Sodium in PDB 7ug3: Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
Enzymatic activity of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
All present enzymatic activity of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae:
2.6.1.62;
Protein crystallography data
The structure of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae, PDB code: 7ug3
was solved by
Seattle Structural Genomics Center For Infectious Disease,
Seattlestructural 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)
|
45.42 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.07,
90.83,
103.86,
90,
93.87,
90
|
R / Rfree (%)
|
22.5 /
26
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
(pdb code 7ug3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae, PDB code: 7ug3:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7ug3
Go back to
Sodium Binding Sites List in 7ug3
Sodium binding site 1 out
of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:35.7
occ:1.00
|
O
|
A:VAL96
|
2.3
|
35.9
|
1.0
|
OG1
|
A:THR99
|
2.3
|
34.5
|
1.0
|
O
|
A:LEU103
|
2.4
|
36.1
|
1.0
|
O
|
A:PRO100
|
2.4
|
39.9
|
1.0
|
O
|
A:HOH762
|
2.6
|
37.2
|
1.0
|
O
|
A:THR99
|
2.7
|
36.5
|
1.0
|
C
|
A:THR99
|
3.1
|
35.8
|
1.0
|
C
|
A:VAL96
|
3.4
|
35.0
|
1.0
|
C
|
A:PRO100
|
3.4
|
41.1
|
1.0
|
CB
|
A:THR99
|
3.4
|
34.5
|
1.0
|
C
|
A:LEU103
|
3.5
|
36.2
|
1.0
|
CA
|
A:THR99
|
3.7
|
35.1
|
1.0
|
CA
|
A:VAL96
|
3.7
|
34.6
|
1.0
|
N
|
A:PRO100
|
3.9
|
40.1
|
1.0
|
N
|
A:THR99
|
3.9
|
35.2
|
1.0
|
CB
|
A:LEU103
|
4.1
|
36.1
|
1.0
|
CG1
|
A:VAL96
|
4.1
|
35.6
|
1.0
|
CA
|
A:LEU103
|
4.1
|
36.6
|
1.0
|
N
|
A:ALA101
|
4.2
|
43.0
|
1.0
|
N
|
A:LEU103
|
4.2
|
36.6
|
1.0
|
CA
|
A:PRO100
|
4.2
|
42.1
|
1.0
|
CA
|
A:ALA101
|
4.2
|
44.5
|
1.0
|
O
|
A:LEU95
|
4.3
|
33.2
|
1.0
|
C
|
A:ALA101
|
4.4
|
44.4
|
1.0
|
O
|
A:ALA101
|
4.5
|
44.3
|
1.0
|
CB
|
A:VAL96
|
4.6
|
34.9
|
1.0
|
N
|
A:ALA97
|
4.6
|
32.5
|
1.0
|
N
|
A:GLU104
|
4.6
|
37.9
|
1.0
|
CG2
|
A:THR99
|
4.7
|
33.2
|
1.0
|
CA
|
A:GLU104
|
4.8
|
37.8
|
1.0
|
N
|
A:VAL96
|
4.9
|
33.7
|
1.0
|
C
|
A:ALA97
|
4.9
|
34.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7ug3
Go back to
Sodium Binding Sites List in 7ug3
Sodium binding site 2 out
of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:35.7
occ:1.00
|
O
|
B:LEU103
|
2.3
|
37.4
|
1.0
|
O
|
B:VAL96
|
2.4
|
33.5
|
1.0
|
OG1
|
B:THR99
|
2.5
|
33.0
|
1.0
|
O
|
B:HOH805
|
2.5
|
36.1
|
1.0
|
O
|
B:PRO100
|
2.5
|
42.8
|
1.0
|
O
|
B:THR99
|
2.7
|
34.4
|
1.0
|
C
|
B:THR99
|
3.2
|
35.0
|
1.0
|
C
|
B:PRO100
|
3.4
|
43.5
|
1.0
|
C
|
B:VAL96
|
3.4
|
32.9
|
1.0
|
C
|
B:LEU103
|
3.4
|
37.6
|
1.0
|
CB
|
B:THR99
|
3.4
|
34.0
|
1.0
|
CA
|
B:THR99
|
3.7
|
34.6
|
1.0
|
CA
|
B:VAL96
|
3.7
|
32.4
|
1.0
|
N
|
B:PRO100
|
3.9
|
42.6
|
1.0
|
N
|
B:THR99
|
4.0
|
33.7
|
1.0
|
CG1
|
B:VAL96
|
4.1
|
33.5
|
1.0
|
CB
|
B:LEU103
|
4.1
|
37.1
|
1.0
|
CA
|
B:LEU103
|
4.1
|
37.8
|
1.0
|
N
|
B:LEU103
|
4.1
|
38.0
|
1.0
|
N
|
B:ALA101
|
4.2
|
37.6
|
1.0
|
CA
|
B:PRO100
|
4.2
|
43.5
|
1.0
|
CA
|
B:ALA101
|
4.3
|
38.4
|
1.0
|
O
|
B:ALA101
|
4.3
|
37.7
|
1.0
|
C
|
B:ALA101
|
4.4
|
38.7
|
1.0
|
O
|
B:HOH838
|
4.4
|
47.8
|
1.0
|
O
|
B:LEU95
|
4.4
|
30.4
|
1.0
|
N
|
B:GLU104
|
4.5
|
37.0
|
1.0
|
CB
|
B:VAL96
|
4.5
|
32.7
|
1.0
|
N
|
B:ALA97
|
4.6
|
33.4
|
1.0
|
CA
|
B:GLU104
|
4.7
|
37.0
|
1.0
|
CG2
|
B:THR99
|
4.8
|
33.4
|
1.0
|
N
|
B:VAL96
|
4.9
|
31.8
|
1.0
|
C
|
B:ALA97
|
5.0
|
35.4
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7ug3
Go back to
Sodium Binding Sites List in 7ug3
Sodium binding site 3 out
of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:35.7
occ:1.00
|
O
|
C:LEU103
|
2.2
|
40.9
|
1.0
|
O
|
C:PRO100
|
2.3
|
47.5
|
1.0
|
O
|
C:HOH721
|
2.3
|
40.2
|
1.0
|
O
|
C:VAL96
|
2.4
|
41.9
|
1.0
|
OG1
|
C:THR99
|
2.6
|
41.4
|
1.0
|
O
|
C:THR99
|
2.7
|
44.0
|
1.0
|
C
|
C:THR99
|
3.2
|
42.7
|
1.0
|
C
|
C:PRO100
|
3.2
|
48.2
|
1.0
|
C
|
C:LEU103
|
3.4
|
41.2
|
1.0
|
C
|
C:VAL96
|
3.4
|
41.0
|
1.0
|
CB
|
C:THR99
|
3.6
|
41.7
|
1.0
|
CA
|
C:THR99
|
3.8
|
42.1
|
1.0
|
CA
|
C:VAL96
|
3.9
|
40.5
|
1.0
|
N
|
C:PRO100
|
3.9
|
47.2
|
1.0
|
N
|
C:ALA101
|
4.0
|
47.7
|
1.0
|
CA
|
C:ALA101
|
4.0
|
47.2
|
1.0
|
CB
|
C:LEU103
|
4.0
|
40.1
|
1.0
|
O
|
C:HOH695
|
4.0
|
35.7
|
1.0
|
CA
|
C:LEU103
|
4.0
|
41.3
|
1.0
|
O
|
C:ALA101
|
4.0
|
47.3
|
1.0
|
N
|
C:LEU103
|
4.1
|
42.5
|
1.0
|
N
|
C:THR99
|
4.1
|
42.5
|
1.0
|
C
|
C:ALA101
|
4.1
|
47.6
|
1.0
|
CA
|
C:PRO100
|
4.1
|
47.8
|
1.0
|
CG1
|
C:VAL96
|
4.2
|
42.1
|
1.0
|
O
|
C:LEU95
|
4.5
|
41.5
|
1.0
|
N
|
C:GLU104
|
4.5
|
45.1
|
1.0
|
N
|
C:ALA97
|
4.6
|
42.1
|
1.0
|
CB
|
C:VAL96
|
4.6
|
41.3
|
1.0
|
CA
|
C:GLU104
|
4.7
|
46.0
|
1.0
|
N
|
C:SER102
|
4.9
|
46.8
|
1.0
|
C
|
C:ALA97
|
4.9
|
44.2
|
1.0
|
CG2
|
C:THR99
|
4.9
|
40.2
|
1.0
|
CA
|
C:ALA97
|
5.0
|
44.1
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7ug3
Go back to
Sodium Binding Sites List in 7ug3
Sodium binding site 4 out
of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/ug/7ug3-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:35.7
occ:1.00
|
O
|
D:LEU103
|
2.2
|
34.7
|
1.0
|
O
|
D:PRO100
|
2.3
|
43.7
|
1.0
|
OG1
|
D:THR99
|
2.3
|
37.3
|
1.0
|
O
|
D:VAL96
|
2.3
|
37.2
|
1.0
|
O
|
D:HOH721
|
2.4
|
37.2
|
1.0
|
O
|
D:THR99
|
2.8
|
39.6
|
1.0
|
C
|
D:THR99
|
3.2
|
40.3
|
1.0
|
C
|
D:PRO100
|
3.3
|
45.9
|
1.0
|
C
|
D:LEU103
|
3.4
|
35.3
|
1.0
|
C
|
D:VAL96
|
3.4
|
37.0
|
1.0
|
CB
|
D:THR99
|
3.4
|
38.8
|
1.0
|
CA
|
D:THR99
|
3.7
|
39.4
|
1.0
|
CA
|
D:VAL96
|
3.8
|
36.0
|
1.0
|
N
|
D:PRO100
|
3.9
|
45.8
|
1.0
|
N
|
D:THR99
|
3.9
|
38.0
|
1.0
|
CA
|
D:LEU103
|
4.0
|
36.0
|
1.0
|
N
|
D:LEU103
|
4.1
|
37.6
|
1.0
|
CB
|
D:LEU103
|
4.1
|
36.7
|
1.0
|
CA
|
D:ALA101
|
4.1
|
47.9
|
1.0
|
N
|
D:ALA101
|
4.2
|
48.7
|
1.0
|
CG1
|
D:VAL96
|
4.2
|
36.8
|
1.0
|
CA
|
D:PRO100
|
4.2
|
46.6
|
1.0
|
C
|
D:ALA101
|
4.3
|
47.8
|
1.0
|
O
|
D:LEU95
|
4.3
|
39.2
|
1.0
|
O
|
D:ALA101
|
4.3
|
47.2
|
1.0
|
N
|
D:GLU104
|
4.4
|
43.4
|
1.0
|
N
|
D:ALA97
|
4.6
|
37.7
|
1.0
|
CB
|
D:VAL96
|
4.6
|
37.0
|
1.0
|
CA
|
D:GLU104
|
4.7
|
42.2
|
1.0
|
CG2
|
D:THR99
|
4.7
|
38.9
|
1.0
|
C
|
D:ALA97
|
4.9
|
39.6
|
1.0
|
N
|
D:VAL96
|
5.0
|
34.7
|
1.0
|
N
|
D:SER102
|
5.0
|
40.6
|
1.0
|
CA
|
D:ALA97
|
5.0
|
39.3
|
1.0
|
|
Reference:
M.Yang,
T.E.Edwards,
P.S.Horanyi,
D.D.Lorimer.
Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae To Be Published.
Page generated: Fri Apr 7 16:39:24 2023
|