Calcium in PDB 8tff: Porx with BEF3 Phosphate Analog
Protein crystallography data
The structure of Porx with BEF3 Phosphate Analog, PDB code: 8tff
was solved by
A.Saran,
N.Zeytuni,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.81 /
2.34
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.32,
97.518,
131.258,
90,
90,
90
|
R / Rfree (%)
|
16.5 /
23.1
|
Other elements in 8tff:
The structure of Porx with BEF3 Phosphate Analog also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Porx with BEF3 Phosphate Analog
(pdb code 8tff). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Porx with BEF3 Phosphate Analog, PDB code: 8tff:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 1 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:21.9
occ:1.00
|
OD1
|
A:ASN238
|
2.1
|
21.2
|
1.0
|
OD2
|
A:ASP414
|
2.2
|
16.1
|
1.0
|
OG1
|
A:THR271
|
2.2
|
16.9
|
1.0
|
OD1
|
A:ASP237
|
2.2
|
24.5
|
1.0
|
NE2
|
A:HIS415
|
2.4
|
15.4
|
1.0
|
CG
|
A:ASP414
|
2.9
|
20.3
|
1.0
|
OD1
|
A:ASP414
|
3.1
|
21.3
|
1.0
|
CG
|
A:ASP237
|
3.1
|
23.6
|
1.0
|
CB
|
A:THR271
|
3.2
|
19.8
|
1.0
|
CE1
|
A:HIS415
|
3.2
|
17.9
|
1.0
|
CD2
|
A:HIS415
|
3.2
|
16.0
|
1.0
|
O
|
A:HOH703
|
3.3
|
32.2
|
1.0
|
CG
|
A:ASN238
|
3.3
|
23.8
|
1.0
|
OD2
|
A:ASP237
|
3.6
|
25.9
|
1.0
|
CA
|
A:THR271
|
3.6
|
20.9
|
1.0
|
CG2
|
A:THR271
|
3.6
|
21.2
|
1.0
|
N
|
A:THR271
|
3.7
|
22.2
|
1.0
|
N
|
A:ASN238
|
3.8
|
19.5
|
1.0
|
ND2
|
A:ASN238
|
4.2
|
23.3
|
1.0
|
ND1
|
A:HIS415
|
4.2
|
16.0
|
1.0
|
CG
|
A:HIS415
|
4.2
|
16.1
|
1.0
|
CA
|
A:ASN238
|
4.3
|
21.1
|
1.0
|
CB
|
A:ASP237
|
4.3
|
22.5
|
1.0
|
CB
|
A:ASN238
|
4.4
|
22.0
|
1.0
|
CB
|
A:ASP414
|
4.4
|
20.5
|
1.0
|
CA
|
A:ASP237
|
4.4
|
22.2
|
1.0
|
C
|
A:ASP237
|
4.5
|
22.0
|
1.0
|
O
|
A:HOH851
|
4.6
|
29.4
|
1.0
|
C
|
A:ALA270
|
4.7
|
21.3
|
1.0
|
NH1
|
A:ARG275
|
4.7
|
24.1
|
1.0
|
|
Calcium binding site 2 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 2 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:35.2
occ:1.00
|
O
|
A:MET467
|
2.3
|
28.6
|
1.0
|
O
|
A:HOH876
|
2.3
|
38.1
|
1.0
|
O
|
A:LYS455
|
2.3
|
34.1
|
1.0
|
O
|
A:HOH748
|
2.4
|
29.2
|
1.0
|
OXT
|
A:ACT604
|
2.6
|
34.6
|
1.0
|
O
|
A:ACT604
|
2.9
|
36.3
|
1.0
|
C
|
A:ACT604
|
3.1
|
44.2
|
1.0
|
C
|
A:MET467
|
3.3
|
30.0
|
1.0
|
C
|
A:LYS455
|
3.5
|
27.1
|
1.0
|
O
|
A:SER469
|
4.0
|
29.4
|
1.0
|
CA
|
A:MET467
|
4.1
|
36.1
|
1.0
|
CA
|
A:LYS455
|
4.2
|
27.7
|
1.0
|
CB
|
A:LYS455
|
4.2
|
35.2
|
1.0
|
OE2
|
A:GLU456
|
4.2
|
37.9
|
1.0
|
N
|
A:SER468
|
4.3
|
29.3
|
1.0
|
CA
|
A:SER468
|
4.4
|
30.8
|
1.0
|
N
|
A:GLU456
|
4.5
|
25.8
|
1.0
|
C
|
A:SER468
|
4.5
|
26.5
|
1.0
|
O
|
A:HOH921
|
4.5
|
12.3
|
1.0
|
CH3
|
A:ACT604
|
4.6
|
41.2
|
1.0
|
CB
|
A:MET467
|
4.7
|
42.5
|
1.0
|
CA
|
A:GLU456
|
4.7
|
30.7
|
1.0
|
N
|
A:SER469
|
4.7
|
24.1
|
1.0
|
CG
|
A:GLU456
|
4.8
|
35.1
|
1.0
|
C
|
A:SER469
|
4.9
|
24.8
|
1.0
|
CD
|
A:GLU456
|
4.9
|
36.6
|
1.0
|
O
|
A:SER468
|
5.0
|
28.7
|
1.0
|
|
Calcium binding site 3 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 3 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:40.2
occ:1.00
|
F3
|
A:BEF605
|
2.1
|
50.3
|
1.0
|
OD2
|
A:ASP54
|
2.3
|
35.6
|
1.0
|
O
|
A:ASN56
|
2.3
|
34.6
|
0.5
|
O
|
A:ASN56
|
2.4
|
34.1
|
0.5
|
O
|
A:HOH728
|
2.4
|
34.0
|
1.0
|
OD1
|
A:ASP11
|
2.5
|
39.6
|
1.0
|
O
|
A:HOH800
|
2.5
|
37.1
|
1.0
|
CG
|
A:ASP11
|
3.3
|
33.7
|
1.0
|
CG
|
A:ASP54
|
3.4
|
36.1
|
1.0
|
OD2
|
A:ASP11
|
3.4
|
36.1
|
1.0
|
BE
|
A:BEF605
|
3.4
|
42.1
|
1.0
|
C
|
A:ASN56
|
3.6
|
32.1
|
0.5
|
C
|
A:ASN56
|
3.6
|
31.4
|
0.5
|
OD1
|
A:ASP54
|
3.9
|
37.7
|
1.0
|
OD1
|
A:ASP10
|
4.1
|
36.5
|
1.0
|
OE1
|
A:GLU12
|
4.2
|
47.3
|
1.0
|
F1
|
A:BEF605
|
4.4
|
39.1
|
1.0
|
CB
|
A:ASN56
|
4.4
|
35.2
|
0.5
|
CG
|
A:MET57
|
4.4
|
35.7
|
1.0
|
CA
|
A:ASN56
|
4.4
|
33.0
|
0.5
|
N
|
A:MET57
|
4.5
|
31.5
|
1.0
|
CA
|
A:ASN56
|
4.5
|
31.7
|
0.5
|
CD
|
A:GLU12
|
4.5
|
50.6
|
1.0
|
CB
|
A:ASN56
|
4.6
|
33.0
|
0.5
|
CA
|
A:MET57
|
4.6
|
31.9
|
1.0
|
F2
|
A:BEF605
|
4.6
|
46.6
|
1.0
|
CB
|
A:ASP54
|
4.7
|
34.5
|
1.0
|
CG
|
A:GLU12
|
4.7
|
44.8
|
1.0
|
CB
|
A:ASP11
|
4.7
|
29.6
|
1.0
|
N
|
A:ASN56
|
4.7
|
32.7
|
0.5
|
N
|
A:ASN56
|
4.8
|
32.1
|
0.5
|
N
|
A:ASP11
|
4.8
|
32.4
|
1.0
|
CG
|
A:ASP10
|
4.9
|
36.9
|
1.0
|
CG
|
A:ASN56
|
5.0
|
32.1
|
0.5
|
|
Calcium binding site 4 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 4 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:40.5
occ:1.00
|
F3
|
B:BEF605
|
2.0
|
40.5
|
1.0
|
O
|
B:ASN56
|
2.3
|
35.3
|
1.0
|
OD1
|
B:ASP11
|
2.4
|
40.4
|
1.0
|
OD2
|
B:ASP54
|
2.4
|
42.0
|
1.0
|
O
|
B:HOH705
|
2.5
|
32.0
|
1.0
|
O
|
B:HOH811
|
2.5
|
45.5
|
1.0
|
O
|
B:HOH756
|
3.0
|
48.1
|
1.0
|
CG
|
B:ASP11
|
3.2
|
40.5
|
1.0
|
OD2
|
B:ASP11
|
3.3
|
62.3
|
1.0
|
CG
|
B:ASP54
|
3.4
|
39.4
|
1.0
|
BE
|
B:BEF605
|
3.5
|
40.9
|
1.0
|
C
|
B:ASN56
|
3.5
|
36.6
|
1.0
|
OD1
|
B:ASP54
|
3.9
|
32.1
|
1.0
|
ND2
|
B:ASN56
|
4.1
|
37.5
|
0.5
|
OD1
|
B:ASP10
|
4.2
|
47.8
|
1.0
|
NZ
|
B:LYS83
|
4.2
|
63.2
|
1.0
|
OE1
|
B:GLU12
|
4.3
|
48.9
|
1.0
|
F2
|
B:BEF605
|
4.4
|
48.9
|
1.0
|
CB
|
B:ASN56
|
4.4
|
36.9
|
0.5
|
CA
|
B:ASN56
|
4.4
|
36.2
|
0.5
|
CA
|
B:ASN56
|
4.4
|
36.2
|
0.5
|
CG
|
B:MET57
|
4.5
|
39.1
|
1.0
|
CB
|
B:ASN56
|
4.5
|
36.9
|
0.5
|
N
|
B:MET57
|
4.5
|
38.7
|
1.0
|
CB
|
B:ASP11
|
4.6
|
35.8
|
1.0
|
CD
|
B:GLU12
|
4.6
|
55.4
|
1.0
|
CA
|
B:MET57
|
4.6
|
37.8
|
1.0
|
CG
|
B:GLU12
|
4.6
|
46.2
|
1.0
|
CE
|
B:LYS83
|
4.7
|
58.4
|
1.0
|
N
|
B:ASN56
|
4.7
|
38.1
|
1.0
|
CB
|
B:ASP54
|
4.7
|
38.7
|
1.0
|
N
|
B:ASP11
|
4.7
|
32.9
|
1.0
|
CG
|
B:ASN56
|
4.8
|
36.8
|
0.5
|
F1
|
B:BEF605
|
4.8
|
42.4
|
1.0
|
CG
|
B:ASP10
|
4.9
|
40.5
|
1.0
|
|
Calcium binding site 5 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 5 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:32.5
occ:1.00
|
OD2
|
B:ASP414
|
2.1
|
28.7
|
1.0
|
OG1
|
B:THR271
|
2.2
|
32.8
|
1.0
|
OD2
|
B:ASP237
|
2.3
|
29.9
|
1.0
|
OD1
|
B:ASP237
|
2.3
|
28.4
|
1.0
|
NE2
|
B:HIS415
|
2.4
|
26.8
|
1.0
|
O
|
B:HOH729
|
2.6
|
36.7
|
1.0
|
CG
|
B:ASP237
|
2.6
|
29.1
|
1.0
|
CG
|
B:ASP414
|
3.0
|
25.7
|
1.0
|
CB
|
B:THR271
|
3.2
|
33.0
|
1.0
|
CE1
|
B:HIS415
|
3.2
|
27.5
|
1.0
|
OD1
|
B:ASP414
|
3.2
|
23.7
|
1.0
|
CD2
|
B:HIS415
|
3.2
|
30.4
|
1.0
|
CA
|
B:THR271
|
3.5
|
32.2
|
1.0
|
CG2
|
B:THR271
|
3.5
|
29.1
|
1.0
|
N
|
B:THR271
|
3.7
|
30.8
|
1.0
|
CB
|
B:ASP237
|
4.1
|
25.8
|
1.0
|
F3
|
B:BEF606
|
4.1
|
51.1
|
1.0
|
ND1
|
B:HIS415
|
4.2
|
29.3
|
1.0
|
CG
|
B:HIS415
|
4.2
|
28.9
|
1.0
|
N
|
B:ASN238
|
4.3
|
25.2
|
1.0
|
CB
|
B:ASP414
|
4.4
|
24.8
|
1.0
|
OD1
|
B:ASP360
|
4.5
|
43.2
|
1.0
|
CA
|
B:ASP237
|
4.6
|
25.2
|
1.0
|
C
|
B:ALA270
|
4.6
|
28.6
|
1.0
|
F2
|
B:BEF606
|
4.6
|
49.4
|
1.0
|
NH1
|
B:ARG275
|
4.8
|
25.6
|
1.0
|
CB
|
B:ASN238
|
4.8
|
30.8
|
1.0
|
CA
|
B:ASN238
|
4.8
|
29.1
|
1.0
|
C
|
B:ASP237
|
4.8
|
26.1
|
1.0
|
BE
|
B:BEF606
|
4.8
|
47.2
|
1.0
|
|
Calcium binding site 6 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 6 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:97.6
occ:1.00
|
NE2
|
B:HIS364
|
2.0
|
49.3
|
0.5
|
OD1
|
B:ASP360
|
2.8
|
43.2
|
1.0
|
CD2
|
B:HIS364
|
2.8
|
46.8
|
0.5
|
F1
|
B:BEF606
|
2.9
|
52.8
|
1.0
|
NE2
|
B:HIS499
|
2.9
|
45.3
|
1.0
|
CE1
|
B:HIS364
|
3.1
|
48.6
|
0.5
|
BE
|
B:BEF606
|
3.2
|
47.2
|
1.0
|
O
|
B:HOH729
|
3.2
|
36.7
|
1.0
|
OD2
|
B:ASP360
|
3.3
|
50.6
|
1.0
|
CG
|
B:ASP360
|
3.4
|
38.9
|
1.0
|
CE1
|
B:HIS499
|
3.8
|
46.7
|
1.0
|
CD2
|
B:HIS499
|
3.8
|
34.1
|
1.0
|
F2
|
B:BEF606
|
3.9
|
49.4
|
1.0
|
CG
|
B:HIS364
|
4.0
|
43.5
|
0.5
|
ND1
|
B:HIS364
|
4.1
|
45.9
|
0.5
|
F3
|
B:BEF606
|
4.1
|
51.1
|
1.0
|
ND2
|
B:ASN238
|
4.4
|
36.9
|
1.0
|
O
|
B:HOH787
|
4.6
|
41.5
|
1.0
|
O
|
B:ASP360
|
4.8
|
31.6
|
1.0
|
ND1
|
B:HIS364
|
4.8
|
48.0
|
0.5
|
CB
|
B:ASP360
|
4.8
|
36.0
|
1.0
|
ND1
|
B:HIS499
|
4.9
|
44.6
|
1.0
|
CG
|
B:HIS499
|
5.0
|
34.9
|
1.0
|
OG
|
B:SER363
|
5.0
|
34.7
|
1.0
|
|
Calcium binding site 7 out
of 7 in 8tff
Go back to
Calcium Binding Sites List in 8tff
Calcium binding site 7 out
of 7 in the Porx with BEF3 Phosphate Analog
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca604
b:94.5
occ:1.00
|
F3
|
B:BEF607
|
2.4
|
61.7
|
1.0
|
BE
|
B:BEF607
|
3.1
|
58.1
|
1.0
|
F1
|
B:BEF607
|
3.3
|
64.2
|
1.0
|
OE2
|
B:GLU68
|
3.9
|
46.9
|
1.0
|
OE1
|
B:GLU68
|
4.0
|
41.5
|
1.0
|
CD
|
B:GLU68
|
4.3
|
38.5
|
1.0
|
F2
|
B:BEF607
|
4.7
|
60.8
|
1.0
|
|
Reference:
A.Saran,
N.Zeytuni.
Porx with BEF3 Phosphate Analog To Be Published.
Page generated: Fri Jul 19 12:02:39 2024
|