Sodium in PDB 8beo: Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
Enzymatic activity of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
All present enzymatic activity of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map:
4.1.1.47;
Protein crystallography data
The structure of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map, PDB code: 8beo
was solved by
B.Shaanan,
E.Binshtein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.35 /
1.96
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
188.641,
188.641,
246.957,
90,
90,
90
|
|
R / Rfree (%)
|
17.6 /
20.4
|
Other elements in 8beo:
The structure of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
(pdb code 8beo). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the
Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map, PDB code: 8beo:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 1 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na622
b:33.4
occ:1.00
|
O
|
A:PHE383
|
2.2
|
35.8
|
1.0
|
|
O
|
A:ASN380
|
2.2
|
25.1
|
1.0
|
|
O
|
A:HOH895
|
2.4
|
26.8
|
1.0
|
|
O
|
A:HOH982
|
2.5
|
33.8
|
1.0
|
|
HD2
|
A:TYR592
|
2.8
|
26.3
|
1.0
|
|
HE2
|
A:TYR592
|
3.3
|
26.0
|
1.0
|
|
CD2
|
A:TYR592
|
3.3
|
26.1
|
1.0
|
|
C
|
A:PHE383
|
3.3
|
31.4
|
1.0
|
|
C
|
A:ASN380
|
3.4
|
24.2
|
1.0
|
|
CE2
|
A:TYR592
|
3.5
|
26.5
|
1.0
|
|
HA2
|
A:GLY384
|
3.6
|
29.9
|
1.0
|
|
HA
|
A:ASN380
|
3.9
|
22.3
|
1.0
|
|
H
|
A:PHE383
|
4.0
|
27.6
|
1.0
|
|
C
|
A:GLY384
|
4.0
|
28.9
|
1.0
|
|
CA
|
A:GLY384
|
4.1
|
28.9
|
1.0
|
|
HA
|
A:LYS381
|
4.1
|
27.9
|
1.0
|
|
N
|
A:GLY384
|
4.1
|
30.8
|
1.0
|
|
O
|
A:GLY384
|
4.1
|
28.6
|
1.0
|
|
CA
|
A:ASN380
|
4.2
|
22.4
|
1.0
|
|
N
|
A:PHE383
|
4.3
|
27.5
|
1.0
|
|
CG
|
A:TYR592
|
4.3
|
27.6
|
1.0
|
|
HA
|
A:TYR592
|
4.4
|
32.9
|
1.0
|
|
CA
|
A:PHE383
|
4.4
|
28.1
|
1.0
|
|
O
|
A:LYS381
|
4.4
|
24.6
|
1.0
|
|
N
|
A:LYS381
|
4.4
|
25.5
|
1.0
|
|
C
|
A:LYS381
|
4.4
|
26.8
|
1.0
|
|
HB3
|
A:TYR592
|
4.4
|
29.6
|
1.0
|
|
HB3
|
A:ASN380
|
4.5
|
22.3
|
1.0
|
|
CA
|
A:LYS381
|
4.5
|
27.8
|
1.0
|
|
N
|
A:ARG385
|
4.6
|
28.0
|
1.0
|
|
HB2
|
A:PHE383
|
4.6
|
28.3
|
1.0
|
|
O
|
A:HOH976
|
4.6
|
31.4
|
1.0
|
|
O
|
A:HOH811
|
4.6
|
22.4
|
1.0
|
|
HA
|
A:ARG385
|
4.6
|
28.4
|
1.0
|
|
CZ
|
A:TYR592
|
4.7
|
26.8
|
1.0
|
|
O
|
A:MET379
|
4.7
|
23.8
|
1.0
|
|
CB
|
A:TYR592
|
4.8
|
30.0
|
1.0
|
|
H
|
A:ARG385
|
4.9
|
29.1
|
1.0
|
|
CB
|
A:ASN380
|
5.0
|
21.6
|
1.0
|
|
N
|
A:ALA382
|
5.0
|
25.9
|
1.0
|
|
H
|
A:GLY384
|
5.0
|
30.2
|
1.0
|
|
Sodium binding site 2 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 2 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na615
b:40.6
occ:1.00
|
O
|
B:HOH1046
|
2.1
|
31.0
|
1.0
|
|
O
|
B:LYS124
|
2.5
|
23.9
|
1.0
|
|
O
|
B:SER127
|
2.6
|
17.7
|
1.0
|
|
HG3
|
B:LYS124
|
3.2
|
45.4
|
1.0
|
|
HA
|
B:LYS124
|
3.5
|
27.3
|
1.0
|
|
C
|
B:LYS124
|
3.5
|
26.0
|
1.0
|
|
C
|
B:SER127
|
3.7
|
20.4
|
1.0
|
|
H
|
B:SER127
|
3.8
|
20.4
|
1.0
|
|
HD3
|
B:LYS124
|
3.8
|
55.7
|
1.0
|
|
CA
|
B:LYS124
|
4.0
|
27.1
|
1.0
|
|
CG
|
B:LYS124
|
4.0
|
46.3
|
1.0
|
|
HA
|
B:LYS128
|
4.1
|
21.8
|
1.0
|
|
OG
|
B:SER127
|
4.1
|
23.2
|
1.0
|
|
HD2
|
B:LYS124
|
4.2
|
56.4
|
1.0
|
|
CD
|
B:LYS124
|
4.3
|
59.8
|
1.0
|
|
C
|
B:LYS128
|
4.3
|
22.6
|
1.0
|
|
O
|
B:HOH1005
|
4.3
|
32.5
|
1.0
|
|
O
|
B:LYS128
|
4.3
|
21.9
|
1.0
|
|
HA
|
B:MET129
|
4.4
|
21.3
|
1.0
|
|
N
|
B:SER127
|
4.5
|
19.8
|
1.0
|
|
HA
|
B:PRO125
|
4.5
|
23.1
|
1.0
|
|
CA
|
B:LYS128
|
4.5
|
21.3
|
1.0
|
|
CB
|
B:LYS124
|
4.5
|
33.4
|
1.0
|
|
N
|
B:LYS128
|
4.6
|
21.0
|
1.0
|
|
CA
|
B:SER127
|
4.6
|
20.2
|
1.0
|
|
N
|
B:PRO125
|
4.6
|
23.3
|
1.0
|
|
HG
|
B:SER127
|
4.7
|
18.7
|
0.0
|
|
N
|
B:MET129
|
4.7
|
21.2
|
1.0
|
|
HG2
|
B:LYS124
|
4.8
|
45.8
|
1.0
|
|
HB3
|
B:LYS124
|
4.9
|
34.2
|
1.0
|
|
CA
|
B:PRO125
|
4.9
|
22.9
|
1.0
|
|
O
|
B:HOH1064
|
5.0
|
49.8
|
1.0
|
|
CB
|
B:SER127
|
5.0
|
22.2
|
1.0
|
|
Sodium binding site 3 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 3 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na616
b:47.9
occ:1.00
|
OE1
|
B:GLU497
|
2.1
|
55.1
|
1.0
|
|
O
|
B:HOH853
|
2.7
|
43.9
|
1.0
|
|
O
|
B:HOH966
|
2.8
|
29.7
|
1.0
|
|
HA
|
B:SER502
|
3.0
|
36.4
|
1.0
|
|
CD
|
B:GLU497
|
3.3
|
55.0
|
1.0
|
|
HB3
|
B:GLU497
|
3.3
|
38.0
|
1.0
|
|
HA
|
B:GLU497
|
3.4
|
31.1
|
1.0
|
|
H
|
B:ASN498
|
3.8
|
28.3
|
1.0
|
|
CB
|
B:GLU497
|
3.9
|
36.7
|
1.0
|
|
H
|
B:GLY506
|
3.9
|
33.2
|
1.0
|
|
CG
|
B:GLU497
|
4.0
|
47.9
|
1.0
|
|
CA
|
B:SER502
|
4.0
|
37.2
|
1.0
|
|
CA
|
B:GLU497
|
4.0
|
31.3
|
1.0
|
|
HG3
|
B:GLU497
|
4.1
|
47.1
|
1.0
|
|
O
|
B:HOH992
|
4.2
|
49.0
|
1.0
|
|
HB2
|
B:SER502
|
4.2
|
39.0
|
1.0
|
|
O
|
B:ASN498
|
4.2
|
27.9
|
1.0
|
|
N
|
B:ASN498
|
4.2
|
28.4
|
1.0
|
|
HA2
|
B:GLY506
|
4.3
|
31.6
|
1.0
|
|
OE2
|
B:GLU497
|
4.3
|
56.3
|
1.0
|
|
HB3
|
B:SER502
|
4.4
|
39.0
|
1.0
|
|
C
|
B:GLU497
|
4.4
|
29.1
|
1.0
|
|
N
|
B:GLY506
|
4.4
|
33.2
|
1.0
|
|
CB
|
B:SER502
|
4.5
|
39.0
|
1.0
|
|
O
|
B:SER502
|
4.5
|
37.7
|
1.0
|
|
O
|
B:SER501
|
4.6
|
29.7
|
1.0
|
|
HA
|
B:ASN505
|
4.6
|
37.5
|
1.0
|
|
C
|
B:SER502
|
4.8
|
36.1
|
1.0
|
|
N
|
B:SER502
|
4.8
|
33.3
|
1.0
|
|
HB2
|
B:GLU497
|
4.8
|
37.7
|
1.0
|
|
CA
|
B:GLY506
|
4.8
|
31.6
|
1.0
|
|
H
|
B:ASN505
|
4.8
|
36.7
|
1.0
|
|
HG2
|
B:GLU497
|
4.9
|
46.3
|
1.0
|
|
C
|
B:ASN498
|
4.9
|
27.8
|
1.0
|
|
Sodium binding site 4 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 4 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na619
b:70.2
occ:0.50
|
O
|
B:HOH1022
|
2.4
|
42.5
|
1.0
|
|
OE1
|
B:GLU52
|
3.1
|
19.4
|
1.0
|
|
HE2
|
B:HIS50
|
3.1
|
15.9
|
0.0
|
|
HB2
|
B:GLU52
|
3.2
|
17.8
|
1.0
|
|
NE2
|
B:HIS50
|
3.7
|
20.5
|
1.0
|
|
CD
|
B:GLU52
|
3.9
|
19.0
|
1.0
|
|
HA
|
B:ASP82
|
3.9
|
18.7
|
1.0
|
|
CB
|
B:GLU52
|
4.0
|
17.5
|
1.0
|
|
OD1
|
B:ASP82
|
4.0
|
17.4
|
1.0
|
|
HE1
|
B:HIS50
|
4.1
|
19.3
|
1.0
|
|
CE1
|
B:HIS50
|
4.2
|
17.8
|
1.0
|
|
HB3
|
B:GLU52
|
4.2
|
17.8
|
1.0
|
|
CG
|
B:GLU52
|
4.3
|
18.6
|
1.0
|
|
HG3
|
B:GLU52
|
4.4
|
18.3
|
1.0
|
|
O
|
B:HOH928
|
4.4
|
23.6
|
1.0
|
|
HB3
|
B:ASP82
|
4.5
|
18.8
|
1.0
|
|
CG
|
B:ASP82
|
4.5
|
19.4
|
1.0
|
|
O
|
B:ASP82
|
4.7
|
21.2
|
1.0
|
|
CD2
|
B:HIS50
|
4.7
|
17.3
|
1.0
|
|
CA
|
B:ASP82
|
4.7
|
18.7
|
1.0
|
|
CB
|
B:ASP82
|
4.8
|
18.8
|
1.0
|
|
OE2
|
B:GLU52
|
4.8
|
19.5
|
1.0
|
|
HG1
|
B:THR85
|
4.9
|
12.1
|
0.0
|
|
HD2
|
B:HIS50
|
5.0
|
18.4
|
1.0
|
|
Sodium binding site 5 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 5 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na621
b:33.0
occ:1.00
|
O
|
B:PHE383
|
2.2
|
39.2
|
1.0
|
|
O
|
B:ASN380
|
2.3
|
25.7
|
1.0
|
|
O
|
B:HOH1032
|
2.4
|
34.9
|
1.0
|
|
O
|
B:HOH892
|
2.4
|
26.8
|
1.0
|
|
O
|
B:HOH1028
|
2.7
|
40.6
|
1.0
|
|
HD2
|
B:TYR592
|
2.8
|
27.5
|
1.0
|
|
CD2
|
B:TYR592
|
3.3
|
27.8
|
1.0
|
|
HE2
|
B:TYR592
|
3.3
|
26.6
|
1.0
|
|
C
|
B:PHE383
|
3.3
|
33.1
|
1.0
|
|
C
|
B:ASN380
|
3.5
|
24.8
|
1.0
|
|
HA2
|
B:GLY384
|
3.5
|
31.4
|
1.0
|
|
CE2
|
B:TYR592
|
3.6
|
26.9
|
1.0
|
|
HA
|
B:ASN380
|
3.9
|
23.8
|
1.0
|
|
H
|
B:PHE383
|
3.9
|
27.9
|
1.0
|
|
C
|
B:GLY384
|
4.0
|
27.7
|
1.0
|
|
CA
|
B:GLY384
|
4.0
|
31.2
|
1.0
|
|
HA
|
B:LYS381
|
4.1
|
28.4
|
1.0
|
|
N
|
B:GLY384
|
4.1
|
33.5
|
1.0
|
|
O
|
B:GLY384
|
4.2
|
28.2
|
1.0
|
|
N
|
B:PHE383
|
4.2
|
27.2
|
1.0
|
|
HA
|
B:TYR592
|
4.3
|
32.1
|
1.0
|
|
CA
|
B:ASN380
|
4.3
|
24.2
|
1.0
|
|
CG
|
B:TYR592
|
4.3
|
28.4
|
1.0
|
|
O
|
B:LYS381
|
4.3
|
26.5
|
1.0
|
|
CA
|
B:PHE383
|
4.4
|
29.3
|
1.0
|
|
C
|
B:LYS381
|
4.4
|
27.9
|
1.0
|
|
N
|
B:LYS381
|
4.4
|
25.1
|
1.0
|
|
HB3
|
B:TYR592
|
4.5
|
30.2
|
1.0
|
|
CA
|
B:LYS381
|
4.5
|
28.6
|
1.0
|
|
N
|
B:ARG385
|
4.5
|
27.1
|
1.0
|
|
HB2
|
B:PHE383
|
4.6
|
28.2
|
1.0
|
|
HB3
|
B:ASN380
|
4.6
|
24.5
|
1.0
|
|
O
|
B:HOH788
|
4.7
|
25.7
|
1.0
|
|
HA
|
B:ARG385
|
4.7
|
27.1
|
1.0
|
|
CZ
|
B:TYR592
|
4.8
|
26.6
|
1.0
|
|
H
|
B:ARG385
|
4.8
|
28.0
|
1.0
|
|
O
|
B:MET379
|
4.8
|
22.6
|
1.0
|
|
O
|
B:HOH1084
|
4.8
|
51.5
|
1.0
|
|
CB
|
B:TYR592
|
4.8
|
30.9
|
1.0
|
|
HA3
|
B:GLY384
|
5.0
|
31.2
|
1.0
|
|
Sodium binding site 6 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 6 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na610
b:60.8
occ:1.00
|
O
|
C:HOH954
|
2.4
|
34.9
|
1.0
|
|
HB3
|
E:ASN283
|
2.6
|
34.0
|
1.0
|
|
OD1
|
C:ASP113
|
2.7
|
40.7
|
1.0
|
|
O
|
C:LYS111
|
2.8
|
49.1
|
1.0
|
|
HB3
|
C:LYS111
|
2.8
|
51.8
|
1.0
|
|
HA
|
C:ASP113
|
2.9
|
39.5
|
1.0
|
|
HE
|
C:ARG108
|
3.3
|
73.5
|
1.0
|
|
HG12
|
E:VAL311
|
3.5
|
40.3
|
1.0
|
|
CB
|
E:ASN283
|
3.5
|
34.0
|
1.0
|
|
N
|
C:ASP113
|
3.5
|
39.7
|
1.0
|
|
CA
|
C:ASP113
|
3.6
|
38.7
|
1.0
|
|
C
|
C:LYS111
|
3.6
|
46.2
|
1.0
|
|
CB
|
C:LYS111
|
3.7
|
50.9
|
1.0
|
|
HB2
|
C:LYS111
|
3.7
|
51.2
|
1.0
|
|
H
|
E:ASN283
|
3.7
|
31.3
|
1.0
|
|
H
|
C:ASP113
|
3.8
|
39.6
|
1.0
|
|
CG
|
C:ASP113
|
3.8
|
45.1
|
1.0
|
|
C
|
C:GLU112
|
3.9
|
40.2
|
1.0
|
|
HG11
|
E:VAL311
|
3.9
|
40.7
|
1.0
|
|
CG
|
E:ASN283
|
4.0
|
34.2
|
1.0
|
|
OD1
|
E:ASN283
|
4.0
|
35.0
|
1.0
|
|
HB2
|
E:ASN283
|
4.0
|
34.4
|
1.0
|
|
NE
|
C:ARG108
|
4.1
|
72.9
|
1.0
|
|
O
|
C:GLU112
|
4.1
|
36.6
|
1.0
|
|
CB
|
C:ASP113
|
4.1
|
42.0
|
1.0
|
|
CG1
|
E:VAL311
|
4.2
|
40.6
|
1.0
|
|
HH21
|
C:ARG108
|
4.2
|
83.5
|
1.0
|
|
O
|
E:HOH818
|
4.2
|
37.1
|
1.0
|
|
N
|
E:ASN283
|
4.2
|
31.5
|
1.0
|
|
HD3
|
C:LYS111
|
4.3
|
56.5
|
1.0
|
|
CA
|
C:LYS111
|
4.3
|
50.6
|
1.0
|
|
CA
|
E:ASN283
|
4.3
|
32.8
|
1.0
|
|
NH2
|
C:ARG108
|
4.4
|
83.0
|
1.0
|
|
HB2
|
C:ASP113
|
4.4
|
41.5
|
1.0
|
|
HA
|
E:ASN283
|
4.5
|
33.4
|
1.0
|
|
HB3
|
C:ARG108
|
4.5
|
54.2
|
1.0
|
|
N
|
C:GLU112
|
4.5
|
41.1
|
1.0
|
|
HB
|
E:VAL311
|
4.6
|
41.3
|
1.0
|
|
HH22
|
C:ARG108
|
4.7
|
82.8
|
1.0
|
|
CZ
|
C:ARG108
|
4.7
|
84.2
|
1.0
|
|
HD2
|
C:ARG108
|
4.8
|
65.3
|
1.0
|
|
CA
|
C:GLU112
|
4.8
|
40.7
|
1.0
|
|
CG
|
C:LYS111
|
4.8
|
54.2
|
1.0
|
|
HB2
|
C:GLU112
|
4.8
|
42.0
|
1.0
|
|
HA
|
E:ALA282
|
4.8
|
31.1
|
1.0
|
|
HA
|
C:LYS111
|
4.8
|
50.1
|
1.0
|
|
HG13
|
E:VAL311
|
4.9
|
40.5
|
1.0
|
|
H
|
C:PHE114
|
4.9
|
34.9
|
1.0
|
|
CD
|
C:LYS111
|
4.9
|
56.1
|
1.0
|
|
C
|
C:ASP113
|
4.9
|
35.9
|
1.0
|
|
ND2
|
E:ASN283
|
4.9
|
34.2
|
1.0
|
|
HD2
|
C:LYS111
|
4.9
|
56.0
|
1.0
|
|
OD2
|
C:ASP113
|
5.0
|
50.4
|
1.0
|
|
Sodium binding site 7 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 7 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na613
b:35.7
occ:1.00
|
O
|
C:ASN380
|
2.2
|
33.1
|
1.0
|
|
O
|
C:PHE383
|
2.3
|
38.7
|
1.0
|
|
O
|
C:HOH797
|
2.4
|
29.7
|
1.0
|
|
O
|
C:HOH962
|
2.5
|
34.3
|
1.0
|
|
HD2
|
C:TYR592
|
2.7
|
35.1
|
1.0
|
|
HE2
|
C:TYR592
|
3.2
|
34.3
|
1.0
|
|
CD2
|
C:TYR592
|
3.2
|
34.8
|
1.0
|
|
C
|
C:ASN380
|
3.4
|
32.3
|
1.0
|
|
C
|
C:PHE383
|
3.4
|
36.4
|
1.0
|
|
CE2
|
C:TYR592
|
3.5
|
34.3
|
1.0
|
|
HA2
|
C:GLY384
|
3.7
|
37.4
|
1.0
|
|
HA
|
C:ASN380
|
3.8
|
31.1
|
1.0
|
|
H
|
C:PHE383
|
4.0
|
34.4
|
1.0
|
|
C
|
C:GLY384
|
4.0
|
37.2
|
1.0
|
|
O
|
C:GLY384
|
4.1
|
34.9
|
1.0
|
|
CA
|
C:GLY384
|
4.2
|
36.9
|
1.0
|
|
CA
|
C:ASN380
|
4.2
|
31.2
|
1.0
|
|
HA
|
C:LYS381
|
4.2
|
36.3
|
1.0
|
|
N
|
C:GLY384
|
4.2
|
36.1
|
1.0
|
|
CG
|
C:TYR592
|
4.3
|
37.2
|
1.0
|
|
N
|
C:PHE383
|
4.3
|
33.8
|
1.0
|
|
HA
|
C:TYR592
|
4.3
|
41.8
|
1.0
|
|
CA
|
C:PHE383
|
4.4
|
35.8
|
1.0
|
|
N
|
C:LYS381
|
4.4
|
34.2
|
1.0
|
|
HB3
|
C:ASN380
|
4.4
|
31.7
|
1.0
|
|
HB3
|
C:TYR592
|
4.4
|
39.0
|
1.0
|
|
O
|
C:LYS381
|
4.5
|
31.4
|
1.0
|
|
C
|
C:LYS381
|
4.5
|
35.1
|
1.0
|
|
HB2
|
C:PHE383
|
4.6
|
35.8
|
1.0
|
|
O
|
C:HOH790
|
4.6
|
26.0
|
1.0
|
|
N
|
C:ARG385
|
4.6
|
35.9
|
1.0
|
|
CA
|
C:LYS381
|
4.6
|
36.1
|
1.0
|
|
CZ
|
C:TYR592
|
4.6
|
35.4
|
1.0
|
|
HA
|
C:ARG385
|
4.7
|
36.6
|
1.0
|
|
CB
|
C:TYR592
|
4.8
|
39.7
|
1.0
|
|
O
|
C:MET379
|
4.8
|
30.0
|
1.0
|
|
H
|
C:ARG385
|
4.9
|
37.3
|
1.0
|
|
CB
|
C:ASN380
|
4.9
|
31.1
|
1.0
|
|
Sodium binding site 8 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 8 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na609
b:47.4
occ:1.00
|
O
|
E:HOH896
|
2.5
|
46.1
|
1.0
|
|
OE2
|
D:GLU135
|
2.9
|
49.4
|
1.0
|
|
HB3
|
D:ARG134
|
2.9
|
42.5
|
1.0
|
|
HG3
|
E:LYS111
|
3.0
|
52.4
|
1.0
|
|
HB2
|
E:HIS110
|
3.0
|
59.8
|
1.0
|
|
HE2
|
E:LYS111
|
3.2
|
60.1
|
1.0
|
|
HB2
|
D:ARG134
|
3.4
|
42.3
|
1.0
|
|
HZ3
|
E:LYS111
|
3.5
|
62.1
|
1.0
|
|
HG2
|
D:GLU135
|
3.5
|
41.5
|
1.0
|
|
CB
|
D:ARG134
|
3.6
|
42.5
|
1.0
|
|
HG2
|
E:LYS111
|
3.6
|
53.0
|
1.0
|
|
O
|
D:ARG134
|
3.7
|
35.1
|
1.0
|
|
CG
|
E:LYS111
|
3.7
|
52.6
|
1.0
|
|
CD
|
D:GLU135
|
3.8
|
45.4
|
1.0
|
|
CB
|
E:HIS110
|
3.9
|
59.3
|
1.0
|
|
CE
|
E:LYS111
|
4.0
|
60.5
|
1.0
|
|
HB3
|
E:HIS110
|
4.0
|
59.7
|
1.0
|
|
CG
|
D:GLU135
|
4.1
|
41.4
|
1.0
|
|
NZ
|
E:LYS111
|
4.1
|
62.8
|
1.0
|
|
H
|
E:HIS110
|
4.2
|
49.8
|
1.0
|
|
HH12
|
D:ARG106
|
4.3
|
55.8
|
1.0
|
|
C
|
D:ARG134
|
4.3
|
36.7
|
1.0
|
|
CD
|
E:LYS111
|
4.3
|
56.7
|
1.0
|
|
HG3
|
D:ARG134
|
4.4
|
46.0
|
1.0
|
|
C
|
E:HIS110
|
4.4
|
50.4
|
1.0
|
|
HD2
|
D:ARG134
|
4.4
|
49.4
|
1.0
|
|
HG3
|
D:GLU135
|
4.5
|
42.1
|
1.0
|
|
CA
|
E:HIS110
|
4.5
|
53.1
|
1.0
|
|
CG
|
D:ARG134
|
4.6
|
46.5
|
1.0
|
|
HD2
|
E:LYS111
|
4.6
|
56.2
|
1.0
|
|
O
|
E:ALA107
|
4.6
|
46.5
|
1.0
|
|
O
|
E:HIS110
|
4.6
|
47.2
|
1.0
|
|
HZ2
|
E:LYS111
|
4.6
|
62.7
|
1.0
|
|
CA
|
D:ARG134
|
4.7
|
37.0
|
1.0
|
|
O
|
E:HOH925
|
4.7
|
52.1
|
1.0
|
|
HD2
|
D:ARG106
|
4.7
|
51.0
|
1.0
|
|
N
|
E:HIS110
|
4.7
|
48.9
|
1.0
|
|
HZ1
|
E:LYS111
|
4.8
|
62.1
|
1.0
|
|
HE3
|
E:LYS111
|
4.8
|
60.4
|
1.0
|
|
N
|
E:LYS111
|
4.8
|
46.5
|
1.0
|
|
NH1
|
D:ARG106
|
4.9
|
55.5
|
1.0
|
|
HA
|
E:LYS111
|
4.9
|
46.9
|
1.0
|
|
HD2
|
E:HIS110
|
4.9
|
66.1
|
1.0
|
|
HH11
|
D:ARG106
|
4.9
|
55.3
|
1.0
|
|
CB
|
E:LYS111
|
4.9
|
48.5
|
1.0
|
|
OE1
|
D:GLU135
|
4.9
|
44.1
|
1.0
|
|
CD
|
D:ARG134
|
5.0
|
48.2
|
1.0
|
|
CG
|
E:HIS110
|
5.0
|
66.3
|
1.0
|
|
Sodium binding site 9 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 9 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na610
b:34.7
occ:1.00
|
O
|
D:PHE383
|
2.2
|
35.7
|
1.0
|
|
O
|
D:HOH972
|
2.3
|
37.3
|
1.0
|
|
O
|
D:ASN380
|
2.3
|
30.1
|
1.0
|
|
O
|
D:HOH968
|
2.5
|
40.0
|
1.0
|
|
O
|
D:HOH908
|
2.6
|
29.1
|
1.0
|
|
HD2
|
D:TYR592
|
2.9
|
32.5
|
1.0
|
|
C
|
D:PHE383
|
3.3
|
34.2
|
1.0
|
|
CD2
|
D:TYR592
|
3.4
|
32.6
|
1.0
|
|
HE2
|
D:TYR592
|
3.4
|
31.6
|
1.0
|
|
C
|
D:ASN380
|
3.5
|
30.7
|
1.0
|
|
HA2
|
D:GLY384
|
3.5
|
33.6
|
1.0
|
|
CE2
|
D:TYR592
|
3.7
|
32.1
|
1.0
|
|
H
|
D:PHE383
|
3.9
|
32.8
|
1.0
|
|
HA
|
D:ASN380
|
4.0
|
30.4
|
1.0
|
|
CA
|
D:GLY384
|
4.1
|
32.9
|
1.0
|
|
C
|
D:GLY384
|
4.1
|
32.9
|
1.0
|
|
HA
|
D:LYS381
|
4.1
|
34.5
|
1.0
|
|
N
|
D:GLY384
|
4.1
|
34.0
|
1.0
|
|
O
|
D:LYS381
|
4.2
|
34.0
|
1.0
|
|
O
|
D:GLY384
|
4.2
|
31.9
|
1.0
|
|
N
|
D:PHE383
|
4.2
|
32.4
|
1.0
|
|
HA
|
D:TYR592
|
4.3
|
40.0
|
1.0
|
|
CA
|
D:ASN380
|
4.3
|
30.7
|
1.0
|
|
CA
|
D:PHE383
|
4.4
|
33.9
|
1.0
|
|
CG
|
D:TYR592
|
4.4
|
33.9
|
1.0
|
|
C
|
D:LYS381
|
4.4
|
33.9
|
1.0
|
|
N
|
D:LYS381
|
4.4
|
31.7
|
1.0
|
|
HB3
|
D:TYR592
|
4.5
|
36.0
|
1.0
|
|
CA
|
D:LYS381
|
4.5
|
34.3
|
1.0
|
|
N
|
D:ARG385
|
4.6
|
33.6
|
1.0
|
|
HB2
|
D:PHE383
|
4.6
|
33.5
|
1.0
|
|
HB3
|
D:ASN380
|
4.6
|
32.2
|
1.0
|
|
HA
|
D:ARG385
|
4.8
|
35.4
|
1.0
|
|
H
|
D:ARG385
|
4.8
|
34.5
|
1.0
|
|
O
|
D:HOH764
|
4.8
|
25.3
|
1.0
|
|
O
|
D:MET379
|
4.8
|
31.1
|
1.0
|
|
CB
|
D:TYR592
|
4.8
|
36.1
|
1.0
|
|
CZ
|
D:TYR592
|
4.8
|
31.4
|
1.0
|
|
O
|
D:GLU593
|
5.0
|
41.9
|
1.0
|
|
Sodium binding site 10 out
of 15 in 8beo
Go back to
Sodium Binding Sites List in 8beo
Sodium binding site 10 out
of 15 in the Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na611
b:57.4
occ:1.00
|
HB3
|
D:LYS111
|
2.6
|
50.5
|
1.0
|
|
O
|
F:HOH927
|
2.7
|
35.4
|
1.0
|
|
OD1
|
D:ASP113
|
2.7
|
42.3
|
1.0
|
|
O
|
D:HOH1039
|
2.7
|
39.8
|
1.0
|
|
O
|
D:LYS111
|
2.7
|
47.0
|
1.0
|
|
HB3
|
F:ASN283
|
2.8
|
33.1
|
1.0
|
|
HA
|
D:ASP113
|
3.1
|
38.6
|
1.0
|
|
HE
|
D:ARG108
|
3.2
|
71.7
|
1.0
|
|
HG12
|
F:VAL311
|
3.4
|
40.8
|
1.0
|
|
CB
|
D:LYS111
|
3.5
|
49.4
|
1.0
|
|
HB2
|
D:LYS111
|
3.5
|
49.8
|
1.0
|
|
C
|
D:LYS111
|
3.6
|
45.0
|
1.0
|
|
N
|
D:ASP113
|
3.6
|
38.5
|
1.0
|
|
CA
|
D:ASP113
|
3.7
|
38.1
|
1.0
|
|
CB
|
F:ASN283
|
3.8
|
32.7
|
1.0
|
|
H
|
D:ASP113
|
3.8
|
38.9
|
1.0
|
|
CG
|
D:ASP113
|
3.8
|
43.3
|
1.0
|
|
HG11
|
F:VAL311
|
3.9
|
41.1
|
1.0
|
|
H
|
F:ASN283
|
3.9
|
32.1
|
1.0
|
|
HD3
|
D:LYS111
|
4.0
|
58.0
|
1.0
|
|
NE
|
D:ARG108
|
4.0
|
71.6
|
1.0
|
|
HH21
|
D:ARG108
|
4.0
|
83.0
|
1.0
|
|
C
|
D:GLU112
|
4.0
|
40.6
|
1.0
|
|
CG1
|
F:VAL311
|
4.1
|
41.6
|
1.0
|
|
CA
|
D:LYS111
|
4.1
|
47.8
|
1.0
|
|
CB
|
D:ASP113
|
4.2
|
40.5
|
1.0
|
|
O
|
F:HOH800
|
4.2
|
32.1
|
1.0
|
|
HB2
|
F:ASN283
|
4.3
|
33.4
|
1.0
|
|
CG
|
F:ASN283
|
4.3
|
33.5
|
1.0
|
|
O
|
D:GLU112
|
4.3
|
38.9
|
1.0
|
|
OD1
|
F:ASN283
|
4.3
|
32.5
|
1.0
|
|
NH2
|
D:ARG108
|
4.4
|
83.0
|
1.0
|
|
HB
|
F:VAL311
|
4.4
|
40.7
|
1.0
|
|
N
|
F:ASN283
|
4.4
|
32.1
|
1.0
|
|
HB2
|
D:ASP113
|
4.5
|
40.3
|
1.0
|
|
HB3
|
D:ARG108
|
4.5
|
52.6
|
1.0
|
|
N
|
D:GLU112
|
4.5
|
39.8
|
1.0
|
|
CA
|
F:ASN283
|
4.6
|
32.5
|
1.0
|
|
CG
|
D:LYS111
|
4.6
|
55.3
|
1.0
|
|
HA
|
F:ASN283
|
4.6
|
33.1
|
1.0
|
|
CZ
|
D:ARG108
|
4.6
|
82.0
|
1.0
|
|
CD
|
D:LYS111
|
4.6
|
58.2
|
1.0
|
|
HD2
|
D:ARG108
|
4.7
|
63.0
|
1.0
|
|
HA
|
D:LYS111
|
4.7
|
47.8
|
1.0
|
|
HD2
|
D:LYS111
|
4.7
|
57.6
|
1.0
|
|
HH22
|
D:ARG108
|
4.8
|
82.2
|
1.0
|
|
HB2
|
D:GLU112
|
4.8
|
42.7
|
1.0
|
|
CA
|
D:GLU112
|
4.8
|
41.4
|
1.0
|
|
CB
|
F:VAL311
|
4.8
|
40.4
|
1.0
|
|
HG13
|
F:VAL311
|
4.8
|
41.0
|
1.0
|
|
OD2
|
D:ASP113
|
4.9
|
54.7
|
1.0
|
|
CD
|
D:ARG108
|
4.9
|
62.9
|
1.0
|
|
HG2
|
D:LYS111
|
5.0
|
54.9
|
1.0
|
|
Reference:
B.Shaanan,
E.Binshtein.
Crystal Structure of E. Coli Glyoxylate Carboligase Mutant I393A with Map To Be Published.
Page generated: Thu Dec 28 11:32:59 2023
|
