Magnesium in PDB 7sr6: Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Protein crystallography data
The structure of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp, PDB code: 7sr6
was solved by
E.T.Baldwin,
C.Nichols,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
88.85 /
2.62
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.697,
177.697,
117.414,
90,
90,
120
|
R / Rfree (%)
|
16.8 /
21.8
|
Other elements in 7sr6:
The structure of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
(pdb code 7sr6). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp, PDB code: 7sr6:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7sr6
Go back to
Magnesium Binding Sites List in 7sr6
Magnesium binding site 1 out
of 5 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:62.0
occ:1.00
|
O3B
|
A:DCP602
|
2.1
|
85.8
|
1.0
|
O
|
A:LEU122
|
2.1
|
100.3
|
1.0
|
O1A
|
A:DCP602
|
2.2
|
56.9
|
1.0
|
OD1
|
A:ASP121
|
2.6
|
102.5
|
1.0
|
O2G
|
A:DCP602
|
2.7
|
75.9
|
1.0
|
OD2
|
A:ASP196
|
2.7
|
89.3
|
1.0
|
PG
|
A:DCP602
|
3.0
|
80.7
|
1.0
|
O1B
|
A:DCP602
|
3.0
|
75.5
|
1.0
|
PB
|
A:DCP602
|
3.1
|
86.2
|
1.0
|
C
|
A:LEU122
|
3.3
|
100.4
|
1.0
|
PA
|
A:DCP602
|
3.4
|
68.9
|
1.0
|
O3A
|
A:DCP602
|
3.6
|
73.0
|
1.0
|
CG
|
A:ASP121
|
3.7
|
99.4
|
1.0
|
CG
|
A:ASP196
|
3.8
|
95.1
|
1.0
|
O1G
|
A:DCP602
|
4.0
|
79.9
|
1.0
|
O3G
|
A:DCP602
|
4.1
|
57.5
|
1.0
|
CA
|
A:LYS123
|
4.1
|
104.3
|
1.0
|
N
|
A:LYS123
|
4.1
|
106.6
|
1.0
|
OD2
|
A:ASP121
|
4.2
|
91.6
|
1.0
|
N
|
A:ASP124
|
4.2
|
94.1
|
1.0
|
OD1
|
A:ASP196
|
4.2
|
97.4
|
1.0
|
C5'
|
A:DCP602
|
4.3
|
56.6
|
1.0
|
O
|
A:HOH736
|
4.3
|
68.3
|
1.0
|
N
|
A:LEU122
|
4.3
|
89.9
|
1.0
|
CA
|
A:LEU122
|
4.4
|
87.9
|
1.0
|
O5'
|
A:DCP602
|
4.4
|
58.2
|
1.0
|
C
|
A:ASP121
|
4.4
|
83.2
|
1.0
|
O2B
|
A:DCP602
|
4.4
|
100.4
|
1.0
|
C
|
A:LYS123
|
4.5
|
102.3
|
1.0
|
O2A
|
A:DCP602
|
4.5
|
61.5
|
1.0
|
O
|
A:ASP121
|
4.6
|
109.4
|
1.0
|
NZ
|
A:LYS230
|
4.6
|
108.3
|
1.0
|
N
|
A:CYS125
|
4.7
|
91.7
|
1.0
|
CB
|
A:ASP121
|
4.9
|
88.2
|
1.0
|
CA
|
A:ASP124
|
5.0
|
92.2
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7sr6
Go back to
Magnesium Binding Sites List in 7sr6
Magnesium binding site 2 out
of 5 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg612
b:45.3
occ:0.50
|
N
|
A:ASP516
|
2.5
|
57.9
|
1.0
|
O
|
A:THR467
|
2.6
|
59.4
|
1.0
|
OE1
|
A:GLU496
|
2.8
|
60.6
|
1.0
|
OD1
|
A:ASP516
|
3.1
|
74.2
|
1.0
|
CB
|
A:ASP516
|
3.2
|
76.1
|
1.0
|
CG
|
A:ASP516
|
3.3
|
84.2
|
1.0
|
C
|
A:SER515
|
3.4
|
58.4
|
1.0
|
CA
|
A:ASP516
|
3.4
|
65.3
|
1.0
|
CA
|
A:SER515
|
3.4
|
57.9
|
1.0
|
OD1
|
A:ASP468
|
3.4
|
53.4
|
1.0
|
O
|
A:HOH738
|
3.5
|
38.2
|
1.0
|
OG
|
A:SER515
|
3.6
|
61.4
|
1.0
|
CD
|
A:GLU496
|
3.6
|
56.0
|
1.0
|
C
|
A:THR467
|
3.6
|
65.7
|
1.0
|
CG
|
A:ASP468
|
3.7
|
66.8
|
1.0
|
CA
|
A:ASP468
|
3.8
|
61.7
|
1.0
|
CB
|
A:ASP468
|
3.8
|
59.4
|
1.0
|
OD1
|
A:ASN577
|
3.8
|
61.7
|
1.0
|
OE2
|
A:GLU496
|
3.9
|
60.4
|
1.0
|
CB
|
A:SER515
|
4.0
|
58.1
|
1.0
|
OD2
|
A:ASP516
|
4.1
|
101.3
|
1.0
|
N
|
A:ASP468
|
4.2
|
64.5
|
1.0
|
N
|
A:SER517
|
4.3
|
55.6
|
1.0
|
C
|
A:ASP516
|
4.3
|
56.9
|
1.0
|
OD2
|
A:ASP468
|
4.6
|
69.0
|
1.0
|
O
|
A:SER515
|
4.6
|
56.3
|
1.0
|
OG1
|
A:THR467
|
4.6
|
62.2
|
1.0
|
N
|
A:SER515
|
4.7
|
57.0
|
1.0
|
CG
|
A:GLU496
|
4.7
|
46.3
|
1.0
|
O
|
A:ILE514
|
4.8
|
49.2
|
1.0
|
CA
|
A:THR467
|
4.8
|
66.8
|
1.0
|
N
|
A:THR467
|
5.0
|
57.3
|
1.0
|
CG
|
A:ASN577
|
5.0
|
58.9
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7sr6
Go back to
Magnesium Binding Sites List in 7sr6
Magnesium binding site 3 out
of 5 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg103
b:67.3
occ:1.00
|
CD1
|
F:LEU333
|
2.8
|
110.8
|
1.0
|
N3
|
D:DA24
|
3.4
|
106.5
|
1.0
|
NZ
|
F:LYS113
|
3.5
|
112.9
|
1.0
|
C2
|
D:DA24
|
3.5
|
106.9
|
1.0
|
CA
|
F:GLY331
|
3.7
|
71.2
|
1.0
|
CB
|
F:ALA334
|
3.7
|
76.1
|
1.0
|
C4
|
D:DA24
|
3.9
|
113.8
|
1.0
|
CG
|
F:LEU333
|
4.0
|
112.2
|
1.0
|
OE1
|
F:GLN353
|
4.0
|
76.4
|
1.0
|
N
|
F:GLY331
|
4.1
|
78.9
|
1.0
|
N1
|
D:DA24
|
4.1
|
98.1
|
1.0
|
N
|
F:ALA334
|
4.4
|
90.5
|
1.0
|
CD
|
F:GLN353
|
4.4
|
81.8
|
1.0
|
C5
|
D:DA24
|
4.4
|
104.2
|
1.0
|
C6
|
D:DA24
|
4.5
|
92.2
|
1.0
|
C
|
F:GLY331
|
4.5
|
69.5
|
1.0
|
N9
|
D:DA24
|
4.6
|
112.0
|
1.0
|
C2'
|
D:DA24
|
4.6
|
135.0
|
1.0
|
CD2
|
F:LEU333
|
4.7
|
120.3
|
1.0
|
CA
|
F:ALA334
|
4.7
|
79.2
|
1.0
|
O
|
F:GLY331
|
4.7
|
82.9
|
1.0
|
ND2
|
F:ASN354
|
4.8
|
111.0
|
1.0
|
CE
|
F:LYS113
|
4.8
|
98.6
|
1.0
|
CG
|
F:GLN353
|
4.8
|
72.7
|
1.0
|
NE2
|
F:GLN353
|
4.9
|
83.0
|
1.0
|
C1'
|
D:DA24
|
5.0
|
125.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7sr6
Go back to
Magnesium Binding Sites List in 7sr6
Magnesium binding site 4 out
of 5 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg602
b:60.8
occ:1.00
|
OD1
|
F:ASP121
|
1.9
|
87.6
|
1.0
|
O2B
|
F:TTP605
|
2.0
|
48.7
|
1.0
|
O1G
|
F:TTP605
|
2.1
|
75.9
|
1.0
|
O1A
|
F:TTP605
|
2.2
|
69.2
|
1.0
|
OD2
|
F:ASP196
|
2.2
|
82.3
|
1.0
|
O
|
F:LEU122
|
2.2
|
76.5
|
1.0
|
CG
|
F:ASP121
|
2.6
|
81.2
|
1.0
|
OD2
|
F:ASP121
|
2.6
|
84.0
|
1.0
|
CG
|
F:ASP196
|
3.2
|
86.1
|
1.0
|
PB
|
F:TTP605
|
3.3
|
71.2
|
1.0
|
C
|
F:LEU122
|
3.4
|
78.7
|
1.0
|
PA
|
F:TTP605
|
3.4
|
87.4
|
1.0
|
PG
|
F:TTP605
|
3.5
|
89.2
|
1.0
|
O3A
|
F:TTP605
|
3.6
|
73.4
|
1.0
|
N
|
F:LEU122
|
3.8
|
71.0
|
1.0
|
OD1
|
F:ASP196
|
3.8
|
75.3
|
1.0
|
C5'
|
F:TTP605
|
3.8
|
69.0
|
1.0
|
O3B
|
F:TTP605
|
3.8
|
66.2
|
1.0
|
O5'
|
F:TTP605
|
4.0
|
70.3
|
1.0
|
NZ
|
F:LYS230
|
4.0
|
66.8
|
1.0
|
CB
|
F:ASP121
|
4.0
|
81.1
|
1.0
|
CA
|
F:LEU122
|
4.1
|
70.0
|
1.0
|
O2G
|
F:TTP605
|
4.3
|
80.4
|
1.0
|
CB
|
F:ASP196
|
4.4
|
74.7
|
1.0
|
C
|
F:ASP121
|
4.4
|
81.8
|
1.0
|
N
|
F:LYS123
|
4.4
|
77.0
|
1.0
|
O1B
|
F:TTP605
|
4.6
|
64.0
|
1.0
|
CB
|
F:CYS125
|
4.6
|
82.6
|
1.0
|
O3G
|
F:TTP605
|
4.6
|
74.6
|
1.0
|
CA
|
F:ASP121
|
4.6
|
80.2
|
1.0
|
O2A
|
F:TTP605
|
4.7
|
72.0
|
1.0
|
CA
|
F:LYS123
|
4.7
|
82.0
|
1.0
|
CB
|
F:LEU122
|
4.7
|
71.9
|
1.0
|
N
|
F:CYS125
|
4.8
|
84.0
|
1.0
|
N
|
F:ASP124
|
4.9
|
81.0
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7sr6
Go back to
Magnesium Binding Sites List in 7sr6
Magnesium binding site 5 out
of 5 in the Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Human Endogenous Retrovirus (Herv-K) Reverse Transcriptase Ternary Complex with Dsdna Template Primer and Dntp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg611
b:69.8
occ:1.00
|
O
|
G:VAL427
|
2.1
|
70.8
|
1.0
|
O
|
G:GLY428
|
2.8
|
74.5
|
1.0
|
O
|
G:ARG89
|
3.0
|
65.1
|
1.0
|
C
|
G:VAL427
|
3.0
|
73.4
|
1.0
|
C
|
G:GLY428
|
3.1
|
63.4
|
1.0
|
CA
|
G:ARG89
|
3.4
|
53.4
|
1.0
|
CA
|
G:GLY428
|
3.5
|
68.0
|
1.0
|
C
|
G:ARG89
|
3.6
|
52.4
|
1.0
|
N
|
G:GLY428
|
3.6
|
79.2
|
1.0
|
CB
|
G:ARG89
|
3.7
|
57.7
|
1.0
|
N
|
G:ILE429
|
3.8
|
57.0
|
1.0
|
ND2
|
G:ASN92
|
3.9
|
58.7
|
1.0
|
CG
|
G:ARG89
|
3.9
|
53.3
|
1.0
|
CA
|
G:VAL427
|
4.2
|
67.5
|
1.0
|
CB
|
G:ALA93
|
4.3
|
55.4
|
1.0
|
N
|
G:ALA93
|
4.3
|
60.7
|
1.0
|
CA
|
G:ILE429
|
4.5
|
56.6
|
1.0
|
CB
|
G:ASN92
|
4.5
|
64.1
|
1.0
|
CG
|
G:ASN92
|
4.6
|
58.0
|
1.0
|
CA
|
G:ALA93
|
4.6
|
57.1
|
1.0
|
N
|
G:ARG89
|
4.7
|
54.4
|
1.0
|
CD
|
G:ARG89
|
4.8
|
52.0
|
1.0
|
N
|
G:ALA90
|
4.8
|
44.9
|
1.0
|
CG1
|
G:ILE429
|
4.8
|
60.7
|
1.0
|
C
|
G:ASN92
|
4.9
|
58.1
|
1.0
|
CB
|
G:VAL427
|
4.9
|
69.2
|
1.0
|
|
Reference:
E.T.Baldwin,
M.Gotte,
E.P.Tchesnokov,
E.Arnold,
M.Hagel,
C.Nichols,
P.Dossang,
M.Lamers,
P.Wan,
S.Steinbacher,
D.L.Romero.
Human Endogenous Retrovirus-K (Herv-K) Reverse Transcriptase (Rt) Structure and Biochemistry Reveals Remarkable Similarities to Hiv-1 Rt and Opportunities For Herv-K-Specific Inhibition. Proc.Natl.Acad.Sci.Usa V. 119 60119 2022.
ISSN: ESSN 1091-6490
PubMed: 35771941
DOI: 10.1073/PNAS.2200260119
Page generated: Thu Oct 3 08:51:41 2024
|