.Querol,
J.A.Perez-Pons,
D.Reverter.
Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma Penetrans. Plos One V. 7 47886 2012.
ISSN: ESSN 1932-6203
PubMed: 23082227
DOI: 10.1371/JOURNAL.PONE.0047886
Page generated: Fri Jul 11 14:38:24 2025
|
