Calcium in PDB 4y90: Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
Enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans:
5.3.1.1;
Protein crystallography data
The structure of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans, PDB code: 4y90
was solved by
S.Romero-Romero,
A.Rodriguez-Romero,
D.A.Fernadez-Velasco,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
36.13 /
2.10
|
|
Space group
|
H 3 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
169.620,
169.620,
202.266,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
13.6 /
18.6
|
Other elements in 4y90:
The structure of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
(pdb code 4y90). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans, PDB code: 4y90:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 4y90
Go back to
Calcium Binding Sites List in 4y90
Calcium binding site 1 out
of 5 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:23.4
occ:1.00
|
HE2
|
A:HIS96
|
2.3
|
25.8
|
1.0
|
|
HD22
|
A:ASN11
|
2.5
|
20.6
|
1.0
|
|
OE2
|
A:GLU164
|
3.0
|
24.1
|
1.0
|
|
HG
|
A:LEU228
|
3.1
|
25.9
|
1.0
|
|
O
|
A:HOH523
|
3.1
|
30.2
|
1.0
|
|
HE2
|
A:LYS13
|
3.1
|
18.8
|
1.0
|
|
NE2
|
A:HIS96
|
3.2
|
21.5
|
1.0
|
|
HB3
|
A:ASN11
|
3.2
|
19.6
|
1.0
|
|
ND2
|
A:ASN11
|
3.3
|
17.1
|
1.0
|
|
HE3
|
A:LYS13
|
3.4
|
18.8
|
1.0
|
|
OE1
|
A:GLU164
|
3.6
|
21.4
|
1.0
|
|
CE
|
A:LYS13
|
3.7
|
15.7
|
1.0
|
|
CD
|
A:GLU164
|
3.7
|
28.8
|
1.0
|
|
HD21
|
A:ASN11
|
3.8
|
20.6
|
1.0
|
|
HD23
|
A:LEU228
|
3.8
|
23.4
|
1.0
|
|
HD21
|
A:LEU228
|
3.8
|
23.4
|
1.0
|
|
HZ1
|
A:LYS13
|
3.8
|
22.0
|
1.0
|
|
HD2
|
A:HIS96
|
3.8
|
19.4
|
1.0
|
|
HA2
|
A:GLY230
|
3.9
|
20.4
|
1.0
|
|
CD2
|
A:HIS96
|
3.9
|
16.1
|
1.0
|
|
CG
|
A:LEU228
|
3.9
|
21.6
|
1.0
|
|
HA3
|
A:GLY230
|
3.9
|
20.4
|
1.0
|
|
CB
|
A:ASN11
|
3.9
|
16.3
|
1.0
|
|
CD2
|
A:LEU228
|
4.0
|
19.5
|
1.0
|
|
HB2
|
A:ASN11
|
4.1
|
19.6
|
1.0
|
|
CG
|
A:ASN11
|
4.1
|
15.2
|
1.0
|
|
N
|
A:GLY230
|
4.2
|
15.0
|
1.0
|
|
CA
|
A:GLY230
|
4.2
|
17.0
|
1.0
|
|
CE1
|
A:HIS96
|
4.2
|
19.5
|
1.0
|
|
NZ
|
A:LYS13
|
4.3
|
18.4
|
1.0
|
|
O
|
A:LEU228
|
4.4
|
17.9
|
1.0
|
|
C
|
A:VAL229
|
4.4
|
18.9
|
1.0
|
|
HE1
|
A:HIS96
|
4.4
|
23.4
|
1.0
|
|
H
|
A:GLY230
|
4.4
|
18.0
|
1.0
|
|
O
|
A:VAL229
|
4.6
|
20.8
|
1.0
|
|
HD11
|
A:LEU228
|
4.6
|
26.9
|
1.0
|
|
HB3
|
A:LEU228
|
4.6
|
22.0
|
1.0
|
|
C
|
A:LEU228
|
4.7
|
22.0
|
1.0
|
|
HZ3
|
A:LYS13
|
4.8
|
22.0
|
1.0
|
|
HG2
|
A:LYS13
|
4.8
|
16.6
|
1.0
|
|
CD1
|
A:LEU228
|
4.8
|
22.4
|
1.0
|
|
CB
|
A:LEU228
|
4.9
|
18.3
|
1.0
|
|
HZ2
|
A:LYS13
|
4.9
|
22.0
|
1.0
|
|
N
|
A:VAL229
|
4.9
|
15.7
|
1.0
|
|
O
|
A:HOH470
|
5.0
|
22.0
|
1.0
|
|
Calcium binding site 2 out
of 5 in 4y90
Go back to
Calcium Binding Sites List in 4y90
Calcium binding site 2 out
of 5 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca306
b:29.7
occ:1.00
|
HE2
|
B:HIS96
|
2.5
|
28.3
|
1.0
|
|
HD22
|
B:ASN11
|
2.5
|
20.1
|
1.0
|
|
HG
|
B:LEU228
|
2.8
|
25.6
|
1.0
|
|
O
|
B:HOH514
|
3.0
|
32.3
|
1.0
|
|
OE2
|
B:GLU164
|
3.0
|
27.7
|
1.0
|
|
HB3
|
B:ASN11
|
3.1
|
24.0
|
1.0
|
|
NE2
|
B:HIS96
|
3.3
|
23.6
|
1.0
|
|
ND2
|
B:ASN11
|
3.3
|
16.8
|
1.0
|
|
HE2
|
B:LYS13
|
3.4
|
21.2
|
1.0
|
|
OE1
|
B:GLU164
|
3.6
|
28.6
|
1.0
|
|
HE3
|
B:LYS13
|
3.6
|
21.2
|
1.0
|
|
HD21
|
B:LEU228
|
3.7
|
29.1
|
1.0
|
|
CD
|
B:GLU164
|
3.7
|
33.8
|
1.0
|
|
CG
|
B:LEU228
|
3.7
|
21.3
|
1.0
|
|
HD2
|
B:HIS96
|
3.8
|
21.1
|
1.0
|
|
HA2
|
B:GLY230
|
3.8
|
30.4
|
1.0
|
|
CB
|
B:ASN11
|
3.8
|
20.0
|
1.0
|
|
HD23
|
B:LEU228
|
3.8
|
29.1
|
1.0
|
|
HB2
|
B:ASN11
|
3.9
|
24.0
|
1.0
|
|
HD21
|
B:ASN11
|
3.9
|
20.1
|
1.0
|
|
HZ1
|
B:LYS13
|
3.9
|
23.6
|
1.0
|
|
CE
|
B:LYS13
|
3.9
|
17.6
|
1.0
|
|
CD2
|
B:HIS96
|
3.9
|
17.6
|
1.0
|
|
CD2
|
B:LEU228
|
4.0
|
24.3
|
1.0
|
|
HA3
|
B:GLY230
|
4.0
|
30.4
|
1.0
|
|
CG
|
B:ASN11
|
4.1
|
18.6
|
1.0
|
|
N
|
B:GLY230
|
4.1
|
23.8
|
1.0
|
|
CA
|
B:GLY230
|
4.2
|
25.4
|
1.0
|
|
HD11
|
B:LEU228
|
4.2
|
19.2
|
1.0
|
|
C
|
B:VAL229
|
4.3
|
23.7
|
1.0
|
|
O
|
B:LEU228
|
4.3
|
20.3
|
1.0
|
|
H
|
B:GLY230
|
4.4
|
28.5
|
1.0
|
|
CE1
|
B:HIS96
|
4.4
|
20.6
|
1.0
|
|
NZ
|
B:LYS13
|
4.4
|
19.6
|
1.0
|
|
O
|
B:VAL229
|
4.5
|
24.1
|
1.0
|
|
CD1
|
B:LEU228
|
4.5
|
16.0
|
1.0
|
|
C
|
B:LEU228
|
4.6
|
18.6
|
1.0
|
|
HB3
|
B:LEU228
|
4.6
|
25.8
|
1.0
|
|
HE1
|
B:HIS96
|
4.6
|
24.7
|
1.0
|
|
HD12
|
B:LEU228
|
4.7
|
19.2
|
1.0
|
|
CB
|
B:LEU228
|
4.8
|
21.5
|
1.0
|
|
N
|
B:VAL229
|
4.8
|
20.5
|
1.0
|
|
HZ3
|
B:LYS13
|
4.9
|
23.6
|
1.0
|
|
HD22
|
B:LEU228
|
4.9
|
29.1
|
1.0
|
|
HG3
|
B:LYS13
|
5.0
|
20.5
|
1.0
|
|
Calcium binding site 3 out
of 5 in 4y90
Go back to
Calcium Binding Sites List in 4y90
Calcium binding site 3 out
of 5 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca307
b:60.6
occ:1.00
|
O
|
B:VAL224
|
2.6
|
30.0
|
1.0
|
|
O
|
B:CYS219
|
2.7
|
30.5
|
1.0
|
|
O
|
B:LYS221
|
2.7
|
26.6
|
1.0
|
|
O
|
B:HOH601
|
3.1
|
59.7
|
1.0
|
|
O
|
B:HOH550
|
3.1
|
43.1
|
1.0
|
|
O
|
B:HOH560
|
3.4
|
41.8
|
1.0
|
|
O
|
B:HOH600
|
3.5
|
60.2
|
1.0
|
|
C
|
B:LYS221
|
3.8
|
28.1
|
1.0
|
|
C
|
B:VAL224
|
3.8
|
26.8
|
1.0
|
|
C
|
B:CYS219
|
3.9
|
31.5
|
1.0
|
|
H
|
B:VAL224
|
4.0
|
38.2
|
1.0
|
|
HA
|
B:ASN225
|
4.0
|
23.4
|
1.0
|
|
HA2
|
B:GLY220
|
4.0
|
32.6
|
1.0
|
|
HD22
|
B:ASN225
|
4.1
|
30.6
|
1.0
|
|
C
|
B:GLY220
|
4.1
|
30.9
|
1.0
|
|
O
|
B:GLY220
|
4.2
|
32.5
|
1.0
|
|
HA
|
B:PRO222
|
4.3
|
45.9
|
1.0
|
|
HB
|
B:VAL224
|
4.3
|
30.4
|
1.0
|
|
N
|
B:LYS221
|
4.3
|
29.9
|
1.0
|
|
O
|
B:PRO222
|
4.4
|
26.8
|
1.0
|
|
N
|
B:VAL224
|
4.4
|
31.8
|
1.0
|
|
CA
|
B:GLY220
|
4.4
|
27.1
|
1.0
|
|
C
|
B:PRO222
|
4.5
|
33.2
|
1.0
|
|
H
|
B:LYS221
|
4.6
|
35.9
|
1.0
|
|
CA
|
B:PRO222
|
4.6
|
38.3
|
1.0
|
|
O
|
B:HOH569
|
4.6
|
39.2
|
1.0
|
|
N
|
B:PRO222
|
4.6
|
29.6
|
1.0
|
|
CA
|
B:VAL224
|
4.7
|
33.0
|
1.0
|
|
N
|
B:GLY220
|
4.7
|
33.9
|
1.0
|
|
ND2
|
B:ASN225
|
4.7
|
25.5
|
1.0
|
|
HA
|
B:CYS219
|
4.7
|
28.8
|
1.0
|
|
CA
|
B:LYS221
|
4.7
|
28.7
|
1.0
|
|
N
|
B:ASN225
|
4.8
|
20.8
|
1.0
|
|
CA
|
B:ASN225
|
4.8
|
19.5
|
1.0
|
|
HD21
|
B:ASN225
|
4.9
|
30.6
|
1.0
|
|
HB3
|
B:CYS219
|
4.9
|
31.9
|
1.0
|
|
CA
|
B:CYS219
|
4.9
|
24.0
|
1.0
|
|
CB
|
B:VAL224
|
5.0
|
25.4
|
1.0
|
|
Calcium binding site 4 out
of 5 in 4y90
Go back to
Calcium Binding Sites List in 4y90
Calcium binding site 4 out
of 5 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca306
b:68.1
occ:1.00
|
HZ1
|
C:LYS113
|
2.5
|
22.9
|
1.0
|
|
HO3
|
C:GOL302
|
2.5
|
36.1
|
1.0
|
|
HE1
|
D:HIS103
|
2.8
|
45.1
|
1.0
|
|
O
|
D:HOH485
|
3.2
|
21.6
|
1.0
|
|
O
|
C:HOH496
|
3.2
|
25.4
|
1.0
|
|
NZ
|
C:LYS113
|
3.3
|
19.0
|
1.0
|
|
HG2
|
C:GLU78
|
3.3
|
19.3
|
1.0
|
|
HZ3
|
C:LYS113
|
3.4
|
22.9
|
1.0
|
|
O
|
C:HOH460
|
3.5
|
19.0
|
1.0
|
|
O3
|
C:GOL302
|
3.5
|
30.1
|
1.0
|
|
HH21
|
C:ARG99
|
3.6
|
26.5
|
1.0
|
|
CE1
|
D:HIS103
|
3.6
|
37.6
|
1.0
|
|
HA
|
C:SER68
|
3.6
|
26.7
|
1.0
|
|
OD2
|
C:ASP66
|
3.7
|
26.3
|
1.0
|
|
HO2
|
C:GOL302
|
3.7
|
45.1
|
1.0
|
|
HZ2
|
C:LYS113
|
3.8
|
22.9
|
1.0
|
|
HE2
|
C:LYS113
|
3.9
|
24.3
|
1.0
|
|
CD
|
C:GLU78
|
3.9
|
26.0
|
1.0
|
|
OE1
|
C:GLU78
|
4.0
|
24.4
|
1.0
|
|
CG
|
C:GLU78
|
4.1
|
16.1
|
1.0
|
|
CE
|
C:LYS113
|
4.1
|
20.2
|
1.0
|
|
H31
|
C:GOL302
|
4.2
|
44.0
|
1.0
|
|
NH2
|
C:ARG99
|
4.2
|
22.1
|
1.0
|
|
O
|
D:HOH581
|
4.3
|
38.3
|
1.0
|
|
HE3
|
C:LYS113
|
4.3
|
24.3
|
1.0
|
|
HH22
|
C:ARG99
|
4.3
|
26.5
|
1.0
|
|
OE2
|
C:GLU78
|
4.4
|
24.0
|
1.0
|
|
C3
|
C:GOL302
|
4.4
|
36.6
|
1.0
|
|
HE2
|
D:HIS103
|
4.4
|
45.6
|
1.0
|
|
NE2
|
D:HIS103
|
4.4
|
38.0
|
1.0
|
|
HB3
|
C:GLU78
|
4.5
|
22.9
|
1.0
|
|
O2
|
C:GOL302
|
4.5
|
37.5
|
1.0
|
|
ND1
|
D:HIS103
|
4.5
|
31.2
|
1.0
|
|
CA
|
C:SER68
|
4.6
|
22.2
|
1.0
|
|
O
|
C:VAL67
|
4.6
|
18.7
|
1.0
|
|
CG
|
C:ASP66
|
4.7
|
29.4
|
1.0
|
|
HA
|
C:GLU78
|
4.7
|
21.3
|
1.0
|
|
OE2
|
C:GLU105
|
4.7
|
26.6
|
1.0
|
|
H
|
C:ALA69
|
4.7
|
23.0
|
1.0
|
|
HG3
|
C:GLU78
|
4.8
|
19.3
|
1.0
|
|
OD1
|
C:ASP66
|
4.8
|
23.2
|
1.0
|
|
CB
|
C:GLU78
|
4.8
|
19.1
|
1.0
|
|
HB2
|
C:SER68
|
4.9
|
21.7
|
1.0
|
|
HE
|
C:ARG99
|
4.9
|
23.3
|
1.0
|
|
HG
|
C:SER68
|
4.9
|
22.2
|
1.0
|
|
HH22
|
D:ARG99
|
5.0
|
24.1
|
1.0
|
|
HH12
|
D:ARG99
|
5.0
|
24.0
|
1.0
|
|
Calcium binding site 5 out
of 5 in 4y90
Go back to
Calcium Binding Sites List in 4y90
Calcium binding site 5 out
of 5 in the Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Triosephosphate Isomerase From Deinococcus Radiodurans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca304
b:61.1
occ:1.00
|
H
|
D:GLY208
|
2.2
|
20.5
|
1.0
|
|
H
|
D:VAL210
|
2.2
|
29.0
|
1.0
|
|
O2
|
D:SO4301
|
2.6
|
51.8
|
1.0
|
|
H
|
D:GLY230
|
2.6
|
24.7
|
1.0
|
|
HA
|
D:VAL229
|
2.7
|
22.8
|
1.0
|
|
HB
|
D:VAL210
|
2.9
|
31.9
|
1.0
|
|
HG23
|
D:VAL210
|
3.0
|
29.7
|
1.0
|
|
N
|
D:GLY208
|
3.0
|
17.1
|
1.0
|
|
N
|
D:VAL210
|
3.1
|
24.2
|
1.0
|
|
O
|
D:LEU228
|
3.2
|
20.9
|
1.0
|
|
H
|
D:SER209
|
3.2
|
24.9
|
1.0
|
|
N
|
D:SER209
|
3.4
|
20.7
|
1.0
|
|
N
|
D:GLY230
|
3.4
|
20.6
|
1.0
|
|
CB
|
D:VAL210
|
3.5
|
26.6
|
1.0
|
|
HA2
|
D:GLY207
|
3.6
|
19.6
|
1.0
|
|
CG2
|
D:VAL210
|
3.6
|
24.7
|
1.0
|
|
CA
|
D:VAL229
|
3.6
|
19.0
|
1.0
|
|
C
|
D:GLY208
|
3.7
|
28.2
|
1.0
|
|
CA
|
D:GLY208
|
3.7
|
25.2
|
1.0
|
|
HA2
|
D:GLY208
|
3.8
|
30.2
|
1.0
|
|
CA
|
D:VAL210
|
3.8
|
27.0
|
1.0
|
|
S
|
D:SO4301
|
3.9
|
37.0
|
1.0
|
|
HG21
|
D:VAL210
|
3.9
|
29.7
|
1.0
|
|
HG13
|
D:VAL229
|
3.9
|
26.8
|
1.0
|
|
O
|
D:HOH531
|
4.0
|
32.3
|
1.0
|
|
HA
|
D:SER209
|
4.0
|
22.4
|
1.0
|
|
CA
|
D:SER209
|
4.0
|
18.7
|
1.0
|
|
O1
|
D:SO4301
|
4.0
|
37.1
|
1.0
|
|
C
|
D:SER209
|
4.0
|
27.9
|
1.0
|
|
C
|
D:VAL229
|
4.0
|
19.1
|
1.0
|
|
C
|
D:GLY207
|
4.0
|
21.9
|
1.0
|
|
C
|
D:LEU228
|
4.1
|
20.6
|
1.0
|
|
CA
|
D:GLY207
|
4.1
|
16.3
|
1.0
|
|
HA3
|
D:GLY207
|
4.2
|
19.6
|
1.0
|
|
HA3
|
D:GLY230
|
4.3
|
22.4
|
1.0
|
|
N
|
D:VAL229
|
4.3
|
20.1
|
1.0
|
|
HG22
|
D:VAL229
|
4.4
|
33.5
|
1.0
|
|
O
|
D:VAL210
|
4.4
|
21.6
|
1.0
|
|
HG22
|
D:VAL210
|
4.4
|
29.7
|
1.0
|
|
O
|
D:GLY208
|
4.5
|
18.6
|
1.0
|
|
CA
|
D:GLY230
|
4.5
|
18.7
|
1.0
|
|
O
|
D:HOH520
|
4.5
|
28.3
|
1.0
|
|
HA
|
D:VAL210
|
4.6
|
32.4
|
1.0
|
|
CG1
|
D:VAL229
|
4.6
|
22.3
|
1.0
|
|
CB
|
D:VAL229
|
4.6
|
28.2
|
1.0
|
|
HA3
|
D:GLY208
|
4.6
|
30.2
|
1.0
|
|
C
|
D:VAL210
|
4.7
|
28.0
|
1.0
|
|
O3
|
D:SO4301
|
4.7
|
29.1
|
1.0
|
|
O4
|
D:SO4301
|
4.7
|
34.9
|
1.0
|
|
HG12
|
D:VAL229
|
4.7
|
26.8
|
1.0
|
|
OE2
|
D:GLU164
|
4.8
|
28.7
|
1.0
|
|
CG1
|
D:VAL210
|
4.9
|
22.2
|
1.0
|
|
Reference:
S.Romero-Romero,
M.Costas,
A.Rodriguez-Romero,
D.Alejandro Fernandez-Velasco.
Reversibility and Two State Behaviour in the Thermal Unfolding of Oligomeric Tim Barrel Proteins. Phys Chem Chem Phys V. 17 20699 2015.
ISSN: ESSN 1463-9084
PubMed: 26206330
DOI: 10.1039/C5CP01599E
Page generated: Sun Jul 14 14:50:44 2024
|
