Chlorine in PDB 2a7d: On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
Enzymatic activity of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
All present enzymatic activity of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength:
3.2.1.17;
Protein crystallography data
The structure of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength, PDB code: 2a7d
was solved by
C.Mueller-Dieckmann,
S.Panjikar,
P.A.Tucker,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.66
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.050,
77.050,
37.210,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
20.2
|
Other elements in 2a7d:
The structure of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
(pdb code 2a7d). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength, PDB code: 2a7d:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 1 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl200
b:17.4
occ:0.68
|
OH
|
A:TYR23
|
3.0
|
16.3
|
1.0
|
O
|
A:HOH371
|
3.0
|
48.1
|
1.0
|
O
|
A:HOH317
|
3.3
|
21.1
|
1.0
|
CZ
|
A:TYR23
|
3.6
|
16.1
|
1.0
|
CE2
|
A:TYR23
|
3.7
|
16.2
|
1.0
|
CA
|
A:GLY104
|
4.2
|
17.3
|
1.0
|
O
|
A:ARG21
|
4.5
|
19.1
|
1.0
|
CE1
|
A:TYR23
|
4.8
|
14.4
|
1.0
|
N
|
A:GLY104
|
4.8
|
17.2
|
1.0
|
CD2
|
A:TYR23
|
5.0
|
13.8
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 2 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:17.1
occ:0.58
|
OG
|
A:SER24
|
3.0
|
22.1
|
1.0
|
N
|
A:GLY26
|
3.1
|
16.8
|
1.0
|
CA
|
A:GLY26
|
3.4
|
15.7
|
1.0
|
CB
|
A:SER24
|
3.5
|
18.9
|
1.0
|
CA
|
A:GLN121
|
3.6
|
24.4
|
1.0
|
CD1
|
A:ILE124
|
3.7
|
34.6
|
1.0
|
N
|
A:GLN121
|
3.9
|
24.2
|
1.0
|
CB
|
A:GLN121
|
4.1
|
26.2
|
1.0
|
N
|
A:LEU25
|
4.2
|
17.1
|
1.0
|
CG1
|
A:ILE124
|
4.2
|
26.9
|
1.0
|
CG2
|
A:VAL120
|
4.2
|
23.9
|
1.0
|
C
|
A:SER24
|
4.2
|
17.5
|
1.0
|
C
|
A:LEU25
|
4.2
|
16.2
|
1.0
|
C
|
A:VAL120
|
4.2
|
22.8
|
1.0
|
CG
|
A:GLN121
|
4.3
|
33.2
|
1.0
|
O
|
A:VAL120
|
4.3
|
23.2
|
1.0
|
CA
|
A:SER24
|
4.5
|
17.3
|
1.0
|
C
|
A:GLY26
|
4.5
|
15.5
|
1.0
|
N
|
A:ASN27
|
4.6
|
15.7
|
1.0
|
O
|
A:SER24
|
4.6
|
17.6
|
1.0
|
CA
|
A:LEU25
|
4.6
|
16.5
|
1.0
|
C
|
A:GLN121
|
4.9
|
22.7
|
1.0
|
CB
|
A:LEU25
|
5.0
|
18.0
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 3 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:16.3
occ:0.52
|
O
|
A:HOH361
|
3.0
|
39.1
|
1.0
|
O
|
A:HOH304
|
3.0
|
17.1
|
1.0
|
N
|
A:THR69
|
3.1
|
20.7
|
1.0
|
O
|
A:THR69
|
3.3
|
20.7
|
1.0
|
O
|
A:HOH389
|
3.3
|
32.3
|
1.0
|
N
|
A:ARG68
|
3.5
|
21.0
|
1.0
|
C
|
A:THR69
|
3.6
|
22.1
|
1.0
|
C
|
A:GLY67
|
3.6
|
22.1
|
1.0
|
OD1
|
A:ASN65
|
3.6
|
19.7
|
1.0
|
CA
|
A:GLY67
|
3.7
|
19.3
|
1.0
|
N
|
A:GLY67
|
3.7
|
18.3
|
1.0
|
CA
|
A:THR69
|
3.8
|
22.3
|
1.0
|
O
|
A:HOH326
|
4.0
|
20.6
|
1.0
|
C
|
A:ARG68
|
4.1
|
22.4
|
1.0
|
CB
|
A:SER72
|
4.1
|
27.2
|
1.0
|
CB
|
A:THR69
|
4.2
|
21.9
|
1.0
|
CA
|
A:ARG68
|
4.2
|
22.2
|
1.0
|
OD1
|
A:ASP66
|
4.2
|
16.1
|
1.0
|
O
|
A:GLY67
|
4.2
|
24.3
|
1.0
|
N
|
A:PRO70
|
4.3
|
25.3
|
1.0
|
OG
|
A:SER72
|
4.6
|
40.3
|
1.0
|
NA
|
A:NA208
|
4.7
|
18.8
|
1.0
|
OG1
|
A:THR69
|
4.7
|
19.5
|
1.0
|
C
|
A:ASP66
|
4.7
|
17.2
|
1.0
|
CG
|
A:ASN65
|
4.8
|
20.1
|
1.0
|
N
|
A:ASP66
|
4.8
|
15.7
|
1.0
|
CA
|
A:PRO70
|
4.9
|
27.8
|
1.0
|
O
|
A:HOH330
|
4.9
|
20.8
|
0.5
|
|
Chlorine binding site 4 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 4 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
|
Chlorine binding site 5 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 5 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl204
b:22.3
occ:0.37
|
O
|
A:HOH384
|
3.2
|
37.0
|
1.0
|
CE2
|
A:PHE38
|
3.6
|
20.4
|
1.0
|
NZ
|
A:LYS33
|
3.8
|
32.2
|
1.0
|
CZ3
|
A:TRP123
|
4.0
|
24.1
|
1.0
|
CD
|
A:ARG5
|
4.1
|
28.6
|
1.0
|
CE
|
A:LYS33
|
4.2
|
28.1
|
1.0
|
CB
|
A:ARG5
|
4.2
|
22.4
|
1.0
|
CD
|
A:LYS33
|
4.3
|
21.7
|
1.0
|
CZ
|
A:PHE38
|
4.4
|
17.4
|
1.0
|
NE
|
A:ARG5
|
4.5
|
30.7
|
1.0
|
CD2
|
A:PHE38
|
4.6
|
20.3
|
1.0
|
CG
|
A:ARG5
|
4.6
|
23.7
|
1.0
|
CE3
|
A:TRP123
|
4.8
|
22.2
|
1.0
|
CH2
|
A:TRP123
|
4.9
|
26.5
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 6 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl205
b:14.0
occ:0.34
|
ND2
|
A:ASN65
|
2.9
|
27.8
|
1.0
|
CA
|
A:GLY67
|
3.4
|
19.3
|
1.0
|
N
|
A:GLY67
|
3.8
|
18.3
|
1.0
|
CG
|
A:ASN65
|
3.9
|
20.1
|
1.0
|
OD1
|
A:ASN65
|
4.1
|
19.7
|
1.0
|
C
|
A:ASP66
|
4.5
|
17.2
|
1.0
|
O
|
A:HOH382
|
4.7
|
40.3
|
1.0
|
C
|
A:GLY67
|
4.8
|
22.1
|
1.0
|
O
|
A:ASP66
|
4.8
|
18.9
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 7 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl206
b:19.3
occ:0.31
|
N
|
A:ASN74
|
3.0
|
20.7
|
1.0
|
NE
|
A:ARG73
|
3.4
|
58.0
|
1.0
|
CB
|
A:ARG73
|
3.5
|
25.3
|
1.0
|
C
|
A:ASN74
|
3.6
|
18.4
|
1.0
|
O
|
A:ASN74
|
3.7
|
20.3
|
1.0
|
CA
|
A:ARG73
|
3.8
|
24.1
|
1.0
|
CA
|
A:ASN74
|
3.8
|
19.4
|
1.0
|
CD2
|
A:LEU75
|
3.9
|
28.6
|
1.0
|
C
|
A:ARG73
|
3.9
|
22.3
|
1.0
|
N
|
A:LEU75
|
4.0
|
20.0
|
1.0
|
NH2
|
A:ARG73
|
4.1
|
65.5
|
1.0
|
CZ
|
A:ARG73
|
4.1
|
65.1
|
1.0
|
CD
|
A:ARG73
|
4.1
|
47.3
|
1.0
|
CB
|
A:ASN74
|
4.3
|
18.5
|
1.0
|
CA
|
A:LEU75
|
4.4
|
21.6
|
1.0
|
CG
|
A:ARG73
|
4.4
|
30.8
|
1.0
|
CG
|
A:LEU75
|
4.5
|
23.2
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 2a7d
Go back to
Chlorine Binding Sites List in 2a7d
Chlorine binding site 8 out
of 8 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl207
b:18.2
occ:0.28
|
O
|
A:HOH322
|
1.8
|
27.1
|
1.0
|
NE1
|
A:TRP108
|
3.5
|
16.9
|
1.0
|
CE2
|
A:TRP108
|
3.7
|
15.2
|
1.0
|
CD1
|
A:TRP108
|
3.8
|
14.5
|
1.0
|
O
|
A:ALA107
|
3.9
|
20.1
|
1.0
|
O
|
A:GLN57
|
4.0
|
16.9
|
1.0
|
O
|
A:HOH338
|
4.0
|
34.5
|
1.0
|
CD1
|
A:ILE98
|
4.1
|
17.1
|
1.0
|
CD2
|
A:TRP108
|
4.2
|
15.5
|
1.0
|
CG
|
A:TRP108
|
4.2
|
16.2
|
1.0
|
CZ2
|
A:TRP108
|
4.3
|
16.6
|
1.0
|
C
|
A:ALA107
|
4.3
|
19.1
|
1.0
|
CA
|
A:ILE58
|
4.4
|
15.0
|
1.0
|
CG2
|
A:ILE98
|
4.4
|
18.1
|
1.0
|
CB
|
A:ALA107
|
4.5
|
17.9
|
1.0
|
O
|
A:HOH350
|
4.5
|
31.5
|
1.0
|
O
|
A:LEU56
|
4.6
|
16.1
|
1.0
|
N
|
A:ASN59
|
4.6
|
16.1
|
1.0
|
N
|
A:TRP108
|
4.7
|
17.2
|
1.0
|
C
|
A:GLN57
|
4.7
|
14.7
|
1.0
|
CA
|
A:TRP108
|
4.7
|
16.1
|
1.0
|
CG1
|
A:ILE58
|
4.7
|
18.7
|
1.0
|
NE1
|
A:TRP63
|
4.8
|
19.5
|
1.0
|
N
|
A:ILE58
|
4.9
|
14.4
|
1.0
|
|
Reference:
C.Mueller-Dieckmann,
S.Panjikar,
P.A.Tucker,
M.S.Weiss.
On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part III. the Optimal Data-Collection Wavelength. Acta Crystallogr.,Sect.D V. 61 1263 2005.
ISSN: ISSN 0907-4449
PubMed: 16131760
DOI: 10.1107/S0907444905021475
Page generated: Sat Jul 20 05:07:06 2024
|