Sodium in PDB 6nlh: Structure of Human Triose Phosphate Isomerase R189A
Enzymatic activity of Structure of Human Triose Phosphate Isomerase R189A
All present enzymatic activity of Structure of Human Triose Phosphate Isomerase R189A:
5.3.1.1;
Protein crystallography data
The structure of Structure of Human Triose Phosphate Isomerase R189A, PDB code: 6nlh
was solved by
K.R.Richards,
B.P.Roland,
M.J.Palladino,
A.P.Vandemark,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.67 /
2.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.142,
73.661,
92.842,
90.03,
90.03,
90.00
|
R / Rfree (%)
|
17.4 /
21.6
|
Other elements in 6nlh:
The structure of Structure of Human Triose Phosphate Isomerase R189A also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Sodium atom in the Structure of Human Triose Phosphate Isomerase R189A
(pdb code 6nlh). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 20 binding sites of Sodium where determined in the
Structure of Human Triose Phosphate Isomerase R189A, PDB code: 6nlh:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 1 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:38.9
occ:1.00
|
O
|
A:VAL226
|
2.4
|
33.4
|
1.0
|
O
|
A:ALA221
|
2.4
|
33.5
|
1.0
|
O
|
A:GLN223
|
2.7
|
38.2
|
1.0
|
O
|
A:HOH502
|
2.7
|
46.9
|
1.0
|
HE2
|
A:LYS247
|
3.2
|
51.0
|
1.0
|
C
|
A:ALA221
|
3.6
|
33.8
|
1.0
|
C
|
A:VAL226
|
3.6
|
31.8
|
1.0
|
HZ1
|
A:LYS247
|
3.7
|
54.9
|
1.0
|
C
|
A:GLN223
|
3.8
|
40.9
|
1.0
|
H
|
A:VAL226
|
3.9
|
39.7
|
1.0
|
O
|
A:PRO224
|
3.9
|
43.2
|
1.0
|
HA
|
A:ASP227
|
3.9
|
38.2
|
1.0
|
HB
|
A:VAL226
|
3.9
|
36.8
|
1.0
|
CE
|
A:LYS247
|
4.0
|
42.5
|
1.0
|
HA
|
A:PRO224
|
4.0
|
53.9
|
1.0
|
HA
|
A:ALA221
|
4.1
|
37.6
|
1.0
|
HE3
|
A:LYS247
|
4.1
|
51.0
|
1.0
|
HA
|
A:SER222
|
4.1
|
49.7
|
1.0
|
NZ
|
A:LYS247
|
4.2
|
45.7
|
1.0
|
C
|
A:PRO224
|
4.2
|
42.5
|
1.0
|
C
|
A:SER222
|
4.2
|
41.8
|
1.0
|
N
|
A:GLN223
|
4.2
|
39.8
|
1.0
|
N
|
A:VAL226
|
4.3
|
33.1
|
1.0
|
H
|
A:GLN223
|
4.3
|
47.8
|
1.0
|
HZ3
|
A:LYS247
|
4.4
|
54.9
|
1.0
|
HE1
|
A:PHE6
|
4.4
|
40.5
|
1.0
|
CA
|
A:VAL226
|
4.4
|
31.2
|
1.0
|
CA
|
A:PRO224
|
4.4
|
44.9
|
1.0
|
CA
|
A:ALA221
|
4.4
|
31.4
|
1.0
|
N
|
A:SER222
|
4.5
|
36.6
|
1.0
|
CA
|
A:SER222
|
4.5
|
41.4
|
1.0
|
N
|
A:ASP227
|
4.6
|
31.5
|
1.0
|
O
|
A:SER222
|
4.6
|
44.0
|
1.0
|
N
|
A:PRO224
|
4.6
|
43.8
|
1.0
|
HG12
|
A:VAL226
|
4.6
|
34.4
|
1.0
|
OD1
|
A:ASP227
|
4.6
|
41.1
|
1.0
|
CB
|
A:VAL226
|
4.6
|
30.6
|
1.0
|
CA
|
A:GLN223
|
4.6
|
40.9
|
1.0
|
CA
|
A:ASP227
|
4.7
|
31.8
|
1.0
|
HB1
|
A:ALA221
|
4.8
|
36.9
|
1.0
|
N
|
A:ASP225
|
4.9
|
40.7
|
1.0
|
HB2
|
A:GLN223
|
5.0
|
46.9
|
1.0
|
|
Sodium binding site 2 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 2 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:38.6
occ:1.00
|
HH22
|
A:ARG99
|
2.0
|
28.0
|
1.0
|
OD1
|
A:ASP106
|
2.5
|
36.0
|
1.0
|
NH2
|
A:ARG99
|
2.8
|
23.3
|
1.0
|
HH12
|
A:ARG99
|
2.8
|
30.5
|
1.0
|
O
|
A:GLN146
|
3.0
|
38.1
|
1.0
|
HG13
|
A:ILE150
|
3.0
|
42.0
|
1.0
|
HA
|
A:GLN146
|
3.1
|
47.2
|
1.0
|
HB
|
A:VAL149
|
3.1
|
51.8
|
1.0
|
HB3
|
A:GLN146
|
3.2
|
49.0
|
1.0
|
HH21
|
A:ARG99
|
3.4
|
28.0
|
1.0
|
HA
|
A:ASP106
|
3.4
|
37.3
|
1.0
|
NH1
|
A:ARG99
|
3.5
|
25.4
|
1.0
|
CZ
|
A:ARG99
|
3.6
|
23.8
|
1.0
|
HG22
|
A:ILE109
|
3.6
|
28.1
|
1.0
|
CG
|
A:ASP106
|
3.6
|
36.5
|
1.0
|
CA
|
A:GLN146
|
3.7
|
39.4
|
1.0
|
C
|
A:GLN146
|
3.7
|
39.0
|
1.0
|
HD13
|
A:ILE150
|
3.8
|
41.9
|
1.0
|
HG21
|
A:ILE109
|
3.8
|
28.1
|
1.0
|
HB
|
A:ILE109
|
3.9
|
29.7
|
1.0
|
CB
|
A:GLN146
|
3.9
|
40.8
|
1.0
|
CG1
|
A:ILE150
|
3.9
|
35.0
|
1.0
|
HB3
|
A:ASP106
|
3.9
|
41.5
|
1.0
|
HD12
|
A:ILE150
|
4.0
|
41.9
|
1.0
|
CB
|
A:VAL149
|
4.0
|
43.2
|
1.0
|
HG2
|
A:GLN146
|
4.0
|
46.7
|
1.0
|
H
|
A:ILE150
|
4.1
|
44.8
|
1.0
|
HG12
|
A:VAL149
|
4.1
|
50.0
|
1.0
|
CD1
|
A:ILE150
|
4.1
|
35.0
|
1.0
|
CG2
|
A:ILE109
|
4.1
|
23.4
|
1.0
|
CB
|
A:ASP106
|
4.1
|
34.6
|
1.0
|
CA
|
A:ASP106
|
4.2
|
31.1
|
1.0
|
HG22
|
A:ILE127
|
4.2
|
35.5
|
1.0
|
HH11
|
A:ARG99
|
4.3
|
30.5
|
1.0
|
HG12
|
A:ILE150
|
4.3
|
42.0
|
1.0
|
HD13
|
A:ILE109
|
4.3
|
33.1
|
1.0
|
HG11
|
A:VAL149
|
4.4
|
50.0
|
1.0
|
CG1
|
A:VAL149
|
4.4
|
41.7
|
1.0
|
HD12
|
A:ILE109
|
4.4
|
33.1
|
1.0
|
O
|
A:ASP106
|
4.5
|
26.8
|
1.0
|
CB
|
A:ILE109
|
4.5
|
24.7
|
1.0
|
N
|
A:ILE150
|
4.5
|
37.4
|
1.0
|
CG
|
A:GLN146
|
4.5
|
39.0
|
1.0
|
HG21
|
A:VAL149
|
4.7
|
53.3
|
1.0
|
HB2
|
A:GLN146
|
4.7
|
49.0
|
1.0
|
OD2
|
A:ASP106
|
4.7
|
38.8
|
1.0
|
CG2
|
A:VAL149
|
4.8
|
44.4
|
1.0
|
HG23
|
A:VAL149
|
4.8
|
53.3
|
1.0
|
CD1
|
A:ILE109
|
4.8
|
27.6
|
1.0
|
C
|
A:ASP106
|
4.8
|
29.3
|
1.0
|
H
|
A:VAL149
|
4.8
|
55.8
|
1.0
|
NE
|
A:ARG99
|
4.9
|
23.9
|
1.0
|
H
|
A:GLY110
|
5.0
|
30.2
|
1.0
|
CA
|
A:VAL149
|
5.0
|
44.6
|
1.0
|
C
|
A:VAL149
|
5.0
|
37.9
|
1.0
|
CB
|
A:ILE150
|
5.0
|
36.1
|
1.0
|
|
Sodium binding site 3 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 3 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:36.3
occ:1.00
|
OD1
|
A:ASN195
|
2.2
|
94.0
|
1.0
|
OG
|
A:SER194
|
2.3
|
69.5
|
1.0
|
CG
|
A:ASN195
|
3.0
|
92.4
|
1.0
|
HD21
|
A:ASN195
|
3.4
|
0.5
|
1.0
|
O
|
A:SER194
|
3.4
|
72.2
|
1.0
|
HA
|
A:ASN195
|
3.4
|
88.9
|
1.0
|
O
|
A:HOH406
|
3.5
|
39.4
|
1.0
|
ND2
|
A:ASN195
|
3.5
|
97.9
|
1.0
|
C
|
A:SER194
|
3.6
|
69.4
|
1.0
|
CB
|
A:SER194
|
3.7
|
68.1
|
1.0
|
N
|
A:ASN195
|
4.0
|
69.4
|
1.0
|
CA
|
A:ASN195
|
4.0
|
74.1
|
1.0
|
CB
|
A:ASN195
|
4.0
|
83.0
|
1.0
|
HB3
|
A:SER194
|
4.1
|
81.7
|
1.0
|
CA
|
A:SER194
|
4.3
|
68.9
|
1.0
|
HB2
|
A:SER194
|
4.3
|
81.7
|
1.0
|
HD22
|
A:ASN195
|
4.3
|
0.5
|
1.0
|
O
|
A:HOH433
|
4.3
|
32.8
|
1.0
|
H
|
A:ASN195
|
4.6
|
83.3
|
1.0
|
HB2
|
A:ASN195
|
4.6
|
99.7
|
1.0
|
HA
|
A:SER194
|
4.6
|
82.7
|
1.0
|
HB3
|
A:ASN195
|
4.7
|
99.7
|
1.0
|
|
Sodium binding site 4 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 4 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na301
b:42.5
occ:1.00
|
O
|
E:ALA221
|
2.5
|
49.3
|
1.0
|
O
|
E:GLN223
|
2.5
|
50.9
|
1.0
|
O
|
E:VAL226
|
2.6
|
45.0
|
1.0
|
HZ1
|
E:LYS247
|
3.0
|
68.3
|
1.0
|
C
|
E:GLN223
|
3.5
|
53.1
|
1.0
|
HA
|
E:PRO224
|
3.6
|
65.6
|
1.0
|
C
|
E:ALA221
|
3.7
|
50.3
|
1.0
|
C
|
E:VAL226
|
3.7
|
44.3
|
1.0
|
H
|
E:VAL226
|
3.7
|
55.8
|
1.0
|
NZ
|
E:LYS247
|
3.9
|
56.9
|
1.0
|
HA
|
E:ASP227
|
3.9
|
53.8
|
1.0
|
HB
|
E:VAL226
|
4.0
|
54.4
|
1.0
|
HZ2
|
E:LYS247
|
4.1
|
68.3
|
1.0
|
C
|
E:PRO224
|
4.1
|
52.6
|
1.0
|
O
|
E:PRO224
|
4.1
|
51.6
|
1.0
|
N
|
E:VAL226
|
4.2
|
46.6
|
1.0
|
CA
|
E:PRO224
|
4.2
|
54.7
|
1.0
|
C
|
E:SER222
|
4.2
|
55.4
|
1.0
|
HA
|
E:ALA221
|
4.2
|
57.1
|
1.0
|
N
|
E:GLN223
|
4.2
|
53.7
|
1.0
|
HA
|
E:SER222
|
4.3
|
66.0
|
1.0
|
HZ3
|
E:LYS247
|
4.3
|
68.3
|
1.0
|
N
|
E:PRO224
|
4.3
|
54.9
|
1.0
|
H
|
E:GLN223
|
4.4
|
64.5
|
1.0
|
HD3
|
E:LYS247
|
4.4
|
64.0
|
1.0
|
CA
|
E:VAL226
|
4.4
|
44.8
|
1.0
|
O
|
E:SER222
|
4.4
|
57.1
|
1.0
|
CA
|
E:GLN223
|
4.5
|
54.1
|
1.0
|
CA
|
E:ALA221
|
4.5
|
47.6
|
1.0
|
N
|
E:SER222
|
4.6
|
52.9
|
1.0
|
CA
|
E:SER222
|
4.6
|
55.0
|
1.0
|
N
|
E:ASP227
|
4.6
|
43.8
|
1.0
|
HE2
|
E:LYS247
|
4.6
|
66.0
|
1.0
|
HE1
|
E:PHE6
|
4.7
|
52.2
|
1.0
|
CB
|
E:VAL226
|
4.7
|
45.3
|
1.0
|
N
|
E:ASP225
|
4.7
|
51.7
|
1.0
|
OD1
|
E:ASP227
|
4.7
|
51.4
|
1.0
|
CA
|
E:ASP227
|
4.7
|
44.8
|
1.0
|
CE
|
E:LYS247
|
4.7
|
54.9
|
1.0
|
HG12
|
E:VAL226
|
4.8
|
52.1
|
1.0
|
HB3
|
E:ALA221
|
4.9
|
55.6
|
1.0
|
HB2
|
E:GLN223
|
4.9
|
62.9
|
1.0
|
|
Sodium binding site 5 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 5 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na301
b:33.7
occ:1.00
|
O
|
B:HOH500
|
2.4
|
36.8
|
1.0
|
O
|
B:HOH429
|
2.4
|
33.3
|
1.0
|
O
|
B:ALA221
|
2.4
|
36.8
|
1.0
|
O
|
B:VAL226
|
2.5
|
34.9
|
1.0
|
O
|
B:GLN223
|
2.6
|
39.4
|
1.0
|
HE2
|
B:LYS247
|
3.2
|
54.1
|
1.0
|
HZ1
|
B:LYS247
|
3.6
|
58.1
|
1.0
|
C
|
B:ALA221
|
3.6
|
35.9
|
1.0
|
C
|
B:VAL226
|
3.6
|
35.3
|
1.0
|
C
|
B:GLN223
|
3.7
|
41.1
|
1.0
|
H
|
B:VAL226
|
3.8
|
42.4
|
1.0
|
CE
|
B:LYS247
|
3.9
|
45.1
|
1.0
|
HB
|
B:VAL226
|
3.9
|
37.3
|
1.0
|
HE3
|
B:LYS247
|
3.9
|
54.1
|
1.0
|
HA
|
B:PRO224
|
4.0
|
56.8
|
1.0
|
O
|
B:PRO224
|
4.0
|
52.2
|
1.0
|
HA
|
B:ASP227
|
4.0
|
40.0
|
1.0
|
HA
|
B:ALA221
|
4.1
|
39.3
|
1.0
|
NZ
|
B:LYS247
|
4.1
|
48.4
|
1.0
|
C
|
B:SER222
|
4.1
|
44.5
|
1.0
|
N
|
B:VAL226
|
4.2
|
35.4
|
1.0
|
C
|
B:PRO224
|
4.2
|
44.0
|
1.0
|
N
|
B:GLN223
|
4.2
|
42.9
|
1.0
|
HA
|
B:SER222
|
4.3
|
50.9
|
1.0
|
HZ3
|
B:LYS247
|
4.4
|
58.1
|
1.0
|
CA
|
B:VAL226
|
4.4
|
38.1
|
1.0
|
HE1
|
B:PHE6
|
4.4
|
46.0
|
1.0
|
O
|
B:SER222
|
4.4
|
48.2
|
1.0
|
CA
|
B:PRO224
|
4.4
|
47.3
|
1.0
|
H
|
B:GLN223
|
4.4
|
51.4
|
1.0
|
CA
|
B:ALA221
|
4.5
|
32.8
|
1.0
|
N
|
B:SER222
|
4.5
|
38.0
|
1.0
|
N
|
B:PRO224
|
4.5
|
44.3
|
1.0
|
CA
|
B:SER222
|
4.5
|
42.4
|
1.0
|
CA
|
B:GLN223
|
4.6
|
43.8
|
1.0
|
CB
|
B:VAL226
|
4.6
|
31.1
|
1.0
|
N
|
B:ASP227
|
4.6
|
32.9
|
1.0
|
OD1
|
B:ASP227
|
4.7
|
40.7
|
1.0
|
HB1
|
B:ALA221
|
4.7
|
37.0
|
1.0
|
N
|
B:ASP225
|
4.8
|
43.1
|
1.0
|
CA
|
B:ASP227
|
4.8
|
33.3
|
1.0
|
HG12
|
B:VAL226
|
4.8
|
35.6
|
1.0
|
HB2
|
B:GLN223
|
4.9
|
49.3
|
1.0
|
HZ2
|
B:LYS247
|
4.9
|
58.1
|
1.0
|
|
Sodium binding site 6 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 6 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na302
b:65.9
occ:1.00
|
H
|
B:VAL39
|
2.6
|
29.1
|
1.0
|
O
|
B:LYS58
|
2.7
|
31.7
|
1.0
|
HA
|
B:GLU38
|
2.8
|
34.5
|
1.0
|
HG11
|
B:VAL33
|
3.1
|
42.7
|
1.0
|
N
|
B:VAL39
|
3.4
|
24.2
|
1.0
|
O
|
B:THR37
|
3.8
|
32.8
|
1.0
|
CA
|
B:GLU38
|
3.8
|
28.7
|
1.0
|
HB
|
B:VAL39
|
3.8
|
30.0
|
1.0
|
C
|
B:LYS58
|
3.9
|
32.3
|
1.0
|
HG23
|
B:VAL39
|
3.9
|
32.8
|
1.0
|
CG1
|
B:VAL33
|
4.0
|
35.6
|
1.0
|
HG3
|
B:GLU38
|
4.0
|
35.7
|
1.0
|
HG12
|
B:VAL33
|
4.0
|
42.7
|
1.0
|
C
|
B:GLU38
|
4.1
|
25.6
|
1.0
|
HA
|
B:ILE59
|
4.1
|
33.3
|
1.0
|
HB2
|
B:LYS58
|
4.2
|
45.3
|
1.0
|
O
|
B:VAL39
|
4.2
|
20.2
|
1.0
|
HD13
|
B:ILE59
|
4.3
|
35.9
|
1.0
|
HG21
|
B:VAL33
|
4.3
|
40.0
|
1.0
|
CA
|
B:VAL39
|
4.4
|
22.6
|
1.0
|
CB
|
B:VAL39
|
4.4
|
25.0
|
1.0
|
HA
|
B:LYS58
|
4.5
|
42.6
|
1.0
|
HG13
|
B:VAL33
|
4.5
|
42.7
|
1.0
|
CB
|
B:GLU38
|
4.6
|
29.5
|
1.0
|
C
|
B:THR37
|
4.6
|
31.7
|
1.0
|
HB2
|
B:GLU38
|
4.6
|
35.4
|
1.0
|
CG2
|
B:VAL39
|
4.6
|
27.3
|
1.0
|
N
|
B:GLU38
|
4.7
|
29.9
|
1.0
|
HE2
|
B:LYS5
|
4.7
|
56.8
|
1.0
|
CA
|
B:LYS58
|
4.7
|
35.5
|
1.0
|
CG
|
B:GLU38
|
4.7
|
29.7
|
1.0
|
HZ1
|
B:LYS5
|
4.8
|
59.9
|
1.0
|
C
|
B:VAL39
|
4.8
|
21.2
|
1.0
|
N
|
B:ILE59
|
4.8
|
30.5
|
1.0
|
H
|
B:ALA60
|
4.9
|
30.8
|
1.0
|
HB
|
B:VAL33
|
4.9
|
42.9
|
1.0
|
CB
|
B:VAL33
|
4.9
|
35.8
|
1.0
|
CA
|
B:ILE59
|
4.9
|
27.7
|
1.0
|
CB
|
B:LYS58
|
4.9
|
37.7
|
1.0
|
|
Sodium binding site 7 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 7 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na303
b:35.8
occ:1.00
|
HH21
|
B:ARG98
|
2.1
|
24.2
|
1.0
|
OE2
|
B:GLU104
|
2.6
|
21.0
|
1.0
|
O
|
B:HOH456
|
2.8
|
34.1
|
1.0
|
NH2
|
B:ARG98
|
2.9
|
20.1
|
1.0
|
O
|
B:HOH412
|
3.1
|
23.5
|
1.0
|
O
|
B:HOH405
|
3.2
|
35.2
|
1.0
|
HG2
|
B:GLU104
|
3.2
|
27.9
|
1.0
|
HH22
|
B:ARG98
|
3.2
|
24.2
|
1.0
|
HD1
|
C:PHE102
|
3.4
|
33.0
|
1.0
|
CD
|
B:GLU104
|
3.5
|
22.2
|
1.0
|
HE
|
B:ARG98
|
3.5
|
21.0
|
1.0
|
HG3
|
B:GLU104
|
3.6
|
27.9
|
1.0
|
CG
|
B:GLU104
|
3.6
|
23.2
|
1.0
|
HB3
|
B:PHE102
|
3.7
|
29.9
|
1.0
|
HD21
|
B:ASN65
|
3.7
|
21.4
|
1.0
|
HZ2
|
B:LYS112
|
3.8
|
19.9
|
1.0
|
CZ
|
B:ARG98
|
3.9
|
19.0
|
1.0
|
CD1
|
C:PHE102
|
4.0
|
27.5
|
1.0
|
NE
|
B:ARG98
|
4.1
|
17.5
|
1.0
|
HB2
|
B:PHE102
|
4.2
|
29.9
|
1.0
|
NA
|
C:NA301
|
4.2
|
48.2
|
1.0
|
HH22
|
C:ARG98
|
4.2
|
23.6
|
1.0
|
HE1
|
C:PHE102
|
4.3
|
33.5
|
1.0
|
CB
|
B:PHE102
|
4.4
|
24.9
|
1.0
|
ND2
|
B:ASN65
|
4.4
|
17.9
|
1.0
|
HD22
|
B:ASN65
|
4.4
|
21.4
|
1.0
|
HB3
|
C:PHE102
|
4.4
|
32.0
|
1.0
|
CE1
|
C:PHE102
|
4.5
|
27.9
|
1.0
|
NZ
|
B:LYS112
|
4.6
|
16.5
|
1.0
|
OE2
|
B:GLU77
|
4.6
|
17.0
|
1.0
|
OE1
|
B:GLU104
|
4.6
|
22.2
|
1.0
|
HZ3
|
B:LYS112
|
4.6
|
19.9
|
1.0
|
HD21
|
B:LEU108
|
4.6
|
33.9
|
1.0
|
O
|
B:PHE102
|
4.7
|
26.8
|
1.0
|
HZ1
|
B:LYS112
|
4.9
|
19.9
|
1.0
|
NH2
|
C:ARG98
|
4.9
|
19.6
|
1.0
|
CG
|
C:PHE102
|
4.9
|
27.2
|
1.0
|
|
Sodium binding site 8 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 8 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na304
b:45.3
occ:1.00
|
OD1
|
B:ASN195
|
2.1
|
0.7
|
1.0
|
HB2
|
B:SER194
|
2.9
|
84.9
|
1.0
|
CG
|
B:ASN195
|
3.2
|
99.4
|
1.0
|
O
|
B:HOH404
|
3.3
|
31.4
|
1.0
|
HA
|
B:ASN195
|
3.4
|
89.9
|
1.0
|
O
|
B:SER194
|
3.5
|
69.8
|
1.0
|
OG
|
B:SER194
|
3.5
|
68.8
|
1.0
|
C
|
B:SER194
|
3.5
|
68.7
|
1.0
|
CB
|
B:SER194
|
3.6
|
70.8
|
1.0
|
HG
|
B:SER194
|
3.6
|
82.5
|
1.0
|
N
|
B:ASN195
|
3.8
|
69.9
|
1.0
|
HD21
|
B:ASN195
|
3.9
|
0.5
|
1.0
|
CA
|
B:ASN195
|
3.9
|
74.9
|
1.0
|
ND2
|
B:ASN195
|
4.0
|
0.5
|
1.0
|
CB
|
B:ASN195
|
4.2
|
88.0
|
1.0
|
CA
|
B:SER194
|
4.2
|
69.6
|
1.0
|
H
|
B:ASN195
|
4.3
|
83.9
|
1.0
|
HB3
|
B:SER194
|
4.4
|
84.9
|
1.0
|
HA
|
B:SER194
|
4.6
|
83.6
|
1.0
|
HB3
|
B:ASN195
|
4.8
|
0.6
|
1.0
|
HD22
|
B:ASN195
|
4.8
|
0.5
|
1.0
|
HB2
|
B:ASN195
|
4.8
|
0.6
|
1.0
|
|
Sodium binding site 9 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 9 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na301
b:48.2
occ:1.00
|
HH22
|
B:ARG98
|
2.0
|
24.2
|
1.0
|
OE2
|
C:GLU77
|
2.4
|
25.5
|
1.0
|
O
|
B:HOH405
|
2.6
|
35.2
|
1.0
|
NH2
|
B:ARG98
|
2.8
|
20.1
|
1.0
|
O
|
C:HOH410
|
2.9
|
21.1
|
1.0
|
HH22
|
C:ARG98
|
3.0
|
23.6
|
1.0
|
HH21
|
C:ARG98
|
3.2
|
23.6
|
1.0
|
HH21
|
B:ARG98
|
3.2
|
24.2
|
1.0
|
NH2
|
C:ARG98
|
3.3
|
19.6
|
1.0
|
HH12
|
B:ARG98
|
3.4
|
21.7
|
1.0
|
O
|
C:HOH411
|
3.4
|
22.4
|
1.0
|
CD
|
C:GLU77
|
3.5
|
24.4
|
1.0
|
OE1
|
C:GLU77
|
3.8
|
24.0
|
1.0
|
CZ
|
B:ARG98
|
3.8
|
19.0
|
1.0
|
O
|
B:HOH462
|
3.8
|
22.7
|
1.0
|
NH1
|
B:ARG98
|
3.9
|
18.1
|
1.0
|
HD22
|
C:ASN65
|
4.1
|
23.7
|
1.0
|
NA
|
B:NA303
|
4.2
|
35.8
|
1.0
|
HD21
|
C:ASN65
|
4.2
|
23.7
|
1.0
|
CD1
|
B:PHE102
|
4.3
|
25.7
|
1.0
|
HD1
|
B:PHE102
|
4.3
|
30.9
|
1.0
|
O
|
C:HOH421
|
4.3
|
15.7
|
1.0
|
HB3
|
B:PHE102
|
4.5
|
29.9
|
1.0
|
CZ
|
C:ARG98
|
4.5
|
20.0
|
1.0
|
ND2
|
C:ASN65
|
4.5
|
19.7
|
1.0
|
CG
|
B:PHE102
|
4.5
|
24.7
|
1.0
|
CE1
|
B:PHE102
|
4.6
|
25.0
|
1.0
|
OE2
|
C:GLU104
|
4.7
|
21.1
|
1.0
|
HH11
|
B:ARG98
|
4.7
|
21.7
|
1.0
|
HE1
|
B:PHE102
|
4.8
|
30.0
|
1.0
|
OE2
|
B:GLU77
|
4.8
|
17.0
|
1.0
|
CG
|
C:GLU77
|
4.8
|
22.6
|
1.0
|
HG2
|
C:GLU77
|
4.8
|
27.1
|
1.0
|
HH12
|
C:ARG98
|
4.9
|
24.2
|
1.0
|
CB
|
B:PHE102
|
5.0
|
24.9
|
1.0
|
|
Sodium binding site 10 out
of 20 in 6nlh
Go back to
Sodium Binding Sites List in 6nlh
Sodium binding site 10 out
of 20 in the Structure of Human Triose Phosphate Isomerase R189A
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure of Human Triose Phosphate Isomerase R189A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na302
b:35.4
occ:1.00
|
O
|
C:GLN223
|
2.2
|
50.4
|
1.0
|
O
|
C:ALA221
|
2.5
|
49.3
|
1.0
|
O
|
C:VAL226
|
2.7
|
45.3
|
1.0
|
HZ1
|
C:LYS247
|
2.7
|
64.4
|
1.0
|
C
|
C:GLN223
|
3.3
|
52.6
|
1.0
|
HA
|
C:PRO224
|
3.4
|
65.2
|
1.0
|
NZ
|
C:LYS247
|
3.5
|
53.7
|
1.0
|
HZ2
|
C:LYS247
|
3.6
|
64.4
|
1.0
|
C
|
C:ALA221
|
3.7
|
50.8
|
1.0
|
H
|
C:VAL226
|
3.7
|
55.2
|
1.0
|
C
|
C:VAL226
|
3.8
|
43.9
|
1.0
|
O
|
C:PRO224
|
3.9
|
50.9
|
1.0
|
CA
|
C:PRO224
|
4.0
|
54.3
|
1.0
|
C
|
C:PRO224
|
4.0
|
52.2
|
1.0
|
C
|
C:SER222
|
4.0
|
54.9
|
1.0
|
HZ3
|
C:LYS247
|
4.1
|
64.4
|
1.0
|
N
|
C:GLN223
|
4.1
|
55.1
|
1.0
|
HB
|
C:VAL226
|
4.1
|
56.8
|
1.0
|
N
|
C:PRO224
|
4.1
|
54.8
|
1.0
|
HA
|
C:ASP227
|
4.1
|
51.0
|
1.0
|
HA
|
C:ALA221
|
4.2
|
59.0
|
1.0
|
O
|
C:SER222
|
4.2
|
56.4
|
1.0
|
HE2
|
C:LYS247
|
4.2
|
62.4
|
1.0
|
N
|
C:VAL226
|
4.2
|
46.1
|
1.0
|
CA
|
C:GLN223
|
4.3
|
55.0
|
1.0
|
H
|
C:GLN223
|
4.3
|
66.1
|
1.0
|
HA
|
C:SER222
|
4.4
|
65.5
|
1.0
|
CE
|
C:LYS247
|
4.4
|
52.0
|
1.0
|
HD3
|
C:LYS247
|
4.4
|
62.1
|
1.0
|
CA
|
C:VAL226
|
4.5
|
44.5
|
1.0
|
CA
|
C:ALA221
|
4.5
|
49.1
|
1.0
|
N
|
C:SER222
|
4.6
|
53.9
|
1.0
|
CA
|
C:SER222
|
4.6
|
54.7
|
1.0
|
HG12
|
C:VAL226
|
4.7
|
51.8
|
1.0
|
N
|
C:ASP225
|
4.7
|
50.3
|
1.0
|
CB
|
C:VAL226
|
4.7
|
47.3
|
1.0
|
N
|
C:ASP227
|
4.7
|
42.3
|
1.0
|
HB2
|
C:GLN223
|
4.7
|
63.3
|
1.0
|
HE1
|
C:PHE6
|
4.8
|
57.1
|
1.0
|
HB1
|
C:ALA221
|
4.9
|
56.0
|
1.0
|
CA
|
C:ASP227
|
4.9
|
42.5
|
1.0
|
CD
|
C:LYS247
|
5.0
|
51.8
|
1.0
|
OD1
|
C:ASP227
|
5.0
|
46.2
|
1.0
|
O
|
C:LEU220
|
5.0
|
48.9
|
1.0
|
|
Reference:
B.P.Roland,
K.R.Richards,
S.L.Hrizo,
S.Eicher,
Z.J.Barile,
T.C.Chang,
G.Savon,
P.Bianchi,
E.Fermo,
B.M.Ricerca,
L.Tortorolo,
J.Vockley,
A.P.Vandemark,
M.J.Palladino.
Missense Variant in TPI1 (ARG189GLN) Causes Neurologic Deficits Through Structural Changes in the Triosephosphate Isomerase Catalytic Site and Reduced Enzyme Levels in Vivo. Biochim Biophys Acta Mol V.1865 2257 2019BASIS Dis.
ISSN: ISSN 1879-260X
PubMed: 31075491
DOI: 10.1016/J.BBADIS.2019.05.002
Page generated: Tue Oct 8 12:19:52 2024
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