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Magnesium in PDB 7jn3: Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048

Enzymatic activity of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048

All present enzymatic activity of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Other elements in 7jn3:

The structure of Cryo-Em Structure of Rous Sarcoma Virus Cleaved Synaptic Complex (Csc) with Hiv-1 Integrase Strand Transfer Inhibitor Mk-2048 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

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 (pdb code 7jn3). 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, PDB code: 7jn3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7jn3

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:39.9
occ:1.00
 OAG A:ZZX302 2.0 53.6 1.0
OE2 A:GLU157 2.0 36.7 1.0
OD1 A:ASP64 2.0 34.7 1.0
OD2 A:ASP64 2.2 34.7 1.0
CG A:ASP64 2.3 34.7 1.0
OE1 A:GLU157 2.5 36.7 1.0
CD A:GLU157 2.6 36.7 1.0
OAF A:ZZX302 2.7 53.6 1.0
CAW A:ZZX302 2.9 53.6 1.0
MG A:MG304 3.3 37.0 1.0
CBA A:ZZX302 3.3 53.6 1.0
CAZ A:ZZX302 3.3 53.6 1.0
CB A:ASP64 3.6 34.7 1.0
CAY A:ZZX302 3.7 53.6 1.0
CG A:GLU157 4.0 36.7 1.0
OD1 A:ASP121 4.2 46.6 1.0
CB A:SER150 4.2 51.5 1.0
OAE A:ZZX302 4.3 53.6 1.0
CAS A:ZZX302 4.4 53.6 1.0
NBE A:ZZX302 4.5 53.6 1.0
CBB A:ZZX302 4.5 53.6 1.0
CA A:ASP64 4.6 34.7 1.0
OG A:SER150 4.6 51.5 1.0
NBF A:ZZX302 4.7 53.6 1.0
N A:PHE65 4.8 36.4 1.0
CG A:ASP121 5.0 46.6 1.0
CB A:GLU157 5.0 36.7 1.0
O A:PHE65 5.0 36.4 1.0

Magnesium binding site 2 out of 4 in 7jn3

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:37.0
occ:1.00
 OD1 A:ASP64 2.2 34.7 1.0
OD1 A:ASP121 2.4 46.6 1.0
OAE A:ZZX302 2.5 53.6 1.0
OD2 A:ASP121 2.6 46.6 1.0
CG A:ASP121 2.7 46.6 1.0
CAS A:ZZX302 2.9 53.6 1.0
OAG A:ZZX302 3.0 53.6 1.0
MG A:MG303 3.3 39.9 1.0
CAY A:ZZX302 3.4 53.6 1.0
CG A:ASP64 3.4 34.7 1.0
CAW A:ZZX302 3.6 53.6 1.0
NBD A:ZZX302 3.7 53.6 1.0
CB A:ASP121 4.1 46.6 1.0
CAM A:ZZX302 4.1 53.6 1.0
CA A:ASP64 4.2 34.7 1.0
N A:PHE65 4.2 36.4 1.0
OD2 A:ASP64 4.3 34.7 1.0
CB A:ASP64 4.3 34.7 1.0
CD2 A:PHE65 4.4 36.4 1.0
C A:ASP64 4.5 34.7 1.0
OE2 A:GLU157 4.6 36.7 1.0
NBF A:ZZX302 4.7 53.6 1.0
CAO A:ZZX302 4.7 53.6 1.0
CBA A:ZZX302 4.8 53.6 1.0
CB A:PHE65 4.9 36.4 1.0

Magnesium binding site 3 out of 4 in 7jn3

Go back to Magnesium Binding Sites List in 7jn3
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:58.8
occ:1.00
 OD1 E:ASP64 2.1 50.6 1.0
OD1 E:ASP121 2.1 60.3 1.0
OD2 E:ASP121 2.4 60.3 1.0
CG E:ASP121 2.5 60.3 1.0
OAE E:ZZX302 2.7 69.2 1.0
CAS E:ZZX302 3.1 69.2 1.0
MG E:MG304 3.1 62.0 1.0
OAG E:ZZX302 3.2 69.2 1.0
CG E:ASP64 3.4 50.6 1.0
CAY E:ZZX302 3.5 69.2 1.0
CAW E:ZZX302 3.7 69.2 1.0
NBD E:ZZX302 3.8 69.2 1.0
CB E:ASP121 3.8 60.3 1.0
CA E:ASP64 4.2 50.6 1.0
OD2 E:ASP64 4.2 50.6 1.0
CAM E:ZZX302 4.2 69.2 1.0
CB E:ASP64 4.3 50.6 1.0
N E:PHE65 4.4 57.1 1.0
OE2 E:GLU157 4.5 52.5 1.0
NE2 E:GLN153 4.5 56.1 1.0
C E:ASP64 4.7 50.6 1.0
CAO E:ZZX302 4.8 69.2 1.0
NBF E:ZZX302 4.8 69.2 1.0
CBA E:ZZX302 4.8 69.2 1.0
O E:THR63 5.0 46.4 1.0
CA E:ASP121 5.0 60.3 1.0

Magnesium binding site 4 out of 4 in 7jn3

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:62.0
occ:1.00
 OAG E:ZZX302 2.0 69.2 1.0
OE2 E:GLU157 2.0 52.5 1.0
OD1 E:ASP64 2.1 50.6 1.0
OD2 E:ASP64 2.2 50.6 1.0
CG E:ASP64 2.3 50.6 1.0
CD E:GLU157 2.6 52.5 1.0
OE1 E:GLU157 2.6 52.5 1.0
OAF E:ZZX302 2.8 69.2 1.0
CAW E:ZZX302 2.8 69.2 1.0
MG E:MG303 3.1 58.8 1.0
CBA E:ZZX302 3.3 69.2 1.0
CAZ E:ZZX302 3.4 69.2 1.0
CB E:ASP64 3.6 50.6 1.0
CAY E:ZZX302 3.7 69.2 1.0
OD1 E:ASP121 3.9 60.3 1.0
NE2 E:GLN153 4.0 56.1 1.0
CG E:GLU157 4.1 52.5 1.0
CB E:SER150 4.2 60.8 1.0
OAE E:ZZX302 4.3 69.2 1.0
CAS E:ZZX302 4.3 69.2 1.0
CBB E:ZZX302 4.5 69.2 1.0
NBE E:ZZX302 4.6 69.2 1.0
CA E:ASP64 4.6 50.6 1.0
OG E:SER150 4.6 60.8 1.0
NBF E:ZZX302 4.6 69.2 1.0
CG E:ASP121 4.7 60.3 1.0
CG E:GLN153 4.8 56.1 1.0
CD E:GLN153 4.9 56.1 1.0
N E:PHE65 4.9 57.1 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 21:56:34 2024

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