Magnesium in PDB 8qrn: Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Other elements in 8qrn:
The structure of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 58 in 8qrn
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Magnesium Binding Sites List in 8qrn
Magnesium binding site 1 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1704
b:71.9
occ:1.00
|
OP2
|
A:G791
|
1.7
|
78.2
|
1.0
|
OP2
|
A:G719
|
2.1
|
78.9
|
1.0
|
OP2
|
A:A718
|
2.1
|
83.2
|
1.0
|
P
|
A:G791
|
3.1
|
78.5
|
1.0
|
P
|
A:A718
|
3.2
|
88.0
|
1.0
|
O5'
|
A:A718
|
3.3
|
78.3
|
1.0
|
P
|
A:G719
|
3.5
|
82.4
|
1.0
|
O5'
|
A:G791
|
3.7
|
76.6
|
1.0
|
OP1
|
A:G791
|
4.0
|
76.4
|
1.0
|
OP1
|
A:A718
|
4.0
|
76.4
|
1.0
|
O3'
|
A:A790
|
4.2
|
83.2
|
1.0
|
C3'
|
A:A790
|
4.2
|
78.7
|
1.0
|
O5'
|
A:A790
|
4.2
|
82.5
|
1.0
|
O3'
|
A:A718
|
4.3
|
81.0
|
1.0
|
OP1
|
A:G719
|
4.4
|
75.1
|
1.0
|
O5'
|
A:G719
|
4.4
|
78.2
|
1.0
|
N7
|
A:G719
|
4.4
|
75.7
|
1.0
|
K
|
A:K1759
|
4.4
|
89.1
|
1.0
|
O3'
|
A:G717
|
4.4
|
71.3
|
1.0
|
C3'
|
A:A718
|
4.5
|
76.4
|
1.0
|
O4
|
A:U720
|
4.6
|
87.9
|
1.0
|
C5'
|
A:A718
|
4.7
|
74.3
|
1.0
|
OP2
|
A:A790
|
4.7
|
82.9
|
1.0
|
C8
|
A:G719
|
4.7
|
77.5
|
1.0
|
P
|
A:A790
|
4.9
|
86.2
|
1.0
|
C5'
|
A:G791
|
5.0
|
76.7
|
1.0
|
|
Magnesium binding site 2 out
of 58 in 8qrn
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Magnesium Binding Sites List in 8qrn
Magnesium binding site 2 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1705
b:39.0
occ:1.00
|
OP2
|
A:A940
|
2.2
|
34.9
|
1.0
|
OP2
|
A:A939
|
2.2
|
46.5
|
1.0
|
OP2
|
A:A938
|
2.5
|
55.0
|
1.0
|
P
|
A:A939
|
3.4
|
54.2
|
1.0
|
P
|
A:A940
|
3.7
|
54.2
|
1.0
|
OP1
|
A:A939
|
3.8
|
48.6
|
1.0
|
P
|
A:A938
|
3.8
|
48.6
|
1.0
|
OP1
|
A:A938
|
4.3
|
40.0
|
1.0
|
OP1
|
A:U937
|
4.3
|
39.6
|
1.0
|
C5'
|
A:A940
|
4.4
|
43.8
|
1.0
|
C3'
|
A:A939
|
4.4
|
41.4
|
1.0
|
C5'
|
A:A938
|
4.4
|
40.0
|
1.0
|
OP1
|
A:A940
|
4.4
|
52.1
|
1.0
|
O5'
|
A:A938
|
4.5
|
39.6
|
1.0
|
O5'
|
A:A939
|
4.5
|
34.1
|
1.0
|
O5'
|
A:A940
|
4.5
|
38.6
|
1.0
|
O3'
|
A:A938
|
4.5
|
42.3
|
1.0
|
O3'
|
A:A939
|
4.6
|
44.5
|
1.0
|
O5'
|
A:U937
|
4.6
|
35.1
|
1.0
|
C3'
|
A:A938
|
4.7
|
30.3
|
1.0
|
C5'
|
A:A939
|
4.8
|
39.9
|
1.0
|
C8
|
A:A940
|
4.8
|
31.8
|
1.0
|
N7
|
A:A940
|
4.9
|
38.1
|
1.0
|
P
|
A:U937
|
4.9
|
44.3
|
1.0
|
|
Magnesium binding site 3 out
of 58 in 8qrn
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Magnesium Binding Sites List in 8qrn
Magnesium binding site 3 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1706
b:43.2
occ:1.00
|
OP2
|
A:G1028
|
3.3
|
40.7
|
1.0
|
OP2
|
A:A1104
|
4.2
|
28.4
|
1.0
|
N1
|
A:A1102
|
4.3
|
26.0
|
1.0
|
P
|
A:G1028
|
4.4
|
39.3
|
1.0
|
O2'
|
A:A1104
|
4.4
|
34.0
|
1.0
|
C4'
|
A:A1104
|
4.5
|
25.8
|
1.0
|
C5'
|
A:A1027
|
4.6
|
15.5
|
1.0
|
OP1
|
A:C1106
|
4.6
|
51.6
|
1.0
|
O3'
|
A:C1591
|
4.6
|
31.2
|
1.0
|
OP1
|
A:G1028
|
4.6
|
35.4
|
1.0
|
OP2
|
A:C1106
|
4.6
|
55.4
|
1.0
|
C2
|
A:A1102
|
4.6
|
27.9
|
1.0
|
O2'
|
A:C1591
|
4.6
|
37.7
|
1.0
|
OP1
|
A:A1027
|
4.7
|
29.7
|
1.0
|
O3'
|
A:A1027
|
4.8
|
35.8
|
1.0
|
|
Magnesium binding site 4 out
of 58 in 8qrn
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Magnesium Binding Sites List in 8qrn
Magnesium binding site 4 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1707
b:43.7
occ:1.00
|
OP2
|
A:A1054
|
2.3
|
42.0
|
1.0
|
O2
|
A:C1100
|
3.6
|
42.1
|
1.0
|
N4
|
A:C1099
|
3.7
|
44.3
|
1.0
|
P
|
A:A1054
|
3.7
|
37.3
|
1.0
|
N3
|
A:C1099
|
3.9
|
31.6
|
1.0
|
O4
|
A:U1101
|
4.1
|
39.3
|
1.0
|
C4
|
A:C1099
|
4.2
|
35.8
|
1.0
|
C2
|
A:C1100
|
4.2
|
37.1
|
1.0
|
N3
|
A:C1100
|
4.3
|
36.1
|
1.0
|
OP1
|
A:A1054
|
4.3
|
37.9
|
1.0
|
C3'
|
A:A1053
|
4.6
|
28.9
|
1.0
|
C4
|
A:U1101
|
4.6
|
32.3
|
1.0
|
O5'
|
A:A1054
|
4.6
|
32.8
|
1.0
|
O3'
|
A:A1053
|
4.6
|
24.8
|
1.0
|
O4
|
A:U1055
|
4.7
|
45.6
|
1.0
|
N6
|
A:A1056
|
4.8
|
44.0
|
1.0
|
C2'
|
A:A1053
|
4.9
|
31.8
|
1.0
|
C2
|
A:C1099
|
5.0
|
39.3
|
1.0
|
|
Magnesium binding site 5 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 5 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1708
b:58.6
occ:1.00
|
OP2
|
A:A1067
|
2.4
|
63.8
|
1.0
|
N7
|
A:A1067
|
3.8
|
58.1
|
1.0
|
OP2
|
A:C1088
|
3.8
|
68.3
|
1.0
|
P
|
A:A1067
|
3.9
|
64.1
|
1.0
|
N6
|
A:A1068
|
4.1
|
56.2
|
1.0
|
C8
|
A:A1067
|
4.2
|
60.7
|
1.0
|
N7
|
A:A1068
|
4.2
|
56.1
|
1.0
|
O5'
|
A:A1067
|
4.3
|
55.2
|
1.0
|
OP1
|
A:A1067
|
4.8
|
62.5
|
1.0
|
O5'
|
A:C1066
|
4.8
|
70.4
|
1.0
|
C3'
|
A:C1066
|
4.8
|
66.8
|
1.0
|
C5
|
A:A1068
|
4.8
|
50.9
|
1.0
|
O3'
|
A:C1066
|
4.9
|
66.1
|
1.0
|
P
|
A:C1088
|
4.9
|
70.5
|
1.0
|
C6
|
A:A1068
|
4.9
|
52.9
|
1.0
|
O5'
|
A:C1088
|
5.0
|
69.6
|
1.0
|
|
Magnesium binding site 6 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 6 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1709
b:72.1
occ:1.00
|
OP1
|
A:A1082
|
1.8
|
61.3
|
1.0
|
OP1
|
A:C1070
|
2.1
|
51.2
|
1.0
|
P
|
A:A1082
|
3.1
|
76.9
|
1.0
|
P
|
A:C1070
|
3.4
|
62.9
|
1.0
|
OP2
|
A:U1071
|
3.6
|
68.3
|
1.0
|
OP2
|
A:A1082
|
3.7
|
67.4
|
1.0
|
O5'
|
A:C1070
|
3.8
|
57.9
|
1.0
|
O5'
|
A:A1082
|
4.1
|
55.0
|
1.0
|
C5'
|
A:C1070
|
4.1
|
49.9
|
1.0
|
O3'
|
A:U1081
|
4.2
|
75.0
|
1.0
|
OP2
|
A:C1070
|
4.3
|
64.5
|
1.0
|
N2
|
A:G1586
|
4.4
|
47.0
|
1.0
|
O3'
|
A:A1069
|
4.5
|
48.7
|
1.0
|
C5'
|
A:A1082
|
4.7
|
54.8
|
1.0
|
O2'
|
A:U1580
|
4.7
|
58.8
|
1.0
|
N3
|
A:G1586
|
4.8
|
34.5
|
1.0
|
P
|
A:U1071
|
4.9
|
70.9
|
1.0
|
|
Magnesium binding site 7 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 7 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1710
b:65.1
occ:1.00
|
OP2
|
A:A1090
|
1.8
|
60.5
|
1.0
|
O4
|
A:U1091
|
2.3
|
56.8
|
1.0
|
P
|
A:A1090
|
3.2
|
70.0
|
1.0
|
C4
|
A:U1091
|
3.2
|
56.2
|
1.0
|
C5
|
A:U1091
|
3.5
|
55.4
|
1.0
|
OP1
|
A:A1090
|
3.8
|
62.7
|
1.0
|
N3
|
A:C1064
|
4.1
|
75.2
|
1.0
|
O5'
|
A:A1090
|
4.1
|
57.4
|
1.0
|
N6
|
A:A1067
|
4.1
|
60.6
|
1.0
|
O3'
|
A:U1089
|
4.2
|
55.8
|
1.0
|
C3'
|
A:U1089
|
4.4
|
55.5
|
1.0
|
N3
|
A:U1091
|
4.5
|
60.0
|
1.0
|
N1
|
A:A1068
|
4.5
|
53.0
|
1.0
|
O5'
|
A:U1089
|
4.6
|
64.2
|
1.0
|
N4
|
A:C1064
|
4.6
|
77.2
|
1.0
|
O6
|
A:G1092
|
4.7
|
57.2
|
1.0
|
O2
|
A:C1064
|
4.7
|
81.9
|
1.0
|
C2
|
A:A1068
|
4.8
|
53.3
|
1.0
|
C6
|
A:U1091
|
4.9
|
55.9
|
1.0
|
C4
|
A:C1064
|
4.9
|
75.7
|
1.0
|
C2
|
A:C1064
|
4.9
|
79.7
|
1.0
|
|
Magnesium binding site 8 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 8 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1711
b:27.0
occ:1.00
|
OP1
|
A:A1266
|
2.7
|
45.0
|
1.0
|
CD2
|
H:HIS130
|
4.0
|
54.0
|
1.0
|
P
|
A:A1266
|
4.0
|
57.6
|
1.0
|
OE1
|
H:GLN122
|
4.1
|
78.0
|
1.0
|
O5'
|
A:A1266
|
4.2
|
45.5
|
1.0
|
OP2
|
A:U1267
|
4.4
|
61.1
|
1.0
|
O6
|
A:G1320
|
4.5
|
57.0
|
1.0
|
NE2
|
H:GLN122
|
4.6
|
73.8
|
1.0
|
CD
|
H:GLN122
|
4.8
|
71.9
|
1.0
|
CG
|
H:HIS130
|
4.8
|
51.6
|
1.0
|
O3'
|
A:C1265
|
4.9
|
37.5
|
1.0
|
NE2
|
H:HIS130
|
4.9
|
59.3
|
1.0
|
C5'
|
A:A1266
|
4.9
|
43.3
|
1.0
|
OD1
|
C:ASN37
|
4.9
|
74.5
|
1.0
|
|
Magnesium binding site 9 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 9 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1712
b:63.3
occ:1.00
|
OP2
|
A:A1434
|
2.4
|
56.8
|
1.0
|
P
|
A:A1434
|
3.8
|
62.0
|
1.0
|
N7
|
A:A1434
|
3.9
|
53.7
|
1.0
|
O5'
|
A:A1434
|
4.0
|
48.3
|
1.0
|
N7
|
A:A1435
|
4.1
|
55.5
|
1.0
|
C8
|
A:A1434
|
4.2
|
52.8
|
1.0
|
O5'
|
A:A1433
|
4.4
|
53.0
|
1.0
|
OP2
|
A:A1435
|
4.5
|
55.2
|
1.0
|
OP2
|
A:A1433
|
4.5
|
57.5
|
1.0
|
OP1
|
A:A1434
|
4.7
|
57.8
|
1.0
|
P
|
A:A1433
|
4.8
|
53.2
|
1.0
|
O3'
|
A:A1433
|
4.9
|
44.8
|
1.0
|
OP1
|
A:A1433
|
4.9
|
55.3
|
1.0
|
C5
|
A:A1434
|
4.9
|
42.2
|
1.0
|
C8
|
A:A1435
|
4.9
|
50.8
|
1.0
|
N6
|
A:A1435
|
5.0
|
54.8
|
1.0
|
C3'
|
A:A1433
|
5.0
|
49.5
|
1.0
|
|
Magnesium binding site 10 out
of 58 in 8qrn
Go back to
Magnesium Binding Sites List in 8qrn
Magnesium binding site 10 out
of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1713
b:41.1
occ:1.00
|
OP2
|
A:A1564
|
2.0
|
42.9
|
1.0
|
OP2
|
A:A1565
|
2.2
|
53.0
|
1.0
|
OP2
|
A:G1570
|
2.5
|
43.3
|
1.0
|
O3'
|
A:U1563
|
2.8
|
52.5
|
1.0
|
P
|
A:A1564
|
2.9
|
59.7
|
1.0
|
O5'
|
A:A1564
|
3.5
|
54.1
|
1.0
|
P
|
A:A1565
|
3.7
|
50.6
|
1.0
|
P
|
A:G1570
|
3.9
|
40.3
|
1.0
|
O2'
|
A:U1563
|
3.9
|
50.8
|
1.0
|
C3'
|
A:U1563
|
4.1
|
51.7
|
1.0
|
N7
|
A:A1565
|
4.1
|
47.8
|
1.0
|
O2'
|
A:G1569
|
4.1
|
38.9
|
1.0
|
OP1
|
A:A1564
|
4.2
|
62.7
|
1.0
|
C3'
|
A:A1564
|
4.3
|
44.1
|
1.0
|
C8
|
A:A1565
|
4.4
|
50.8
|
1.0
|
O3'
|
A:G1569
|
4.4
|
48.6
|
1.0
|
O3'
|
A:A1564
|
4.4
|
57.5
|
1.0
|
O5'
|
A:A1565
|
4.5
|
32.2
|
1.0
|
C5'
|
A:A1564
|
4.5
|
46.0
|
1.0
|
OP1
|
A:G1570
|
4.6
|
53.6
|
1.0
|
OP1
|
A:A1565
|
4.6
|
51.4
|
1.0
|
C2'
|
A:U1563
|
4.6
|
52.4
|
1.0
|
|
Reference:
M.Cipullo,
G.Valentin Gese,
S.Gopalakrishna,
A.Krueger,
V.Lobo,
M.A.Pirozhkova,
J.Marks,
P.Palenkova,
D.Shiriaev,
Y.Liu,
J.Misic,
Y.Cai,
M.Nguyen,
A.Abdelbagi,
X.Li,
M.Minczuk,
M.Hafner,
D.Benhalevy,
A.A.Sarshad,
I.Attanasov,
B.M.Hallberg,
J.Rorbach.
GTPBP8 Plays A Role in Mitoribosome Formation in Human Mitochondria Nat Commun 2024.
ISSN: ESSN 2041-1723
Page generated: Fri Oct 4 16:50:09 2024
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