Cadmium in PDB 7ryw: Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Protein crystallography data
The structure of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose, PDB code: 7ryw
was solved by
S.Aditya,
R.Priyadharshine,
I.Maham,
D.J.Miller,
V.Stojanoff,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.70 /
2.09
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.507,
181.507,
181.507,
90,
90,
90
|
R / Rfree (%)
|
17 /
19.6
|
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
(pdb code 7ryw). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the
Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose, PDB code: 7ryw:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 1 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd201
b:29.5
occ:0.50
|
OD2
|
A:ASP80
|
2.4
|
25.0
|
1.0
|
OD1
|
A:ASP80
|
2.6
|
26.3
|
1.0
|
CD
|
A:CD204
|
2.6
|
36.6
|
0.3
|
CG
|
A:ASP80
|
2.8
|
26.5
|
1.0
|
CD
|
A:CD207
|
4.3
|
60.8
|
0.3
|
CB
|
A:ASP80
|
4.3
|
22.9
|
1.0
|
|
Cadmium binding site 2 out
of 13 in 7ryw
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Cadmium Binding Sites List in 7ryw
Cadmium binding site 2 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd202
b:68.0
occ:0.30
|
OE1
|
A:GLU130
|
2.7
|
50.5
|
1.0
|
OE2
|
A:GLU130
|
3.5
|
41.7
|
1.0
|
CD
|
A:GLU130
|
3.5
|
41.6
|
1.0
|
CD
|
A:CD203
|
3.8
|
93.7
|
0.2
|
CG
|
A:GLU130
|
4.9
|
37.0
|
1.0
|
|
Cadmium binding site 3 out
of 13 in 7ryw
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Cadmium Binding Sites List in 7ryw
Cadmium binding site 3 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:93.7
occ:0.18
|
OD1
|
A:ASP127
|
3.1
|
55.4
|
1.0
|
OE1
|
A:GLU130
|
3.6
|
50.5
|
1.0
|
CD
|
A:CD202
|
3.8
|
68.0
|
0.3
|
CG
|
A:ASP127
|
4.4
|
45.5
|
1.0
|
CD
|
A:GLU130
|
4.8
|
41.6
|
1.0
|
OG
|
A:SER131
|
4.8
|
62.3
|
1.0
|
CB
|
A:GLU130
|
4.9
|
38.0
|
1.0
|
|
Cadmium binding site 4 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 4 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:36.6
occ:0.31
|
CD
|
A:CD201
|
2.6
|
29.5
|
0.5
|
CD
|
A:CD207
|
3.4
|
60.8
|
0.3
|
OD2
|
A:ASP80
|
3.7
|
25.0
|
1.0
|
OD1
|
A:ASP80
|
4.1
|
26.3
|
1.0
|
CG
|
A:ASP80
|
4.3
|
26.5
|
1.0
|
|
Cadmium binding site 5 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 5 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:88.2
occ:0.46
|
OE1
|
A:GLU56
|
2.9
|
69.1
|
1.0
|
O
|
A:HOH372
|
3.2
|
64.8
|
1.0
|
OE1
|
A:GLU53
|
3.2
|
71.9
|
1.0
|
CD
|
A:GLU56
|
3.6
|
64.8
|
1.0
|
OE2
|
A:GLU56
|
3.8
|
65.3
|
1.0
|
OE2
|
A:GLU53
|
3.9
|
76.0
|
1.0
|
CD
|
A:GLU53
|
4.0
|
65.5
|
1.0
|
CG
|
A:GLU56
|
4.9
|
46.4
|
1.0
|
|
Cadmium binding site 6 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 6 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd206
b:78.4
occ:0.41
|
OE2
|
A:GLU60
|
2.8
|
56.9
|
1.0
|
OE2
|
A:GLU56
|
2.9
|
65.3
|
1.0
|
OE1
|
A:GLU60
|
2.9
|
60.0
|
1.0
|
CD
|
A:CD209
|
3.0
|
92.2
|
0.4
|
CD
|
A:GLU60
|
3.2
|
58.3
|
1.0
|
OE2
|
A:GLU57
|
3.2
|
72.4
|
1.0
|
O
|
A:HOH390
|
3.3
|
65.4
|
1.0
|
CD
|
A:GLU56
|
3.7
|
64.8
|
1.0
|
CG
|
A:GLU56
|
3.9
|
46.4
|
1.0
|
CD
|
A:GLU57
|
4.3
|
67.0
|
1.0
|
CG
|
A:GLU60
|
4.7
|
44.2
|
1.0
|
OE1
|
A:GLU56
|
4.7
|
69.1
|
1.0
|
OE1
|
A:GLU57
|
4.8
|
74.5
|
1.0
|
|
Cadmium binding site 7 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 7 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd207
b:60.8
occ:0.26
|
OE1
|
A:GLN79
|
2.9
|
47.2
|
1.0
|
N
|
A:ASP80
|
3.0
|
26.2
|
1.0
|
OD2
|
A:ASP80
|
3.3
|
25.0
|
1.0
|
CD
|
A:CD204
|
3.4
|
36.6
|
0.3
|
CG
|
A:ASP80
|
3.4
|
26.5
|
1.0
|
CB
|
A:GLN79
|
3.5
|
29.0
|
1.0
|
CA
|
A:GLN79
|
3.5
|
26.5
|
1.0
|
OD1
|
A:ASP80
|
3.7
|
26.3
|
1.0
|
C
|
A:GLN79
|
3.7
|
23.9
|
1.0
|
CB
|
A:ASP80
|
3.8
|
22.9
|
1.0
|
CD
|
A:GLN79
|
3.9
|
49.9
|
1.0
|
CA
|
A:ASP80
|
4.0
|
23.4
|
1.0
|
CD
|
A:CD201
|
4.3
|
29.5
|
0.5
|
CG
|
A:GLN79
|
4.3
|
36.3
|
1.0
|
N
|
A:GLN79
|
4.9
|
24.9
|
1.0
|
O
|
A:GLN79
|
5.0
|
20.5
|
1.0
|
|
Cadmium binding site 8 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 8 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:104.1
occ:0.56
|
SG
|
A:CYS126
|
3.2
|
40.0
|
1.0
|
O
|
A:HOH396
|
3.2
|
44.5
|
1.0
|
CB
|
A:CYS126
|
3.5
|
30.7
|
1.0
|
CA
|
A:PRO123
|
4.4
|
29.4
|
1.0
|
CA
|
A:SER118
|
4.4
|
34.7
|
1.0
|
CB
|
A:SER118
|
4.5
|
41.1
|
1.0
|
OG
|
A:SER118
|
4.7
|
48.6
|
1.0
|
CB
|
A:PRO123
|
4.8
|
30.7
|
1.0
|
CE1
|
A:HIS114
|
4.8
|
31.3
|
1.0
|
O
|
A:ASP122
|
5.0
|
30.9
|
1.0
|
N
|
A:PRO123
|
5.0
|
30.2
|
1.0
|
N
|
A:SER118
|
5.0
|
36.0
|
1.0
|
|
Cadmium binding site 9 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 9 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd209
b:92.2
occ:0.39
|
OE2
|
A:GLU60
|
2.8
|
56.9
|
1.0
|
O
|
A:HOH390
|
2.9
|
65.4
|
1.0
|
OE2
|
A:GLU57
|
3.0
|
72.4
|
1.0
|
OE1
|
A:GLU57
|
3.0
|
74.5
|
1.0
|
CD
|
A:CD206
|
3.0
|
78.4
|
0.4
|
CD
|
A:GLU57
|
3.4
|
67.0
|
1.0
|
CD
|
A:GLU60
|
4.0
|
58.3
|
1.0
|
OE1
|
A:GLU60
|
4.6
|
60.0
|
1.0
|
NH1
|
A:ARG64
|
4.6
|
67.0
|
1.0
|
CG
|
A:GLU57
|
4.9
|
44.2
|
1.0
|
CB
|
A:GLU60
|
5.0
|
30.0
|
1.0
|
|
Cadmium binding site 10 out
of 13 in 7ryw
Go back to
Cadmium Binding Sites List in 7ryw
Cadmium binding site 10 out
of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd210
b:78.5
occ:0.45
|
SG
|
A:CYS48
|
2.8
|
34.1
|
1.0
|
CE1
|
A:HIS49
|
3.2
|
39.9
|
0.5
|
ND1
|
A:HIS49
|
3.3
|
38.9
|
0.5
|
CB
|
A:CYS48
|
3.6
|
25.5
|
1.0
|
NE2
|
A:HIS49
|
3.6
|
39.5
|
0.5
|
CG
|
A:HIS49
|
3.8
|
35.6
|
0.5
|
CD2
|
A:HIS49
|
3.9
|
39.7
|
0.5
|
N
|
A:HIS49
|
4.0
|
25.4
|
1.0
|
C
|
A:CYS48
|
4.1
|
27.3
|
1.0
|
NH1
|
A:ARG52
|
4.2
|
58.4
|
1.0
|
CA
|
A:HIS49
|
4.3
|
29.3
|
0.5
|
CA
|
A:HIS49
|
4.3
|
29.3
|
0.5
|
CD
|
A:ARG52
|
4.3
|
45.5
|
1.0
|
O
|
A:GLU45
|
4.4
|
28.6
|
1.0
|
CA
|
A:CYS48
|
4.5
|
26.1
|
1.0
|
O
|
A:HOH309
|
4.5
|
47.3
|
1.0
|
O
|
A:CYS48
|
4.5
|
22.4
|
1.0
|
CG
|
A:GLU45
|
4.5
|
48.2
|
1.0
|
CB
|
A:HIS49
|
4.6
|
31.5
|
0.5
|
CB
|
A:HIS49
|
4.7
|
31.6
|
0.5
|
|
Reference:
S.Aditya,
R.Priyadharshine,
I.Maham,
D.J.Miller,
V.Stojanoff.
Crystal Structure of Ferritin Grown By Microbatch Method in the Presence of Agarose To Be Published.
Page generated: Fri Jul 19 20:09:36 2024
|