Sodium in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Protein crystallography data
The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6
was solved by
G.Blaha,
G.Gurel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.95 /
2.75
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
212.805,
299.997,
576.002,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
24.1
|
Other elements in 3cd6:
The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin also contains other interesting chemical elements:
Sodium Binding Sites:
Sodium binding site 1 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 1 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na8552
b:78.5
occ:1.00
|
O
|
0:HOH4956
|
3.0
|
69.7
|
1.0
|
O
|
B:GLN230
|
3.1
|
36.5
|
1.0
|
O
|
0:HOH4635
|
3.3
|
63.4
|
1.0
|
O
|
0:HOH6877
|
3.3
|
47.6
|
1.0
|
O
|
0:HOH5157
|
3.4
|
53.7
|
1.0
|
OP1
|
0:U837
|
3.6
|
32.2
|
1.0
|
O
|
0:HOH9284
|
3.8
|
79.4
|
1.0
|
OP2
|
0:U837
|
4.0
|
33.0
|
1.0
|
CZ3
|
B:TRP232
|
4.0
|
39.7
|
1.0
|
O
|
0:HOH7392
|
4.2
|
57.4
|
1.0
|
C
|
B:GLN230
|
4.3
|
36.4
|
1.0
|
P
|
0:U837
|
4.3
|
30.3
|
1.0
|
CH2
|
B:TRP232
|
4.3
|
40.2
|
1.0
|
O
|
0:HOH6110
|
4.3
|
56.1
|
1.0
|
CA
|
B:GLY231
|
4.4
|
39.0
|
1.0
|
N4
|
0:C839
|
4.5
|
32.4
|
1.0
|
OP2
|
0:C838
|
4.5
|
28.4
|
1.0
|
O
|
0:HOH3378
|
4.8
|
61.5
|
1.0
|
N
|
B:GLY231
|
4.8
|
38.1
|
1.0
|
CE3
|
B:TRP232
|
4.8
|
39.8
|
1.0
|
O
|
0:HOH9567
|
4.9
|
49.6
|
1.0
|
O
|
0:HOH4501
|
4.9
|
49.0
|
1.0
|
|
Sodium binding site 2 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 2 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na8503
b:36.2
occ:1.00
|
OD1
|
C:ASP45
|
2.8
|
45.6
|
1.0
|
O
|
C:THR94
|
2.9
|
41.3
|
1.0
|
O
|
C:LYS96
|
2.9
|
42.2
|
1.0
|
OD2
|
C:ASP45
|
3.2
|
44.3
|
1.0
|
CG
|
C:ASP45
|
3.2
|
44.1
|
1.0
|
O
|
C:HOH8507
|
3.2
|
23.2
|
1.0
|
C
|
C:LYS96
|
3.7
|
40.4
|
1.0
|
O
|
C:GLU95
|
3.8
|
39.8
|
1.0
|
C
|
C:GLU95
|
3.9
|
41.0
|
1.0
|
C
|
C:THR94
|
4.1
|
40.7
|
1.0
|
O
|
C:HOH8617
|
4.1
|
45.7
|
1.0
|
N
|
C:LYS96
|
4.2
|
39.6
|
1.0
|
O
|
C:HOH8586
|
4.3
|
38.0
|
1.0
|
CA
|
C:GLU95
|
4.4
|
42.5
|
1.0
|
N
|
C:ASP97
|
4.4
|
40.3
|
1.0
|
CB
|
C:ASP45
|
4.4
|
40.7
|
1.0
|
CA
|
C:ASP97
|
4.6
|
38.5
|
1.0
|
CA
|
C:LYS96
|
4.6
|
39.7
|
1.0
|
N
|
C:GLU95
|
4.7
|
41.2
|
1.0
|
|
Sodium binding site 3 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 3 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na8518
b:69.5
occ:1.00
|
O
|
H:HOH8539
|
3.6
|
78.6
|
1.0
|
N
|
H:ASP114
|
3.6
|
88.0
|
1.0
|
O
|
0:HOH7764
|
3.8
|
49.2
|
1.0
|
CD
|
H:ARG117
|
4.0
|
56.6
|
1.0
|
NH1
|
H:ARG117
|
4.0
|
60.6
|
1.0
|
O6
|
0:G2286
|
4.1
|
69.3
|
1.0
|
CA
|
H:ASP114
|
4.2
|
88.2
|
1.0
|
O
|
0:HOH4832
|
4.3
|
43.3
|
1.0
|
N4
|
0:C2287
|
4.5
|
72.2
|
1.0
|
NE
|
H:ARG117
|
4.6
|
59.2
|
1.0
|
CZ
|
H:ARG117
|
4.6
|
58.7
|
1.0
|
N3
|
0:C2287
|
4.9
|
70.7
|
1.0
|
CG
|
H:ARG117
|
5.0
|
56.2
|
1.0
|
|
Sodium binding site 4 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 4 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na8538
b:57.0
occ:1.00
|
O
|
J:TYR69
|
2.7
|
59.6
|
1.0
|
O
|
0:HOH9501
|
2.9
|
79.1
|
1.0
|
O
|
0:HOH5802
|
2.9
|
50.7
|
1.0
|
O
|
J:VAL61
|
3.0
|
53.3
|
1.0
|
O
|
J:ILE63
|
3.0
|
54.0
|
1.0
|
O
|
J:ARG60
|
3.0
|
46.3
|
1.0
|
OP1
|
0:A2677
|
3.5
|
58.1
|
1.0
|
C
|
J:VAL61
|
3.5
|
51.2
|
1.0
|
CA
|
J:VAL61
|
3.6
|
48.3
|
1.0
|
N
|
J:TYR71
|
3.7
|
57.1
|
1.0
|
C
|
J:TYR69
|
3.9
|
59.3
|
1.0
|
CB
|
J:TYR71
|
4.0
|
53.1
|
1.0
|
C
|
J:ARG60
|
4.0
|
43.9
|
1.0
|
C
|
J:ILE63
|
4.2
|
52.9
|
1.0
|
N
|
J:VAL61
|
4.3
|
45.5
|
1.0
|
CA
|
J:TYR71
|
4.4
|
55.3
|
1.0
|
CD2
|
J:TYR69
|
4.4
|
55.7
|
1.0
|
N
|
J:ASP62
|
4.5
|
52.8
|
1.0
|
CB
|
J:TYR69
|
4.6
|
56.8
|
1.0
|
C
|
J:PHE70
|
4.6
|
59.3
|
1.0
|
N
|
J:ILE63
|
4.6
|
54.2
|
1.0
|
CA
|
J:PHE70
|
4.7
|
61.5
|
1.0
|
N
|
J:PHE70
|
4.8
|
60.5
|
1.0
|
O
|
J:TYR71
|
4.8
|
55.7
|
1.0
|
CB
|
J:VAL61
|
4.9
|
48.1
|
1.0
|
CA
|
J:TYR69
|
4.9
|
57.9
|
1.0
|
P
|
0:A2677
|
4.9
|
58.5
|
1.0
|
CA
|
J:ILE63
|
5.0
|
52.9
|
1.0
|
C
|
J:ASP62
|
5.0
|
55.0
|
1.0
|
|
Sodium binding site 5 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 5 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Na8539
b:38.1
occ:1.00
|
O
|
M:LEU112
|
2.7
|
38.6
|
1.0
|
O
|
M:HOH8924
|
2.8
|
51.8
|
1.0
|
O
|
M:SER106
|
2.9
|
42.1
|
1.0
|
OG
|
M:SER106
|
2.9
|
38.2
|
1.0
|
O
|
M:PHE109
|
3.1
|
39.6
|
1.0
|
O
|
M:PRO110
|
3.3
|
40.6
|
1.0
|
C
|
M:PRO110
|
3.5
|
39.0
|
1.0
|
CA
|
M:PRO110
|
3.7
|
38.4
|
1.0
|
C
|
M:SER106
|
3.8
|
41.8
|
1.0
|
C
|
M:LEU112
|
3.9
|
37.9
|
1.0
|
C
|
M:PHE109
|
4.0
|
39.8
|
1.0
|
CB
|
M:SER106
|
4.0
|
39.4
|
1.0
|
OD1
|
M:ASP157
|
4.1
|
52.7
|
1.0
|
CA
|
M:SER106
|
4.2
|
40.6
|
1.0
|
N
|
M:PRO110
|
4.3
|
39.3
|
1.0
|
N
|
M:LEU112
|
4.3
|
36.9
|
1.0
|
N
|
M:ASN111
|
4.3
|
38.7
|
1.0
|
CL
|
M:CL8818
|
4.4
|
40.5
|
1.0
|
CA
|
M:LEU112
|
4.6
|
36.6
|
1.0
|
C
|
M:ASN111
|
4.7
|
37.5
|
1.0
|
O
|
M:HOH8857
|
4.7
|
71.9
|
1.0
|
CE1
|
M:PHE160
|
4.7
|
33.9
|
1.0
|
N
|
M:ARG113
|
4.9
|
36.9
|
1.0
|
N
|
M:ARG107
|
4.9
|
42.3
|
1.0
|
CA
|
M:ASN111
|
5.0
|
37.8
|
1.0
|
|
Sodium binding site 6 out
of 75 in 3cd6
Go back to
Sodium Binding Sites List in 3cd6
Sodium binding site 6 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Na8540
b:74.3
occ:1.00
|
O
|
Q:ASP20
|
2.8
|
73.0
|
1.0
|
O
|
Q:GLY22
|
2.9
|
66.2
|
1.0
|
O
|
Q:HOH1795
|
3.0
|
54.6
|
1.0
|
OG
|
Q:SER24
|
3.0
|
57.5
|
1.0
|
OG
|
Q:SER46
|
3.0
|
52.6
|
1.0
|
O
|
Q:HOH5427
|
3.0
|
87.6
|
1.0
|
O
|
Q:ARG21
|
3.2
|
71.9
|
1.0
|
O
|
Q:HOH7505
|
3.3
|
76.9
|
1.0
|
CA
|
Q:SER24
|
3.7
|
60.1
|
1.0
|
C
|
Q:ASP20
|
3.7
|
73.5
|
1.0
|
N
|
Q:SER24
|
3.8
|
61.5
|
1.0
|
CB
|
Q:SER46
|
3.8
|
52.0
|
1.0
|
C
|
Q:ARG21
|
3.9
|
70.2
|
1.0
|
C
|
Q:GLY22
|
3.9
|
66.0
|
1.0
|
CB
|
Q:SER24
|
3.9
|
60.4
|
1.0
|
C
|
Q:THR23
|
4.0
|
62.6
|
1.0
|
O
|
Q:THR23
|
4.1
|
62.9
|
1.0
|
OD1
|
Q:ASN16
|
4.4
|
64.5
|
1.0
|
N
|
Q:ARG21
|
4.5
|
71.9
|
1.0
|
N
|
Q:GLY22
|
4.5
|
69.0
|
1.0
|
CA
|
Q:ARG21
|
4.6
|
70.8
|
1.0
|
CA
|
Q:ASP20
|
4.6
|
75.3
|
1.0
|
OD1
|
Q:ASP44
|
4.7
|
59.2
|
1.0
|
N
|
Q:THR23
|
4.7
|
65.3
|
1.0
|
CA
|
Q:GLY22
|
4.7
|
66.9
|
1.0
|
OP1
|
0:C2366
|
4.7
|
51.3
|
1.0
|
NH2
|
Q:ARG28
|
4.8
|
58.8
|
1.0
|
CA
|
Q:THR23
|
4.8
|
63.9
|
1.0
|
O
|
Q:HOH7164
|
4.9
|
61.5
|
1.0
|
CG
|
Q:ASN16
|
5.0
|
64.5
|
1.0
|
CB
|
Q:ASP20
|
5.0
|
77.5
|
1.0
|
|
Sodium binding site 7 out
of 75 in 3cd6
Go back to
Sodium Binding Sites List in 3cd6
Sodium binding site 7 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Na8532
b:57.0
occ:1.00
|
O
|
R:SER70
|
2.8
|
45.4
|
1.0
|
O
|
0:HOH3779
|
2.8
|
90.3
|
1.0
|
O
|
0:HOH3105
|
3.1
|
79.8
|
1.0
|
O
|
0:HOH3791
|
3.1
|
0.1
|
1.0
|
O
|
R:VAL72
|
3.2
|
52.0
|
1.0
|
O
|
0:HOH5967
|
3.4
|
87.3
|
1.0
|
NA
|
0:NA8533
|
3.5
|
70.3
|
1.0
|
OD1
|
R:ASP73
|
3.7
|
64.4
|
1.0
|
C
|
R:VAL72
|
3.7
|
52.5
|
1.0
|
CA
|
R:ASP73
|
3.9
|
55.1
|
1.0
|
C
|
R:SER70
|
4.0
|
45.4
|
1.0
|
N
|
R:ASP73
|
4.0
|
53.9
|
1.0
|
C
|
R:LYS71
|
4.0
|
49.7
|
1.0
|
O
|
0:HOH7046
|
4.1
|
56.3
|
1.0
|
O
|
R:LYS71
|
4.2
|
51.1
|
1.0
|
N
|
R:VAL72
|
4.3
|
49.7
|
1.0
|
CB
|
R:ASP73
|
4.3
|
58.4
|
1.0
|
CA
|
R:LYS71
|
4.3
|
48.7
|
1.0
|
CG
|
R:ASP73
|
4.4
|
62.5
|
1.0
|
N
|
R:LYS71
|
4.7
|
46.5
|
1.0
|
CA
|
R:VAL72
|
4.7
|
51.7
|
1.0
|
OP1
|
0:G2660
|
4.7
|
42.4
|
1.0
|
|
Sodium binding site 8 out
of 75 in 3cd6
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Sodium Binding Sites List in 3cd6
Sodium binding site 8 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Na8510
b:47.6
occ:1.00
|
NE2
|
S:HIS7
|
2.8
|
59.5
|
1.0
|
OE2
|
S:GLU61
|
2.9
|
66.8
|
1.0
|
O
|
S:HOH2519
|
3.0
|
65.1
|
1.0
|
OE1
|
S:GLU61
|
3.1
|
65.9
|
1.0
|
CD
|
S:GLU61
|
3.3
|
65.4
|
1.0
|
CE1
|
S:HIS7
|
3.5
|
60.9
|
1.0
|
CD2
|
S:HIS7
|
3.8
|
60.2
|
1.0
|
ND1
|
S:HIS7
|
4.6
|
60.1
|
1.0
|
CG
|
S:HIS7
|
4.8
|
59.3
|
1.0
|
CG
|
S:GLU61
|
4.8
|
61.5
|
1.0
|
|
Sodium binding site 9 out
of 75 in 3cd6
Go back to
Sodium Binding Sites List in 3cd6
Sodium binding site 9 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Na8501
b:39.4
occ:1.00
|
OP2
|
0:C1069
|
2.7
|
27.7
|
1.0
|
N7
|
0:G1072
|
2.8
|
32.9
|
1.0
|
O
|
0:HOH3195
|
2.9
|
42.9
|
1.0
|
O
|
0:HOH3226
|
2.9
|
50.5
|
1.0
|
O
|
0:HOH5025
|
3.0
|
73.2
|
1.0
|
O6
|
0:G1072
|
3.1
|
36.7
|
1.0
|
O6
|
0:G1087
|
3.2
|
34.5
|
1.0
|
C5
|
0:G1072
|
3.4
|
32.6
|
1.0
|
O
|
0:HOH9076
|
3.5
|
30.6
|
1.0
|
C6
|
0:G1072
|
3.6
|
32.1
|
1.0
|
C8
|
0:G1072
|
3.9
|
33.1
|
1.0
|
P
|
0:C1069
|
4.0
|
31.0
|
1.0
|
C6
|
0:G1087
|
4.1
|
32.1
|
1.0
|
O
|
0:HOH5382
|
4.2
|
48.3
|
1.0
|
C5'
|
0:C1068
|
4.3
|
41.4
|
1.0
|
O
|
0:HOH3561
|
4.4
|
34.7
|
1.0
|
O3'
|
0:C1068
|
4.5
|
32.1
|
1.0
|
C3'
|
0:C1068
|
4.5
|
35.7
|
1.0
|
C4
|
0:G1072
|
4.7
|
32.5
|
1.0
|
OP1
|
0:C1069
|
4.7
|
28.0
|
1.0
|
N1
|
0:G1087
|
4.8
|
28.9
|
1.0
|
OP2
|
0:C1068
|
4.8
|
45.4
|
1.0
|
O
|
0:HOH4310
|
4.8
|
76.2
|
1.0
|
N9
|
0:G1072
|
4.9
|
32.2
|
1.0
|
N1
|
0:G1072
|
4.9
|
31.8
|
1.0
|
|
Sodium binding site 10 out
of 75 in 3cd6
Go back to
Sodium Binding Sites List in 3cd6
Sodium binding site 10 out
of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Na8502
b:49.5
occ:1.00
|
O
|
0:HOH7838
|
2.9
|
63.4
|
1.0
|
O2'
|
0:G1119
|
2.9
|
41.5
|
1.0
|
O
|
0:HOH4591
|
3.0
|
43.9
|
1.0
|
O3'
|
0:G1119
|
3.1
|
40.8
|
1.0
|
OP2
|
0:U1120
|
3.1
|
45.6
|
1.0
|
O6
|
0:G1121
|
3.2
|
36.0
|
1.0
|
N7
|
0:G1121
|
3.4
|
36.9
|
1.0
|
O
|
0:HOH4208
|
3.5
|
30.8
|
1.0
|
O4
|
0:U1122
|
3.6
|
43.2
|
1.0
|
P
|
0:U1120
|
3.7
|
45.4
|
1.0
|
O
|
0:HOH5728
|
3.7
|
61.3
|
1.0
|
O
|
0:HOH6988
|
3.7
|
74.5
|
1.0
|
C2'
|
0:G1119
|
3.8
|
39.6
|
1.0
|
C6
|
0:G1121
|
3.9
|
35.6
|
1.0
|
C3'
|
0:G1119
|
4.0
|
41.1
|
1.0
|
C5
|
0:G1121
|
4.0
|
35.4
|
1.0
|
C1'
|
0:G1119
|
4.2
|
37.4
|
1.0
|
MG
|
0:MG8018
|
4.4
|
37.5
|
1.0
|
C4
|
0:U1122
|
4.4
|
40.8
|
1.0
|
OP1
|
0:U1120
|
4.5
|
44.4
|
1.0
|
C8
|
0:G1121
|
4.6
|
36.6
|
1.0
|
N4
|
0:C1243
|
4.8
|
39.0
|
1.0
|
C5
|
0:U1122
|
4.8
|
40.0
|
1.0
|
N6
|
0:A1242
|
4.8
|
36.8
|
1.0
|
O5'
|
0:U1120
|
4.9
|
41.9
|
1.0
|
|
Reference:
G.Blaha,
G.Gurel,
S.J.Schroeder,
P.B.Moore,
T.A.Steitz.
Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Mon Oct 7 07:07:49 2024
|