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Magnesium in PDB 8wvz: Structure of Adp-Form Asfvprimpol Hexamer

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Adp-Form Asfvprimpol Hexamer (pdb code 8wvz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Adp-Form Asfvprimpol Hexamer, PDB code: 8wvz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8wvz

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Magnesium binding site 1 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:30.0
occ:1.00
 O2B A:ADP1001 2.0 20.0 1.0
OG1 A:THR643 2.2 143.6 1.0
O1A A:ADP1001 2.3 20.0 1.0
N A:THR643 2.4 143.6 1.0
CB A:THR643 2.7 143.6 1.0
CG2 A:THR643 2.8 143.6 1.0
CA A:THR643 3.1 143.6 1.0
PA A:ADP1001 3.1 20.0 1.0
N A:LYS642 3.1 144.8 1.0
PB A:ADP1001 3.2 20.0 1.0
O2A A:ADP1001 3.3 20.0 1.0
C A:GLY641 3.3 157.8 1.0
C A:LYS642 3.5 144.8 1.0
CA A:GLY641 3.5 157.8 1.0
O3A A:ADP1001 3.6 20.0 1.0
O1B A:ADP1001 3.6 20.0 1.0
N A:PHE644 3.7 130.2 1.0
CA A:LYS642 3.8 144.8 1.0
C A:THR643 3.8 143.6 1.0
N A:GLY641 3.9 157.8 1.0
O A:GLY641 4.0 157.8 1.0
CB A:LYS642 4.4 144.8 1.0
O3B A:ADP1001 4.5 20.0 1.0
O5' A:ADP1001 4.6 20.0 1.0
O A:LYS642 4.6 144.8 1.0
CD1 A:ILE781 4.7 149.8 1.0
CG A:LYS642 4.8 144.8 1.0
CA A:PHE644 5.0 130.2 1.0
O A:THR643 5.0 143.6 1.0

Magnesium binding site 2 out of 6 in 8wvz

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Magnesium binding site 2 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:30.0
occ:1.00
 O1B B:ADP1001 1.7 20.0 1.0
OG1 B:THR643 1.8 135.9 1.0
O3A B:ADP1001 1.8 20.0 1.0
PB B:ADP1001 1.9 20.0 1.0
O2B B:ADP1001 2.4 20.0 1.0
CB B:THR643 2.8 135.9 1.0
N B:THR643 2.9 135.9 1.0
N B:PHE644 3.1 120.9 1.0
CG2 B:THR643 3.2 135.9 1.0
CA B:THR643 3.2 135.9 1.0
PA B:ADP1001 3.4 20.0 1.0
O3B B:ADP1001 3.4 20.0 1.0
C B:THR643 3.6 135.9 1.0
N B:LYS642 3.8 131.0 1.0
C B:GLY641 3.8 138.6 1.0
O1A B:ADP1001 3.9 20.0 1.0
O5' B:ADP1001 3.9 20.0 1.0
C B:LYS642 4.0 131.0 1.0
CA B:GLY641 4.0 138.6 1.0
N B:GLY641 4.0 138.6 1.0
CA B:PHE644 4.2 120.9 1.0
CB B:PHE644 4.2 120.9 1.0
O B:GLY641 4.3 138.6 1.0
O2A B:ADP1001 4.3 20.0 1.0
CA B:LYS642 4.4 131.0 1.0
O B:THR643 4.8 135.9 1.0
O B:LYS642 4.9 131.0 1.0
CB B:LYS642 5.0 131.0 1.0

Magnesium binding site 3 out of 6 in 8wvz

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Magnesium binding site 3 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:30.0
occ:1.00
 O3B C:ADP1001 1.9 20.0 1.0
OG1 C:THR643 2.1 123.7 1.0
O1B C:ADP1001 2.1 20.0 1.0
O1A C:ADP1001 2.2 20.0 1.0
PB C:ADP1001 2.2 20.0 1.0
O2A C:ADP1001 2.3 20.0 1.0
PA C:ADP1001 2.3 20.0 1.0
CG2 C:THR643 2.5 123.7 1.0
O3A C:ADP1001 2.7 20.0 1.0
CB C:THR643 2.8 123.7 1.0
N C:THR643 3.4 123.7 1.0
CA C:THR643 3.6 123.7 1.0
O2B C:ADP1001 3.7 20.0 1.0
O5' C:ADP1001 3.9 20.0 1.0
N C:PHE644 4.1 108.4 1.0
C C:THR643 4.3 123.7 1.0
N C:LYS642 4.5 121.3 1.0
C C:GLY641 4.5 124.3 1.0
CA C:GLY641 4.6 124.3 1.0
N C:GLY641 4.6 124.3 1.0
C C:LYS642 4.6 121.3 1.0
C5' C:ADP1001 4.8 20.0 1.0
O C:GLY638 4.9 140.2 1.0
OE2 C:GLU693 4.9 131.4 1.0

Magnesium binding site 4 out of 6 in 8wvz

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Magnesium binding site 4 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:30.0
occ:1.00
 O3A D:ADP1001 1.8 20.0 1.0
O1B D:ADP1001 1.8 20.0 1.0
OG1 D:THR643 2.0 132.1 1.0
PB D:ADP1001 2.2 20.0 1.0
N D:THR643 2.9 132.1 1.0
N D:PHE644 3.0 114.5 1.0
O2B D:ADP1001 3.1 20.0 1.0
CB D:THR643 3.1 132.1 1.0
PA D:ADP1001 3.2 20.0 1.0
CA D:THR643 3.3 132.1 1.0
O3B D:ADP1001 3.4 20.0 1.0
C D:THR643 3.5 132.1 1.0
O1A D:ADP1001 3.6 20.0 1.0
N D:LYS642 3.8 129.7 1.0
O5' D:ADP1001 3.8 20.0 1.0
C D:GLY641 3.9 136.4 1.0
CA D:PHE644 4.0 114.5 1.0
CG2 D:THR643 4.0 132.1 1.0
CA D:GLY641 4.1 136.4 1.0
C D:LYS642 4.1 129.7 1.0
CB D:PHE644 4.1 114.5 1.0
O2A D:ADP1001 4.2 20.0 1.0
O D:GLY641 4.4 136.4 1.0
CA D:LYS642 4.4 129.7 1.0
N D:GLY641 4.5 136.4 1.0
CG D:LYS642 4.6 129.7 1.0
O D:THR643 4.6 132.1 1.0
CB D:LYS642 4.9 129.7 1.0

Magnesium binding site 5 out of 6 in 8wvz

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Magnesium binding site 5 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:30.0
occ:1.00
 OG1 E:THR643 1.7 144.8 1.0
O3A E:ADP1001 1.8 20.0 1.0
CG2 E:THR643 2.0 144.8 1.0
CB E:THR643 2.2 144.8 1.0
O1B E:ADP1001 2.4 20.0 1.0
PB E:ADP1001 2.5 20.0 1.0
PA E:ADP1001 2.7 20.0 1.0
O2A E:ADP1001 2.7 20.0 1.0
N E:THR643 2.7 144.8 1.0
CA E:THR643 2.9 144.8 1.0
O3B E:ADP1001 3.1 20.0 1.0
O1A E:ADP1001 3.4 20.0 1.0
N E:PHE644 3.8 131.7 1.0
C E:THR643 3.8 144.8 1.0
O2B E:ADP1001 3.8 20.0 1.0
C E:LYS642 4.0 145.0 1.0
O5' E:ADP1001 4.0 20.0 1.0
N E:LYS642 4.1 145.0 1.0
C E:GLY641 4.3 153.7 1.0
NH2 E:ARG647 4.5 128.0 1.0
CA E:LYS642 4.5 145.0 1.0
CA E:GLY641 4.6 153.7 1.0
O E:GLY641 4.8 153.7 1.0
N E:GLY641 4.8 153.7 1.0
CG E:LYS642 4.9 145.0 1.0
O E:THR643 4.9 144.8 1.0
CB E:LYS642 4.9 145.0 1.0
O E:LYS642 5.0 145.0 1.0

Magnesium binding site 6 out of 6 in 8wvz

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Magnesium binding site 6 out of 6 in the Structure of Adp-Form Asfvprimpol Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Adp-Form Asfvprimpol Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1002

b:30.0
occ:1.00
 OG1 F:THR643 1.7 149.3 1.0
CG2 F:THR643 1.9 149.3 1.0
PB F:ADP1001 2.0 20.0 1.0
O1B F:ADP1001 2.0 20.0 1.0
O2B F:ADP1001 2.0 20.0 1.0
CB F:THR643 2.2 149.3 1.0
O3B F:ADP1001 2.5 20.0 1.0
CA F:THR643 3.2 149.3 1.0
N F:THR643 3.3 149.3 1.0
O3A F:ADP1001 3.6 20.0 1.0
C F:THR643 4.0 149.3 1.0
N F:PHE644 4.0 139.8 1.0
CD1 F:ILE781 4.2 157.9 1.0
O1A F:ADP1001 4.2 20.0 1.0
NH2 F:ARG647 4.3 130.9 1.0
PA F:ADP1001 4.5 20.0 1.0
C F:LYS642 4.5 157.8 1.0
C F:GLY641 4.6 163.8 1.0
N F:LYS642 4.6 157.8 1.0
CA F:GLY641 4.7 163.8 1.0
O F:GLY641 5.0 163.8 1.0

Reference:

T.H.Shi, Y.Y.Guo, R.H.Yan. Structure of Adp-Form Asfvprimpol Hexamer To Be Published.
Page generated: Fri Aug 15 20:03:59 2025

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