Magnesium in PDB 7xd9: Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)

The structure of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form), PDB code: 7xd9 was solved by J.Wu, X.Wang, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.84 / 2.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	139.43, 154.58, 172.351, 90, 94.68, 90
R / Rfree (%)	19.1 / 22.1

The structure of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) (pdb code 7xd9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form), PDB code: 7xd9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:72.2 occ:1.00 OD1 A:ASP664 2.2 56.1 1.0 O A:HOH1186 2.5 54.2 1.0 O A:HOH1172 2.5 61.5 1.0 OP1 C:U1101 2.7 45.5 1.0 O A:HOH1170 3.0 60.1 1.0 CG A:ASP664 3.1 50.6 1.0 OD2 A:ASP534 3.5 82.7 1.0 OD2 A:ASP664 3.5 57.8 1.0 N A:SER710 3.7 47.0 1.0 OG A:SER710 4.1 50.7 1.0 N A:CYS709 4.1 41.1 1.0 CA A:CYS709 4.1 46.6 1.0 P C:U1101 4.1 44.5 1.0 CB A:ASP664 4.4 47.5 1.0 O A:HOH1101 4.4 56.4 1.0 C A:CYS709 4.4 45.0 1.0 C5' C:U1101 4.4 42.4 1.0 CA A:SER710 4.5 47.2 1.0 O5' C:U1101 4.5 42.4 1.0 CG A:ASP534 4.7 76.7 1.0 CB A:SER710 4.9 46.1 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:70.7 occ:1.00 O2B A:CTP1007 1.9 59.5 0.7 OD2 A:ASP663 2.1 70.1 1.0 O A:THR535 2.2 55.5 1.0 OD1 A:ASP534 2.3 79.3 1.0 O2G A:CTP1007 2.3 62.8 0.7 O2A A:CTP1007 2.6 58.7 0.7 CG A:ASP663 3.2 66.4 1.0 PB A:CTP1007 3.3 65.0 0.7 C A:THR535 3.4 51.9 1.0 CG A:ASP534 3.5 76.7 1.0 PG A:CTP1007 3.6 71.1 0.7 N A:THR535 3.7 57.5 1.0 PA A:CTP1007 3.9 60.8 0.7 O3B A:CTP1007 3.9 69.3 0.7 OD1 A:ASP663 3.9 70.7 1.0 O3A A:CTP1007 3.9 69.6 0.7 CA A:THR535 4.0 54.6 1.0 OD2 A:ASP534 4.3 82.7 1.0 CB A:ASP663 4.3 54.0 1.0 C5' A:CTP1007 4.4 58.4 0.7 CB A:THR535 4.4 50.2 1.0 N A:ALA536 4.5 53.6 1.0 N A:GLY537 4.5 54.5 1.0 O3G A:CTP1007 4.5 64.8 0.7 CB A:ASP534 4.5 56.1 1.0 O1B A:CTP1007 4.5 62.2 0.7 N A:TRP538 4.5 53.9 1.0 C A:ASP534 4.6 54.3 1.0 CB A:TRP538 4.6 49.1 1.0 O1G A:CTP1007 4.7 65.4 0.7 O5' A:CTP1007 4.7 59.9 0.7 CA A:ALA536 4.7 57.7 1.0 O A:HOH1172 4.8 61.5 1.0 CA A:ASP534 4.9 56.5 1.0 C A:ALA536 5.0 55.5 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:69.3 occ:0.77 O F:HOH1204 2.2 68.1 1.0 O1A D:CTP1009 2.5 60.6 0.7 OD2 D:ASP664 2.8 58.1 1.0 O3' F:U1101 3.6 53.9 1.0 PA D:CTP1009 3.6 71.2 0.7 CG D:ASP664 3.6 53.4 1.0 OD2 D:ASP663 3.8 78.2 1.0 O2A D:CTP1009 3.9 70.9 0.7 OP1 F:U1101 3.9 51.7 1.0 OD1 D:ASP534 4.0 77.2 1.0 OD2 D:ASP534 4.3 84.7 1.0 MG D:MG1002 4.3 71.3 1.0 C3' F:U1101 4.4 50.3 1.0 OD1 D:ASP664 4.4 61.4 1.0 CB D:ASP664 4.4 49.2 1.0 CG D:ASP534 4.4 75.5 1.0 O D:HOH1180 4.4 51.1 1.0 C5' F:U1101 4.4 44.7 1.0 O D:HOH1199 4.4 54.0 1.0 O5' F:U1101 4.5 47.4 1.0 CG D:ASP663 4.6 68.7 1.0 O3A D:CTP1009 4.6 74.2 0.7 O F:HOH1205 4.7 54.2 1.0 CA D:ASP664 4.7 46.7 1.0 N D:ASP664 4.8 48.3 1.0 O5' D:CTP1009 4.8 69.5 0.7 P F:U1101 4.8 49.2 1.0 C5' D:CTP1009 4.9 64.8 0.7 C4' F:U1101 4.9 47.9 1.0 O3G D:CTP1009 4.9 67.1 0.7 CB D:ASP663 4.9 54.9 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:71.3 occ:1.00 O3G D:CTP1009 2.0 67.1 0.7 O2B D:CTP1009 2.2 61.3 0.7 OD2 D:ASP663 2.2 78.2 1.0 O D:THR535 2.4 58.8 1.0 OD1 D:ASP534 2.6 77.2 1.0 O1A D:CTP1009 3.1 60.6 0.7 PB D:CTP1009 3.1 66.9 0.7 PG D:CTP1009 3.3 66.3 0.7 CG D:ASP663 3.3 68.7 1.0 O3A D:CTP1009 3.4 74.2 0.7 O3B D:CTP1009 3.4 67.2 0.7 C D:THR535 3.6 51.9 1.0 CG D:ASP534 3.6 75.5 1.0 OD1 D:ASP663 3.8 72.8 1.0 PA D:CTP1009 3.8 71.2 0.7 OD2 D:ASP534 4.0 84.7 1.0 N D:GLY537 4.1 50.2 1.0 O1G D:CTP1009 4.2 65.3 0.7 N D:THR535 4.2 55.5 1.0 MG D:MG1001 4.3 69.3 0.8 O2G D:CTP1009 4.3 70.8 0.7 N D:TRP538 4.4 51.4 1.0 CA D:THR535 4.4 50.7 1.0 CB D:ASP663 4.5 54.9 1.0 O1B D:CTP1009 4.5 65.8 0.7 NZ D:LYS689 4.6 74.0 1.0 O5' D:CTP1009 4.6 69.5 0.7 CB D:TRP538 4.6 49.6 1.0 N D:ALA536 4.6 52.6 1.0 CB D:THR535 4.6 52.2 1.0 C5' D:CTP1009 4.7 64.8 0.7 CA D:ALA536 4.7 55.9 1.0 C D:ALA536 4.8 50.5 1.0 C D:ASP534 4.9 52.4 1.0 CA D:GLY537 4.9 51.7 1.0 CB D:ASP534 4.9 59.6 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1001 b:78.0 occ:0.92 O I:HOH1201 2.1 75.1 1.0 O2A G:CTP1005 2.4 68.6 0.8 OD2 G:ASP664 3.2 62.2 1.0 OD1 G:ASP534 3.3 83.1 1.0 O G:HOH1110 3.4 67.5 1.0 OD2 G:ASP534 3.4 88.2 1.0 PA G:CTP1005 3.5 65.5 0.8 O3' I:U1101 3.6 60.7 1.0 O1A G:CTP1005 3.6 69.9 0.8 CG G:ASP534 3.7 80.3 1.0 CG G:ASP664 3.9 64.3 1.0 OP1 I:U1101 4.0 50.5 1.0 OD2 G:ASP663 4.0 72.0 1.0 MG G:MG1002 4.2 74.6 1.0 C3' I:U1101 4.3 57.2 1.0 C5' I:U1101 4.5 53.4 1.0 CB G:ASP664 4.5 60.5 1.0 O3A G:CTP1005 4.5 75.3 0.8 O5' I:U1101 4.5 59.0 1.0 OD1 G:ASP664 4.6 75.4 1.0 O5' G:CTP1005 4.7 62.3 0.8 CG G:ASP663 4.8 71.4 1.0 O1G G:CTP1005 4.9 70.1 0.8 CA G:ASP664 4.9 58.8 1.0 P I:U1101 4.9 50.3 1.0 C4' I:U1101 4.9 56.2 1.0 C5' G:CTP1005 5.0 63.5 0.8 N G:ASP664 5.0 55.7 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1002 b:74.6 occ:1.00 OD2 G:ASP663 2.0 72.0 1.0 O2B G:CTP1005 2.2 67.1 0.8 O1G G:CTP1005 2.2 70.1 0.8 O G:THR535 2.4 68.3 1.0 O2A G:CTP1005 2.8 68.6 0.8 OD1 G:ASP534 2.9 83.1 1.0 PB G:CTP1005 3.1 69.9 0.8 O3A G:CTP1005 3.2 75.3 0.8 CG G:ASP663 3.2 71.4 1.0 PG G:CTP1005 3.4 64.6 0.8 O3B G:CTP1005 3.5 64.9 0.8 CG G:ASP534 3.5 80.3 1.0 OD2 G:ASP534 3.5 88.2 1.0 C G:THR535 3.5 62.4 1.0 PA G:CTP1005 3.6 65.5 0.8 OD1 G:ASP663 3.9 74.8 1.0 N G:THR535 4.1 59.1 1.0 MG G:MG1001 4.2 78.0 0.9 CB G:ASP663 4.2 63.0 1.0 N G:GLY537 4.3 59.3 1.0 CA G:THR535 4.3 63.7 1.0 N G:TRP538 4.3 59.8 1.0 C5' G:CTP1005 4.4 63.5 0.8 O2G G:CTP1005 4.4 70.3 0.8 O5' G:CTP1005 4.4 62.3 0.8 O3G G:CTP1005 4.5 69.8 0.8 O1B G:CTP1005 4.5 63.7 0.8 N G:ALA536 4.6 64.5 1.0 CB G:TRP538 4.6 59.5 1.0 CB G:THR535 4.6 63.9 1.0 CB G:ASP534 4.7 62.5 1.0 CA G:ALA536 4.7 65.9 1.0 C G:ASP534 4.8 65.8 1.0 C G:ALA536 4.8 64.6 1.0 O1A G:CTP1005 4.9 69.9 0.8 CA G:GLY537 4.9 59.8 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1001 b:76.4 occ:0.87 O J:HOH1145 2.5 74.2 1.0 O2A J:CTP1006 2.5 66.5 0.8 OD2 J:ASP664 2.7 70.7 1.0 OD1 J:ASP534 3.0 82.6 1.0 OD2 J:ASP534 3.2 85.7 1.0 OD2 J:ASP663 3.3 75.8 1.0 O3' L:U1101 3.4 64.3 1.0 CG J:ASP664 3.4 64.7 1.0 CG J:ASP534 3.5 84.7 1.0 PA J:CTP1006 3.7 70.8 0.8 MG J:MG1002 3.8 72.0 1.0 CB J:ASP664 4.0 64.7 1.0 O1A J:CTP1006 4.1 72.8 0.8 CG J:ASP663 4.2 74.9 1.0 OP1 L:U1101 4.2 58.4 1.0 N J:ASP664 4.2 65.1 1.0 CA J:ASP664 4.2 68.6 1.0 OD1 J:ASP664 4.3 69.4 1.0 C3' L:U1101 4.3 60.6 1.0 O J:HOH1152 4.4 63.2 1.0 C5' L:U1101 4.4 58.9 1.0 CB J:ASP663 4.7 62.8 1.0 C J:ASP663 4.7 64.9 1.0 O5' L:U1101 4.7 58.0 1.0 O3A J:CTP1006 4.8 74.1 0.8 C4' L:U1101 4.8 57.3 1.0 O5' J:CTP1006 4.8 70.4 0.8 C5' J:CTP1006 4.9 64.3 0.8 CB J:ASP534 5.0 73.9 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1002 b:72.0 occ:1.00 OD2 J:ASP663 2.1 75.8 1.0 O2B J:CTP1006 2.2 63.9 0.8 O J:THR535 2.3 71.2 1.0 O3G J:CTP1006 2.3 68.8 0.8 OD1 J:ASP534 2.6 82.6 1.0 O2A J:CTP1006 2.8 66.5 0.8 PB J:CTP1006 3.2 60.1 0.8 CG J:ASP663 3.2 74.9 1.0 O3A J:CTP1006 3.3 74.1 0.8 C J:THR535 3.4 66.4 1.0 PG J:CTP1006 3.6 70.2 0.8 CG J:ASP534 3.6 84.7 1.0 O3B J:CTP1006 3.7 69.2 0.8 PA J:CTP1006 3.7 70.8 0.8 OD1 J:ASP663 3.8 75.5 1.0 MG J:MG1001 3.8 76.4 0.9 N J:THR535 4.0 71.1 1.0 CA J:THR535 4.2 66.9 1.0 OD2 J:ASP534 4.3 85.7 1.0 CB J:ASP663 4.3 62.8 1.0 O2G J:CTP1006 4.5 73.1 0.8 N J:ALA536 4.5 68.3 1.0 CB J:ASP534 4.5 73.9 1.0 C J:ASP534 4.5 76.5 1.0 N J:GLY537 4.5 65.7 1.0 O J:HOH1145 4.5 74.2 1.0 O5' J:CTP1006 4.6 70.4 0.8 O1B J:CTP1006 4.6 63.4 0.8 O1G J:CTP1006 4.6 70.4 0.8 C5' J:CTP1006 4.6 64.3 0.8 CB J:THR535 4.6 64.9 1.0 CA J:ALA536 4.6 71.1 1.0 N J:TRP538 4.7 61.3 1.0 CA J:ASP534 4.8 74.7 1.0 CE J:LYS689 4.8 77.5 1.0 C J:ALA536 4.8 69.5 1.0 O1A J:CTP1006 4.9 72.8 0.8 CB J:TRP538 4.9 56.8 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg1001 b:69.7 occ:0.71 O1A M:CTP1006 2.0 61.8 0.7 O M:HOH1108 2.2 67.9 1.0 OD1 M:ASP664 2.3 72.6 1.0 OD2 M:ASP663 2.8 75.9 1.0 OD2 M:ASP534 3.1 88.4 1.0 PA M:CTP1006 3.4 70.0 0.7 O3' O:U1101 3.4 59.3 1.0 OD1 M:ASP534 3.5 85.0 1.0 MG M:MG1002 3.5 69.2 1.0 CG M:ASP664 3.5 61.2 1.0 CG M:ASP534 3.6 80.8 1.0 CG M:ASP663 3.8 72.1 1.0 O2A M:CTP1006 4.0 71.0 0.7 N M:ASP664 4.3 49.0 1.0 OD2 M:ASP664 4.4 60.0 1.0 O M:HOH1134 4.4 53.1 1.0 O3A M:CTP1006 4.4 77.4 0.7 C5' M:CTP1006 4.4 63.6 0.7 O5' M:CTP1006 4.4 68.3 0.7 C3' O:U1101 4.4 52.3 1.0 CA M:ASP664 4.4 52.4 1.0 CB M:ASP664 4.4 54.3 1.0 O2G M:CTP1006 4.5 72.6 0.7 CB M:ASP663 4.5 59.2 1.0 OP1 O:U1101 4.6 53.3 1.0 OD1 M:ASP663 4.6 75.9 1.0 C M:ASP663 4.7 51.0 1.0 O1B M:CTP1006 4.8 64.0 0.7 O5' O:U1101 4.8 56.7 1.0 C5' O:U1101 4.8 51.1 1.0 CB M:ASP534 4.9 59.9 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Ctp Form) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg1002 b:69.2 occ:1.00 O1B M:CTP1006 2.1 64.0 0.7 O2G M:CTP1006 2.2 72.6 0.7 OD1 M:ASP534 2.2 85.0 1.0 OD2 M:ASP663 2.4 75.9 1.0 O M:THR535 2.4 62.4 1.0 O1A M:CTP1006 2.9 61.8 0.7 PB M:CTP1006 3.1 67.2 0.7 CG M:ASP534 3.3 80.8 1.0 O3A M:CTP1006 3.3 77.4 0.7 PG M:CTP1006 3.4 69.1 0.7 CG M:ASP663 3.4 72.1 1.0 O3B M:CTP1006 3.4 65.9 0.7 MG M:MG1001 3.5 69.7 0.7 C M:THR535 3.6 58.0 1.0 OD2 M:ASP534 3.6 88.4 1.0 PA M:CTP1006 3.7 70.0 0.7 OD1 M:ASP663 3.9 75.9 1.0 N M:THR535 4.1 64.3 1.0 O3G M:CTP1006 4.2 73.9 0.7 CA M:THR535 4.4 55.3 1.0 N M:GLY537 4.4 54.8 1.0 C5' M:CTP1006 4.4 63.6 0.7 O1G M:CTP1006 4.5 75.3 0.7 O2B M:CTP1006 4.5 60.9 0.7 O5' M:CTP1006 4.6 68.3 0.7 CB M:ASP663 4.6 59.2 1.0 CB M:ASP534 4.6 59.9 1.0 N M:ALA536 4.6 62.4 1.0 N M:TRP538 4.7 56.7 1.0 CB M:THR535 4.7 54.0 1.0 C M:ASP534 4.7 58.5 1.0 CA M:ALA536 4.8 62.5 1.0 CB M:TRP538 4.9 52.8 1.0 CE M:LYS689 5.0 81.2 1.0 CA M:ASP534 5.0 55.3 1.0 C M:ALA536 5.0 59.5 1.0 O2A M:CTP1006 5.0 71.0 0.7

J.Wu, X.Wang, Q.Liu, G.Lu, P.Gong. Structural Basis of Transition From Initiation to Elongation in De Novo Viral Rna-Dependent Rna Polymerases Proc.Natl.Acad.Sci.Usa 2022.
ISSN: ESSN 1091-6490