Chlorine in PDB 7u56: Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
Enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
All present enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp:
6.3.2.4;
Protein crystallography data
The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56
was solved by
Seattle Structural Genomics Center For Infectious Disease (Ssgcid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.13 /
1.85
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.35,
115.42,
68.48,
90,
90,
90
|
R / Rfree (%)
|
16.2 /
19.9
|
Other elements in 7u56:
The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
(pdb code 7u56). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 7u56
Go back to
Chlorine Binding Sites List in 7u56
Chlorine binding site 1 out
of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl407
b:23.7
occ:1.00
|
O
|
A:HOH685
|
2.8
|
30.1
|
1.0
|
NH1
|
A:ARG311
|
3.1
|
23.2
|
1.0
|
N
|
A:TYR339
|
3.2
|
15.4
|
1.0
|
N
|
A:GLY332
|
3.3
|
25.9
|
1.0
|
O
|
A:GLY332
|
3.5
|
29.6
|
1.0
|
CB
|
A:TYR339
|
3.6
|
15.6
|
1.0
|
N
|
A:MET338
|
3.7
|
18.1
|
1.0
|
CB
|
A:PRO331
|
3.7
|
22.5
|
1.0
|
CB
|
A:MET338
|
3.8
|
16.9
|
1.0
|
CD
|
A:ARG311
|
3.8
|
16.2
|
1.0
|
CA
|
A:GLY332
|
3.8
|
27.7
|
1.0
|
CA
|
A:TYR339
|
4.0
|
15.2
|
1.0
|
CA
|
A:MET338
|
4.0
|
16.7
|
1.0
|
C
|
A:MET338
|
4.1
|
18.5
|
1.0
|
C
|
A:PRO331
|
4.1
|
21.2
|
1.0
|
C
|
A:GLY332
|
4.1
|
23.2
|
1.0
|
CB
|
A:SER337
|
4.1
|
23.3
|
1.0
|
CA
|
A:PRO331
|
4.1
|
22.3
|
1.0
|
O
|
A:HOH673
|
4.2
|
35.8
|
1.0
|
CZ
|
A:ARG311
|
4.2
|
23.8
|
1.0
|
O
|
A:HOH524
|
4.3
|
22.9
|
1.0
|
C
|
A:SER337
|
4.4
|
19.4
|
1.0
|
NE
|
A:ARG311
|
4.5
|
17.0
|
1.0
|
O
|
A:HOH657
|
4.5
|
31.7
|
1.0
|
CA
|
A:SER337
|
4.7
|
23.5
|
1.0
|
CG
|
A:MET338
|
4.9
|
16.0
|
1.0
|
CG
|
A:ARG311
|
4.9
|
12.8
|
1.0
|
OG
|
A:SER337
|
4.9
|
21.3
|
1.0
|
CD
|
A:PRO340
|
4.9
|
20.8
|
1.0
|
CG
|
A:TYR339
|
4.9
|
15.0
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 7u56
Go back to
Chlorine Binding Sites List in 7u56
Chlorine binding site 2 out
of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl408
b:26.4
occ:1.00
|
N
|
A:ASN247
|
3.1
|
14.4
|
1.0
|
O2
|
A:EDO405
|
3.1
|
35.4
|
1.0
|
O
|
A:HOH699
|
3.1
|
25.8
|
1.0
|
N
|
A:HIS249
|
3.2
|
16.7
|
1.0
|
O
|
A:HIS249
|
3.5
|
22.6
|
1.0
|
N
|
A:ASP248
|
3.6
|
18.3
|
1.0
|
C
|
A:HIS249
|
3.7
|
21.6
|
1.0
|
CA
|
A:HIS249
|
3.7
|
19.0
|
1.0
|
C
|
A:ASN247
|
3.8
|
17.8
|
1.0
|
CB
|
A:HIS249
|
3.8
|
20.7
|
1.0
|
O
|
A:HOH516
|
3.8
|
37.7
|
1.0
|
CA
|
A:ASN247
|
3.9
|
17.4
|
1.0
|
CA
|
A:GLY246
|
3.9
|
15.3
|
1.0
|
C2
|
A:EDO405
|
3.9
|
36.0
|
1.0
|
C
|
A:GLY246
|
4.0
|
14.6
|
1.0
|
CD2
|
A:LEU360
|
4.1
|
21.3
|
1.0
|
CB
|
A:ASN247
|
4.2
|
15.2
|
1.0
|
C
|
A:ASP248
|
4.2
|
21.7
|
1.0
|
CA
|
A:ASP248
|
4.4
|
21.7
|
1.0
|
N
|
A:PRO250
|
4.5
|
20.0
|
1.0
|
NH2
|
A:ARG356
|
4.5
|
34.0
|
1.0
|
O
|
A:ASN247
|
4.6
|
18.7
|
1.0
|
CG
|
A:HIS249
|
4.6
|
27.0
|
1.0
|
CD2
|
A:HIS249
|
4.6
|
27.3
|
1.0
|
O
|
A:HOH565
|
4.9
|
26.9
|
1.0
|
CB
|
A:ASP248
|
5.0
|
19.5
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 7u56
Go back to
Chlorine Binding Sites List in 7u56
Chlorine binding site 3 out
of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl407
b:21.2
occ:1.00
|
O
|
B:HOH785
|
2.9
|
34.5
|
1.0
|
NH1
|
B:ARG311
|
3.1
|
22.3
|
1.0
|
N
|
B:GLY332
|
3.2
|
23.0
|
1.0
|
N
|
B:TYR339
|
3.2
|
11.7
|
1.0
|
CB
|
B:PRO331
|
3.6
|
19.6
|
1.0
|
CB
|
B:TYR339
|
3.6
|
12.7
|
1.0
|
N
|
B:MET338
|
3.7
|
17.0
|
1.0
|
O
|
B:HOH792
|
3.8
|
38.5
|
1.0
|
CD
|
B:ARG311
|
3.8
|
14.4
|
1.0
|
CB
|
B:MET338
|
3.9
|
16.1
|
1.0
|
O
|
B:GLY332
|
3.9
|
21.5
|
1.0
|
CA
|
B:GLY332
|
4.0
|
21.9
|
1.0
|
CA
|
B:PRO331
|
4.0
|
18.0
|
1.0
|
CA
|
B:TYR339
|
4.0
|
13.8
|
1.0
|
C
|
B:PRO331
|
4.0
|
18.4
|
1.0
|
CA
|
B:MET338
|
4.1
|
16.1
|
1.0
|
C
|
B:MET338
|
4.1
|
14.2
|
1.0
|
CZ
|
B:ARG311
|
4.2
|
22.6
|
1.0
|
CB
|
B:SER337
|
4.3
|
21.6
|
1.0
|
C
|
B:GLY332
|
4.4
|
20.7
|
1.0
|
NE
|
B:ARG311
|
4.4
|
16.9
|
1.0
|
C
|
B:SER337
|
4.4
|
20.6
|
1.0
|
O
|
B:HOH551
|
4.5
|
24.7
|
1.0
|
CA
|
B:SER337
|
4.7
|
25.5
|
1.0
|
CG
|
B:ARG311
|
4.9
|
12.4
|
1.0
|
CG
|
B:TYR339
|
4.9
|
13.6
|
1.0
|
CD
|
B:PRO340
|
5.0
|
17.2
|
1.0
|
CG
|
B:PRO331
|
5.0
|
18.4
|
1.0
|
CG
|
B:MET338
|
5.0
|
18.5
|
1.0
|
OG
|
B:SER337
|
5.0
|
22.9
|
1.0
|
CB
|
B:ARG311
|
5.0
|
11.9
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 7u56
Go back to
Chlorine Binding Sites List in 7u56
Chlorine binding site 4 out
of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp
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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl408
b:21.7
occ:1.00
|
O1
|
B:EDO405
|
3.0
|
30.5
|
1.0
|
N
|
B:ASN247
|
3.0
|
12.5
|
1.0
|
N
|
B:HIS249
|
3.2
|
14.2
|
1.0
|
O
|
B:HOH748
|
3.3
|
23.6
|
1.0
|
O
|
B:HOH529
|
3.4
|
29.9
|
1.0
|
O
|
B:HIS249
|
3.6
|
15.1
|
1.0
|
N
|
B:ASP248
|
3.6
|
12.5
|
1.0
|
C
|
B:HIS249
|
3.7
|
16.5
|
1.0
|
CA
|
B:HIS249
|
3.7
|
19.1
|
1.0
|
O
|
B:HOH507
|
3.7
|
32.3
|
1.0
|
CA
|
B:ASN247
|
3.8
|
13.5
|
1.0
|
C
|
B:ASN247
|
3.8
|
16.6
|
1.0
|
CA
|
B:GLY246
|
3.9
|
11.4
|
1.0
|
CB
|
B:HIS249
|
3.9
|
19.2
|
1.0
|
C
|
B:GLY246
|
3.9
|
13.0
|
1.0
|
C1
|
B:EDO405
|
4.0
|
26.1
|
1.0
|
CB
|
B:ASN247
|
4.1
|
12.6
|
1.0
|
CD2
|
B:LEU360
|
4.1
|
15.2
|
1.0
|
C
|
B:ASP248
|
4.2
|
16.5
|
1.0
|
NH2
|
B:ARG356
|
4.4
|
26.7
|
1.0
|
N
|
B:PRO250
|
4.4
|
16.4
|
1.0
|
CA
|
B:ASP248
|
4.5
|
17.4
|
1.0
|
O
|
B:ASN247
|
4.6
|
15.8
|
1.0
|
ND1
|
B:HIS249
|
4.6
|
28.7
|
1.0
|
CG
|
B:HIS249
|
4.8
|
27.8
|
1.0
|
O
|
B:HOH577
|
4.9
|
27.5
|
1.0
|
O
|
B:HOH555
|
5.0
|
21.4
|
1.0
|
CA
|
B:PRO250
|
5.0
|
14.3
|
1.0
|
CG
|
B:ASN247
|
5.0
|
13.7
|
1.0
|
|
Reference:
J.Abendroth,
M.J.Bolejack,
D.D.Lorimer,
P.S.Horanyi,
T.E.Edwards.
Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp To Be Published.
Page generated: Tue Jul 30 04:57:16 2024
|