Magnesium in PDB 7ku7: Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
Other elements in 7ku7:
The structure of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc. also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
(pdb code 7ku7). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc., PDB code: 7ku7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7ku7
Go back to
Magnesium Binding Sites List in 7ku7
Magnesium binding site 1 out
of 4 in the Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:154.0
occ:1.00
|
OAG
|
J:ZZX401
|
1.9
|
147.9
|
1.0
|
OE2
|
A:GLU157
|
1.9
|
148.2
|
1.0
|
OAF
|
J:ZZX401
|
1.9
|
147.9
|
1.0
|
OD2
|
A:ASP64
|
2.0
|
141.3
|
1.0
|
OE1
|
A:GLU157
|
2.3
|
148.2
|
1.0
|
CD
|
A:GLU157
|
2.4
|
148.2
|
1.0
|
CAW
|
J:ZZX401
|
2.7
|
147.9
|
1.0
|
CAZ
|
J:ZZX401
|
2.7
|
147.9
|
1.0
|
CG
|
A:ASP64
|
2.9
|
141.3
|
1.0
|
CBA
|
J:ZZX401
|
3.0
|
147.9
|
1.0
|
MG
|
A:MG303
|
3.0
|
153.4
|
1.0
|
OD1
|
A:ASP64
|
3.5
|
141.3
|
1.0
|
NBE
|
J:ZZX401
|
3.8
|
147.9
|
1.0
|
CG
|
A:GLU157
|
3.9
|
148.2
|
1.0
|
CAY
|
J:ZZX401
|
3.9
|
147.9
|
1.0
|
CB
|
A:ASP64
|
4.1
|
141.3
|
1.0
|
CB
|
A:SER150
|
4.2
|
145.0
|
1.0
|
CBB
|
J:ZZX401
|
4.2
|
147.9
|
1.0
|
CAN
|
J:ZZX401
|
4.4
|
147.9
|
1.0
|
OG
|
A:SER150
|
4.4
|
145.0
|
1.0
|
OAE
|
J:ZZX401
|
4.5
|
147.9
|
1.0
|
CAS
|
J:ZZX401
|
4.7
|
147.9
|
1.0
|
NBF
|
J:ZZX401
|
4.7
|
147.9
|
1.0
|
CAL
|
J:ZZX401
|
4.8
|
147.9
|
1.0
|
OP1
|
J:DA36
|
4.8
|
148.6
|
1.0
|
C8
|
J:DA36
|
4.8
|
148.6
|
1.0
|
CB
|
A:GLU157
|
4.8
|
148.2
|
1.0
|
O
|
A:PHE65
|
4.8
|
148.2
|
1.0
|
NAP
|
J:ZZX401
|
4.9
|
147.9
|
1.0
|
N7
|
J:DA36
|
4.9
|
148.6
|
1.0
|
ND2
|
A:ASN160
|
5.0
|
144.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7ku7
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Magnesium Binding Sites List in 7ku7
Magnesium binding site 2 out
of 4 in the Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:153.4
occ:1.00
|
OAE
|
J:ZZX401
|
2.0
|
147.9
|
1.0
|
OAG
|
J:ZZX401
|
2.0
|
147.9
|
1.0
|
OD1
|
A:ASP64
|
2.0
|
141.3
|
1.0
|
CAS
|
J:ZZX401
|
2.4
|
147.9
|
1.0
|
CAW
|
J:ZZX401
|
2.5
|
147.9
|
1.0
|
CAY
|
J:ZZX401
|
2.6
|
147.9
|
1.0
|
OD2
|
A:ASP121
|
2.8
|
147.9
|
1.0
|
CG
|
A:ASP64
|
2.8
|
141.3
|
1.0
|
OD2
|
A:ASP64
|
3.0
|
141.3
|
1.0
|
MG
|
A:MG302
|
3.0
|
154.0
|
1.0
|
CG
|
A:ASP121
|
3.5
|
147.9
|
1.0
|
NBD
|
J:ZZX401
|
3.6
|
147.9
|
1.0
|
CBA
|
J:ZZX401
|
3.6
|
147.9
|
1.0
|
OE2
|
A:GLU157
|
3.8
|
148.2
|
1.0
|
NBF
|
J:ZZX401
|
3.9
|
147.9
|
1.0
|
OD1
|
A:ASP121
|
3.9
|
147.9
|
1.0
|
CAO
|
J:ZZX401
|
4.0
|
147.9
|
1.0
|
OG
|
A:SER150
|
4.1
|
145.0
|
1.0
|
CB
|
A:ASP64
|
4.2
|
141.3
|
1.0
|
N7
|
J:DA36
|
4.3
|
148.6
|
1.0
|
OAF
|
J:ZZX401
|
4.4
|
147.9
|
1.0
|
CBB
|
J:ZZX401
|
4.4
|
147.9
|
1.0
|
CB
|
A:ASP121
|
4.4
|
147.9
|
1.0
|
CAZ
|
J:ZZX401
|
4.4
|
147.9
|
1.0
|
CAM
|
J:ZZX401
|
4.6
|
147.9
|
1.0
|
CB
|
A:SER150
|
4.8
|
145.0
|
1.0
|
CA
|
A:ASP64
|
4.8
|
141.3
|
1.0
|
N
|
A:PHE65
|
4.8
|
148.2
|
1.0
|
CD
|
A:GLU157
|
4.9
|
148.2
|
1.0
|
C8
|
J:DA36
|
4.9
|
148.6
|
1.0
|
CBC
|
J:ZZX401
|
5.0
|
147.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7ku7
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Magnesium Binding Sites List in 7ku7
Magnesium binding site 3 out
of 4 in the Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:146.3
occ:1.00
|
OD1
|
E:ASP64
|
2.0
|
136.1
|
1.0
|
OD2
|
E:ASP121
|
2.1
|
141.7
|
1.0
|
OAE
|
L:ZZX401
|
2.3
|
138.8
|
1.0
|
CG
|
E:ASP121
|
2.5
|
141.7
|
1.0
|
OD1
|
E:ASP121
|
2.7
|
141.7
|
1.0
|
CG
|
E:ASP64
|
3.0
|
136.1
|
1.0
|
CAS
|
L:ZZX401
|
3.0
|
138.8
|
1.0
|
OAG
|
L:ZZX401
|
3.2
|
138.8
|
1.0
|
OD2
|
E:ASP64
|
3.5
|
136.1
|
1.0
|
CAY
|
L:ZZX401
|
3.5
|
138.8
|
1.0
|
CAW
|
L:ZZX401
|
3.6
|
138.8
|
1.0
|
CB
|
E:ASP121
|
3.6
|
141.7
|
1.0
|
NBD
|
L:ZZX401
|
3.9
|
138.8
|
1.0
|
MG
|
E:MG303
|
3.9
|
145.4
|
1.0
|
CB
|
E:ASP64
|
4.1
|
136.1
|
1.0
|
OE2
|
E:GLU157
|
4.1
|
141.3
|
1.0
|
CAO
|
L:ZZX401
|
4.5
|
138.8
|
1.0
|
CA
|
E:ASP64
|
4.5
|
136.1
|
1.0
|
CAM
|
L:ZZX401
|
4.5
|
138.8
|
1.0
|
N
|
E:PHE65
|
4.7
|
137.4
|
1.0
|
NBF
|
L:ZZX401
|
4.7
|
138.8
|
1.0
|
CBA
|
L:ZZX401
|
4.8
|
138.8
|
1.0
|
CA
|
E:ASP121
|
5.0
|
141.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7ku7
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Magnesium Binding Sites List in 7ku7
Magnesium binding site 4 out
of 4 in the Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048. Cluster Identified By 3-Dimensional Variability Analysis in Cryosparc. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg303
b:145.4
occ:1.00
|
OAG
|
L:ZZX401
|
1.9
|
138.8
|
1.0
|
OE2
|
E:GLU157
|
2.0
|
141.3
|
1.0
|
OD2
|
E:ASP64
|
2.0
|
136.1
|
1.0
|
OE1
|
E:GLU157
|
2.1
|
141.3
|
1.0
|
OAF
|
L:ZZX401
|
2.1
|
138.8
|
1.0
|
CD
|
E:GLU157
|
2.3
|
141.3
|
1.0
|
CAW
|
L:ZZX401
|
2.8
|
138.8
|
1.0
|
CAZ
|
L:ZZX401
|
2.9
|
138.8
|
1.0
|
CG
|
E:ASP64
|
3.0
|
136.1
|
1.0
|
CBA
|
L:ZZX401
|
3.2
|
138.8
|
1.0
|
OD1
|
E:ASP64
|
3.6
|
136.1
|
1.0
|
CG
|
E:GLU157
|
3.8
|
141.3
|
1.0
|
MG
|
E:MG302
|
3.9
|
146.3
|
1.0
|
CAY
|
L:ZZX401
|
4.0
|
138.8
|
1.0
|
NBE
|
L:ZZX401
|
4.1
|
138.8
|
1.0
|
CB
|
E:ASP64
|
4.2
|
136.1
|
1.0
|
OAE
|
L:ZZX401
|
4.5
|
138.8
|
1.0
|
CBB
|
L:ZZX401
|
4.5
|
138.8
|
1.0
|
CB
|
E:SER150
|
4.5
|
138.5
|
1.0
|
CAN
|
L:ZZX401
|
4.6
|
138.8
|
1.0
|
CB
|
E:GLU157
|
4.6
|
141.3
|
1.0
|
ND2
|
E:ASN160
|
4.7
|
133.6
|
1.0
|
CAS
|
L:ZZX401
|
4.7
|
138.8
|
1.0
|
O
|
E:PHE65
|
4.8
|
137.4
|
1.0
|
O3'
|
L:DC35
|
4.8
|
145.2
|
1.0
|
CAL
|
L:ZZX401
|
4.8
|
138.8
|
1.0
|
NBF
|
L:ZZX401
|
4.9
|
138.8
|
1.0
|
C2'
|
L:DC35
|
4.9
|
145.2
|
1.0
|
OG
|
E:SER150
|
5.0
|
138.5
|
1.0
|
|
Reference:
K.K.Pandey,
S.Bera,
K.Shi,
H.Aihara,
D.P.Grandgenett,
M.J.Rau,
A.V.Oleru,
J.A.J.Fitzpatrick,
A.N.Engelman.
Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048 Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01855-2
Page generated: Wed Oct 2 22:40:28 2024
|