Calcium in PDB 6p06: Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
Protein crystallography data
The structure of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp, PDB code: 6p06
was solved by
B.Selvaraj,
M.J.Cuneo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.98 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.710,
97.950,
100.700,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.1 /
22.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
(pdb code 6p06). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp, PDB code: 6p06:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6p06
Go back to
Calcium Binding Sites List in 6p06
Calcium binding site 1 out
of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:30.4
occ:1.00
|
OE2
|
B:GLU145
|
2.3
|
31.9
|
1.0
|
OD1
|
A:ASP52
|
2.4
|
36.1
|
1.0
|
O
|
A:HOH408
|
2.4
|
30.8
|
1.0
|
O4
|
A:NMY301
|
2.4
|
28.7
|
1.0
|
O2A
|
A:APC302
|
2.6
|
21.5
|
1.0
|
OD2
|
A:ASP50
|
2.6
|
28.6
|
1.0
|
OE1
|
B:GLU145
|
2.8
|
30.9
|
1.0
|
CD
|
B:GLU145
|
2.9
|
27.8
|
1.0
|
OD1
|
A:ASP50
|
3.2
|
27.1
|
1.0
|
O3
|
A:NMY301
|
3.2
|
27.7
|
1.0
|
CG
|
A:ASP50
|
3.3
|
31.1
|
1.0
|
CG
|
A:ASP52
|
3.4
|
31.1
|
1.0
|
C4
|
A:NMY301
|
3.6
|
35.0
|
1.0
|
PA
|
A:APC302
|
3.6
|
25.6
|
1.0
|
OD2
|
A:ASP52
|
3.7
|
28.1
|
1.0
|
C3
|
A:NMY301
|
3.7
|
30.9
|
1.0
|
O1A
|
A:APC302
|
3.7
|
27.7
|
1.0
|
CA
|
A:CA304
|
3.8
|
27.0
|
1.0
|
NZ
|
A:LYS74
|
4.2
|
37.2
|
1.0
|
OE1
|
A:GLU76
|
4.4
|
31.4
|
1.0
|
O5'
|
A:APC302
|
4.4
|
36.1
|
1.0
|
CG
|
B:GLU145
|
4.4
|
27.2
|
1.0
|
O
|
B:HOH426
|
4.6
|
33.3
|
1.0
|
C5'
|
A:APC302
|
4.6
|
32.3
|
1.0
|
C5
|
A:NMY301
|
4.7
|
30.0
|
1.0
|
CB
|
A:ASP52
|
4.7
|
23.6
|
1.0
|
CB
|
A:ASP50
|
4.8
|
23.6
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6p06
Go back to
Calcium Binding Sites List in 6p06
Calcium binding site 2 out
of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:27.0
occ:1.00
|
O2A
|
A:APC302
|
2.3
|
21.5
|
1.0
|
O1B
|
A:APC302
|
2.3
|
26.6
|
1.0
|
O
|
A:HOH409
|
2.3
|
28.4
|
1.0
|
OD2
|
A:ASP52
|
2.3
|
28.1
|
1.0
|
OD1
|
A:ASP50
|
2.4
|
27.1
|
1.0
|
O1G
|
A:APC302
|
2.7
|
40.7
|
1.0
|
CG
|
A:ASP52
|
3.4
|
31.1
|
1.0
|
PB
|
A:APC302
|
3.5
|
26.6
|
1.0
|
PA
|
A:APC302
|
3.5
|
25.6
|
1.0
|
CG
|
A:ASP50
|
3.6
|
31.1
|
1.0
|
O
|
A:ASP50
|
3.6
|
29.7
|
1.0
|
OD1
|
A:ASP52
|
3.7
|
36.1
|
1.0
|
CA
|
A:CA303
|
3.8
|
30.4
|
1.0
|
C3A
|
A:APC302
|
3.8
|
30.2
|
1.0
|
PG
|
A:APC302
|
4.0
|
34.3
|
1.0
|
O
|
B:HOH426
|
4.1
|
33.3
|
1.0
|
C
|
A:ASP50
|
4.1
|
26.6
|
1.0
|
OE2
|
B:GLU145
|
4.1
|
31.9
|
1.0
|
N
|
A:ASP50
|
4.2
|
28.1
|
1.0
|
O3B
|
A:APC302
|
4.2
|
30.4
|
1.0
|
OD2
|
A:ASP50
|
4.2
|
28.6
|
1.0
|
OG
|
A:SER39
|
4.2
|
30.1
|
1.0
|
O
|
A:HOH420
|
4.3
|
30.1
|
1.0
|
C5'
|
A:APC302
|
4.3
|
32.3
|
1.0
|
N
|
A:SER39
|
4.4
|
26.6
|
1.0
|
O5'
|
A:APC302
|
4.4
|
36.1
|
1.0
|
CA
|
A:ASP50
|
4.5
|
24.5
|
1.0
|
O3G
|
A:APC302
|
4.6
|
31.8
|
1.0
|
CB
|
A:ASP50
|
4.6
|
23.6
|
1.0
|
O1A
|
A:APC302
|
4.6
|
27.7
|
1.0
|
O2B
|
A:APC302
|
4.7
|
30.8
|
1.0
|
CB
|
A:ASP52
|
4.7
|
23.6
|
1.0
|
N
|
A:ILE51
|
4.8
|
21.7
|
1.0
|
CA
|
A:GLY38
|
4.8
|
29.5
|
1.0
|
N
|
A:ASP52
|
5.0
|
26.8
|
1.0
|
CB
|
A:SER39
|
5.0
|
25.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6p06
Go back to
Calcium Binding Sites List in 6p06
Calcium binding site 3 out
of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca306
b:22.2
occ:1.00
|
OD1
|
B:ASP52
|
2.3
|
17.1
|
1.0
|
O4
|
A:NMY305
|
2.3
|
21.9
|
1.0
|
OE2
|
A:GLU145
|
2.4
|
22.8
|
1.0
|
O
|
B:HOH406
|
2.4
|
17.1
|
1.0
|
OD2
|
B:ASP50
|
2.4
|
24.1
|
1.0
|
O2A
|
B:APC301
|
2.4
|
18.6
|
1.0
|
CD
|
A:GLU145
|
3.0
|
26.3
|
1.0
|
OD1
|
B:ASP50
|
3.1
|
21.4
|
1.0
|
OE1
|
A:GLU145
|
3.1
|
25.7
|
1.0
|
CG
|
B:ASP50
|
3.1
|
24.4
|
1.0
|
CG
|
B:ASP52
|
3.3
|
20.4
|
1.0
|
O3
|
A:NMY305
|
3.5
|
21.2
|
1.0
|
C4
|
A:NMY305
|
3.6
|
30.4
|
1.0
|
PA
|
B:APC301
|
3.6
|
21.2
|
1.0
|
CA
|
B:CA302
|
3.7
|
21.2
|
1.0
|
OD2
|
B:ASP52
|
3.7
|
20.5
|
1.0
|
O1A
|
B:APC301
|
3.7
|
25.9
|
1.0
|
C3
|
A:NMY305
|
3.9
|
26.1
|
1.0
|
O
|
A:HOH433
|
4.2
|
25.7
|
1.0
|
O5'
|
B:APC301
|
4.3
|
28.3
|
1.0
|
NZ
|
B:LYS74
|
4.3
|
23.2
|
1.0
|
CG
|
A:GLU145
|
4.4
|
27.8
|
1.0
|
OE2
|
B:GLU76
|
4.5
|
27.2
|
1.0
|
C5
|
A:NMY305
|
4.5
|
29.5
|
1.0
|
C5'
|
B:APC301
|
4.5
|
23.9
|
1.0
|
O
|
B:HOH401
|
4.6
|
19.0
|
1.0
|
CB
|
B:ASP50
|
4.6
|
16.4
|
1.0
|
CB
|
B:ASP52
|
4.6
|
19.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6p06
Go back to
Calcium Binding Sites List in 6p06
Calcium binding site 4 out
of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:21.2
occ:1.00
|
O
|
B:HOH401
|
2.2
|
19.0
|
1.0
|
OD2
|
B:ASP52
|
2.3
|
20.5
|
1.0
|
O2A
|
B:APC301
|
2.3
|
18.6
|
1.0
|
OD1
|
B:ASP50
|
2.4
|
21.4
|
1.0
|
O1B
|
B:APC301
|
2.4
|
22.4
|
1.0
|
O
|
B:HOH415
|
2.4
|
19.6
|
1.0
|
O3G
|
B:APC301
|
3.2
|
32.0
|
1.0
|
CG
|
B:ASP52
|
3.3
|
20.4
|
1.0
|
PA
|
B:APC301
|
3.4
|
21.2
|
1.0
|
CG
|
B:ASP50
|
3.5
|
24.4
|
1.0
|
PB
|
B:APC301
|
3.6
|
18.8
|
1.0
|
OD1
|
B:ASP52
|
3.6
|
17.1
|
1.0
|
CA
|
A:CA306
|
3.7
|
22.2
|
1.0
|
O
|
B:ASP50
|
3.7
|
23.2
|
1.0
|
O
|
A:HOH433
|
3.7
|
25.7
|
1.0
|
C3A
|
B:APC301
|
3.8
|
21.0
|
1.0
|
C5'
|
B:APC301
|
4.1
|
23.9
|
1.0
|
C
|
B:ASP50
|
4.1
|
21.6
|
1.0
|
OD2
|
B:ASP50
|
4.1
|
24.1
|
1.0
|
OG
|
B:SER39
|
4.2
|
23.6
|
1.0
|
O5'
|
B:APC301
|
4.2
|
28.3
|
1.0
|
O
|
B:HOH413
|
4.3
|
18.3
|
1.0
|
PG
|
B:APC301
|
4.3
|
30.7
|
1.0
|
N
|
B:ASP50
|
4.4
|
27.2
|
1.0
|
OE2
|
A:GLU145
|
4.4
|
22.8
|
1.0
|
O3B
|
B:APC301
|
4.4
|
23.5
|
1.0
|
N
|
B:SER39
|
4.5
|
22.5
|
1.0
|
CB
|
B:ASP52
|
4.6
|
19.0
|
1.0
|
CA
|
B:ASP50
|
4.6
|
22.4
|
1.0
|
O1A
|
B:APC301
|
4.6
|
25.9
|
1.0
|
CB
|
B:ASP50
|
4.7
|
16.4
|
1.0
|
CA
|
B:GLY38
|
4.7
|
21.4
|
1.0
|
O2B
|
B:APC301
|
4.7
|
24.1
|
1.0
|
O2G
|
B:APC301
|
4.7
|
31.1
|
1.0
|
N
|
B:ILE51
|
4.7
|
19.8
|
1.0
|
N
|
B:ASP52
|
4.9
|
13.4
|
1.0
|
|
Reference:
B.Selvaraj,
M.J.Cuneo.
Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.
Page generated: Tue Jul 16 12:40:51 2024
|