Chlorine in PDB 3zzh: Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
Enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
All present enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine:
2.7.2.8;
Protein crystallography data
The structure of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine, PDB code: 3zzh
was solved by
S.De Cima,
F.Gil-Ortiz,
M.Crabeel,
I.Fita,
V.Rubio,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.489,
99.596,
189.238,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.037 /
21.544
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
(pdb code 3zzh). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine, PDB code: 3zzh:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 3zzh
Go back to
Chlorine Binding Sites List in 3zzh
Chlorine binding site 1 out
of 5 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
 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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1359
b:25.9
occ:1.00
|
NZ
|
A:LYS283
|
3.0
|
16.9
|
1.0
|
O
|
A:HOH2120
|
3.3
|
6.5
|
1.0
|
O
|
A:GLY273
|
3.5
|
14.2
|
1.0
|
N
|
A:GLY345
|
3.5
|
21.6
|
1.0
|
CA
|
A:GLY345
|
4.0
|
19.7
|
1.0
|
C
|
A:GLY273
|
4.3
|
13.2
|
1.0
|
CA
|
A:GLY273
|
4.3
|
14.0
|
1.0
|
CE
|
A:LYS283
|
4.4
|
17.0
|
1.0
|
C
|
A:ALA344
|
4.5
|
23.3
|
1.0
|
CA
|
A:ALA344
|
4.6
|
25.8
|
1.0
|
OD2
|
A:ASP333
|
4.6
|
24.2
|
1.0
|
CG
|
A:LYS283
|
4.6
|
16.4
|
1.0
|
O
|
A:LYS272
|
4.7
|
15.6
|
1.0
|
CB
|
A:ALA344
|
4.7
|
26.0
|
1.0
|
O
|
A:HOH2123
|
4.8
|
2.9
|
1.0
|
CD
|
A:LYS283
|
4.8
|
16.1
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 3zzh
Go back to
Chlorine Binding Sites List in 3zzh
Chlorine binding site 2 out
of 5 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
 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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl1367
b:21.2
occ:1.00
|
O
|
B:HOH2040
|
2.9
|
4.2
|
1.0
|
O
|
B:HOH2142
|
3.0
|
11.6
|
1.0
|
N
|
B:GLU271
|
3.4
|
11.4
|
1.0
|
CA
|
B:ASN270
|
3.6
|
10.2
|
1.0
|
CG
|
B:GLU271
|
3.7
|
12.7
|
1.0
|
CB
|
B:ASN270
|
3.8
|
10.7
|
1.0
|
O
|
B:HOH2110
|
3.9
|
8.7
|
1.0
|
C
|
B:ASN270
|
4.0
|
10.7
|
1.0
|
CB
|
B:ALA107
|
4.0
|
9.8
|
1.0
|
CA
|
B:GLY105
|
4.2
|
9.3
|
1.0
|
CB
|
B:GLU271
|
4.2
|
12.7
|
1.0
|
CG1
|
B:ILE108
|
4.3
|
9.7
|
1.0
|
CA
|
B:GLU271
|
4.4
|
12.2
|
1.0
|
CD
|
B:GLU271
|
4.4
|
14.0
|
1.0
|
O
|
B:LEU269
|
4.5
|
9.1
|
1.0
|
O
|
B:HOH2037
|
4.6
|
7.2
|
1.0
|
C
|
B:GLY105
|
4.6
|
9.0
|
1.0
|
CD1
|
B:ILE108
|
4.7
|
10.3
|
1.0
|
N
|
B:ALA107
|
4.7
|
9.1
|
1.0
|
OE1
|
B:GLU271
|
4.8
|
15.7
|
1.0
|
N
|
B:ILE108
|
4.8
|
9.0
|
1.0
|
C2
|
B:EDO1364
|
4.8
|
32.7
|
1.0
|
O2
|
B:EDO1364
|
4.8
|
32.9
|
1.0
|
CA
|
B:ALA107
|
4.8
|
9.4
|
1.0
|
O
|
B:GLY105
|
4.8
|
8.6
|
1.0
|
N
|
B:ASN270
|
4.8
|
9.7
|
1.0
|
O
|
B:HOH2141
|
4.9
|
26.5
|
1.0
|
C2
|
B:EDO1359
|
4.9
|
39.3
|
1.0
|
O2
|
B:EDO1359
|
4.9
|
39.0
|
1.0
|
OE2
|
B:GLU271
|
5.0
|
14.0
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 3zzh
Go back to
Chlorine Binding Sites List in 3zzh
Chlorine binding site 3 out
of 5 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
 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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl1360
b:36.9
occ:1.00
|
ND2
|
C:ASN141
|
3.0
|
13.8
|
1.0
|
CA
|
C:PRO138
|
3.8
|
14.1
|
1.0
|
CG
|
C:ASN141
|
4.0
|
14.0
|
1.0
|
CB
|
C:ASN141
|
4.1
|
14.2
|
1.0
|
CB
|
C:PRO138
|
4.1
|
14.5
|
1.0
|
CG
|
C:PRO138
|
4.5
|
14.5
|
1.0
|
N
|
C:PRO138
|
4.5
|
13.4
|
1.0
|
O
|
C:PRO138
|
4.6
|
13.7
|
1.0
|
C
|
C:PRO138
|
4.7
|
13.7
|
1.0
|
O
|
C:GLY137
|
4.8
|
13.6
|
1.0
|
C
|
C:GLY137
|
5.0
|
13.1
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 3zzh
Go back to
Chlorine Binding Sites List in 3zzh
Chlorine binding site 4 out
of 5 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
 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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl1367
b:19.2
occ:1.00
|
O
|
D:HOH2137
|
2.9
|
16.1
|
1.0
|
O
|
D:HOH2030
|
2.9
|
3.8
|
1.0
|
O
|
D:HOH2106
|
3.1
|
21.5
|
1.0
|
N
|
D:GLU271
|
3.4
|
11.4
|
1.0
|
CA
|
D:ASN270
|
3.6
|
10.2
|
1.0
|
CG
|
D:GLU271
|
3.7
|
13.7
|
1.0
|
CB
|
D:ASN270
|
3.8
|
10.6
|
1.0
|
O
|
D:HOH2103
|
3.9
|
8.0
|
1.0
|
C
|
D:ASN270
|
3.9
|
10.5
|
1.0
|
CA
|
D:GLY105
|
4.0
|
8.9
|
1.0
|
CB
|
D:ALA107
|
4.1
|
9.9
|
1.0
|
CB
|
D:GLU271
|
4.2
|
12.7
|
1.0
|
O
|
D:HOH2029
|
4.3
|
4.7
|
1.0
|
CG1
|
D:ILE108
|
4.3
|
8.8
|
1.0
|
CA
|
D:GLU271
|
4.4
|
12.4
|
1.0
|
CD1
|
D:ILE108
|
4.4
|
8.9
|
1.0
|
CD
|
D:GLU271
|
4.5
|
15.4
|
1.0
|
C
|
D:GLY105
|
4.5
|
8.8
|
1.0
|
O
|
D:LEU269
|
4.5
|
9.4
|
1.0
|
O
|
D:HOH2138
|
4.5
|
30.9
|
1.0
|
N
|
D:ALA107
|
4.7
|
9.1
|
1.0
|
O
|
D:GLY105
|
4.7
|
8.8
|
1.0
|
N
|
D:ILE108
|
4.8
|
8.9
|
1.0
|
O
|
D:HOH2101
|
4.8
|
18.6
|
1.0
|
N
|
D:ASN270
|
4.8
|
9.8
|
1.0
|
CA
|
D:ALA107
|
4.9
|
9.6
|
1.0
|
C1
|
D:EDO1364
|
4.9
|
35.5
|
1.0
|
OE1
|
D:GLU271
|
4.9
|
17.0
|
1.0
|
N
|
D:GLY105
|
4.9
|
8.8
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 3zzh
Go back to
Chlorine Binding Sites List in 3zzh
Chlorine binding site 5 out
of 5 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine
 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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase in Complex with Its Feed-Back Inhibitor L-Arginine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl1368
b:29.2
occ:1.00
|
O
|
D:HOH2068
|
3.2
|
20.2
|
1.0
|
NH2
|
D:ARG169
|
3.2
|
14.2
|
1.0
|
OG
|
C:SER195
|
3.2
|
15.1
|
1.0
|
NE
|
D:ARG169
|
3.5
|
14.2
|
1.0
|
CE
|
D:MET245
|
3.6
|
21.8
|
1.0
|
CZ
|
D:ARG169
|
3.8
|
14.8
|
1.0
|
N
|
C:GLY196
|
3.8
|
14.9
|
1.0
|
CB
|
C:SER195
|
3.8
|
15.0
|
1.0
|
CA
|
C:GLY196
|
3.9
|
14.9
|
1.0
|
SD
|
D:MET245
|
3.9
|
20.8
|
1.0
|
C
|
C:SER195
|
4.3
|
14.6
|
1.0
|
O
|
D:HOH2079
|
4.3
|
15.3
|
1.0
|
CB
|
D:ARG169
|
4.7
|
11.8
|
1.0
|
CD
|
D:ARG169
|
4.7
|
13.4
|
1.0
|
CA
|
C:SER195
|
4.7
|
14.3
|
1.0
|
CG
|
D:ARG169
|
4.8
|
12.2
|
1.0
|
O
|
C:SER195
|
4.9
|
14.8
|
1.0
|
|
Reference:
S.De Cima,
F.Gil-Ortiz,
M.Crabeel,
I.Fita,
V.Rubio.
Insight on An Arginine Synthesis Metabolon From the Tetrameric Structure of Yeast Acetylglutamate Kinase Plos One V. 7 34734 2012.
ISSN: ISSN 1932-6203
PubMed: 22529931
DOI: 10.1371/JOURNAL.PONE.0034734
Page generated: Sun Jul 21 08:41:05 2024
|