Magnesium in PDB 9iz1: Dmctps Tetramer with Datp Dutp Dgtp and Don

All present enzymatic activity of Dmctps Tetramer with Datp Dutp Dgtp and Don:
6.3.4.2;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Dmctps Tetramer with Datp Dutp Dgtp and Don (pdb code 9iz1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Dmctps Tetramer with Datp Dutp Dgtp and Don, PDB code: 9iz1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:86.4 occ:1.00 O1G A:DGT606 3.0 109.2 1.0 O2A A:DGT606 3.0 106.9 1.0 N2 A:DGT606 3.4 102.1 1.0 O1B A:DGT606 3.4 108.9 1.0 O3A A:DGT606 3.8 108.0 1.0 PA A:DGT606 4.0 108.1 1.0 PB A:DGT606 4.1 113.4 1.0 PG A:DGT606 4.1 111.7 1.0 O3G A:DGT606 4.4 107.7 1.0 O3B A:DGT606 4.4 107.0 1.0 C2 A:DGT606 4.7 106.4 1.0 C5' A:DGT606 4.8 106.9 1.0 O5' A:DGT606 4.8 104.6 1.0

Magnesium binding site 2 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:50.0 occ:1.00 OD2 A:ASP70 2.1 75.4 1.0 O3B A:DAT605 2.1 66.3 1.0 O33 A:5ZL607 2.2 64.0 1.0 OD1 A:ASP70 2.2 71.5 1.0 CG A:ASP70 2.3 70.2 1.0 OE2 A:GLU145 2.6 41.2 1.0 CD A:GLU145 3.4 47.6 1.0 OE1 A:GLU145 3.6 58.2 1.0 PB A:DAT605 3.6 59.3 1.0 P30 A:5ZL607 3.6 83.1 1.0 CB A:ASP70 3.7 63.9 1.0 CA A:GLY17 3.8 36.7 1.0 N A:GLY17 3.8 48.1 1.0 O2A A:DAT605 3.9 62.3 1.0 NZ A:LYS38 4.1 41.5 1.0 MG A:MG604 4.1 53.4 1.0 O32 A:5ZL607 4.2 77.2 1.0 O3A A:DAT605 4.3 59.3 1.0 O2B A:DAT605 4.4 61.2 1.0 O12 A:5ZL607 4.4 68.7 1.0 O1B A:DAT605 4.5 55.2 1.0 CE A:LYS38 4.5 38.0 1.0 O31 A:5ZL607 4.6 66.0 1.0 CA A:ASP70 4.7 59.4 1.0 PA A:DAT605 4.8 55.9 1.0 CD A:LYS38 4.8 45.4 1.0 C A:LYS16 4.8 37.5 1.0 CG A:GLU145 4.8 32.0 1.0

Magnesium binding site 3 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:53.4 occ:1.00 O32 A:5ZL607 2.0 77.2 1.0 O2B A:DAT605 2.6 61.2 1.0 P30 A:5ZL607 3.2 83.1 1.0 O33 A:5ZL607 3.3 64.0 1.0 O3B A:DAT605 3.5 66.3 1.0 PB A:DAT605 3.5 59.3 1.0 O A:SER12 3.7 68.6 1.0 MG A:MG603 4.1 50.0 1.0 O12 A:5ZL607 4.1 68.7 1.0 O31 A:5ZL607 4.3 66.0 1.0 O2A A:DAT605 4.4 62.3 1.0 O1B A:DAT605 4.5 55.2 1.0 O A:HIS55 4.7 80.0 1.0 O3A A:DAT605 4.7 59.3 1.0 C A:SER12 4.8 64.9 1.0 C28 A:5ZL607 4.9 63.5 1.0 OD2 A:ASP70 4.9 75.4 1.0 O5' A:DAT605 4.9 59.7 1.0 C29 A:5ZL607 4.9 67.9 1.0 PA A:DAT605 5.0 55.9 1.0

Magnesium binding site 4 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:69.2 occ:1.00 O17 B:5ZL608 2.3 73.8 1.0 O15 B:5ZL608 2.4 73.6 1.0 O11 B:5ZL608 2.4 68.0 1.0 P02 B:5ZL608 3.6 66.0 1.0 P03 B:5ZL608 3.7 66.6 1.0 P01 B:5ZL608 3.7 74.5 1.0 NZ A:LYS228 4.0 71.3 1.0 O13 B:5ZL608 4.1 63.1 1.0 O09 B:5ZL608 4.1 73.7 1.0 O16 B:5ZL608 4.4 63.7 1.0 O B:GLU54 4.4 84.7 1.0 O07 B:5ZL608 4.5 64.7 1.0 O18 B:5ZL608 4.8 65.4 1.0 O14 B:5ZL608 4.8 69.0 1.0 O10 B:5ZL608 4.8 62.6 1.0 OG B:SER12 4.9 73.6 1.0 OE1 A:GLU190 5.0 76.5 1.0 OE2 A:GLU190 5.0 71.6 1.0

Magnesium binding site 5 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:69.8 occ:1.00 O17 A:5ZL607 2.3 72.9 1.0 O15 A:5ZL607 2.4 73.4 1.0 O11 A:5ZL607 2.4 68.3 1.0 P02 A:5ZL607 3.6 65.3 1.0 P03 A:5ZL607 3.7 66.5 1.0 P01 A:5ZL607 3.7 75.4 1.0 NZ B:LYS228 4.0 71.3 1.0 O13 A:5ZL607 4.1 61.9 1.0 O09 A:5ZL607 4.1 73.2 1.0 O16 A:5ZL607 4.4 64.0 1.0 O A:GLU54 4.4 83.3 1.0 O07 A:5ZL607 4.5 65.5 1.0 O18 A:5ZL607 4.8 65.8 1.0 O14 A:5ZL607 4.8 69.5 1.0 O10 A:5ZL607 4.8 63.2 1.0 OG A:SER12 4.9 73.2 1.0 OE1 B:GLU190 5.0 75.7 1.0 OE2 B:GLU190 5.0 70.4 1.0

Magnesium binding site 6 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:86.7 occ:1.00 O1G B:DGT607 3.0 109.0 1.0 O2A B:DGT607 3.0 106.5 1.0 N2 B:DGT607 3.4 102.0 1.0 O1B B:DGT607 3.4 108.6 1.0 O3A B:DGT607 3.8 107.7 1.0 PA B:DGT607 4.0 108.3 1.0 PB B:DGT607 4.1 113.3 1.0 PG B:DGT607 4.1 111.8 1.0 O3G B:DGT607 4.4 107.5 1.0 O3B B:DGT607 4.4 107.2 1.0 C2 B:DGT607 4.7 106.3 1.0 C5' B:DGT607 4.8 106.9 1.0 O5' B:DGT607 4.8 104.7 1.0

Magnesium binding site 7 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:48.7 occ:1.00 OD2 B:ASP70 2.1 75.7 1.0 O3B B:DAT606 2.1 66.6 1.0 O33 B:5ZL608 2.2 64.4 1.0 OD1 B:ASP70 2.2 70.9 1.0 CG B:ASP70 2.3 70.2 1.0 OE2 B:GLU145 2.6 41.4 1.0 CD B:GLU145 3.4 48.0 1.0 OE1 B:GLU145 3.6 58.7 1.0 PB B:DAT606 3.6 58.8 1.0 P30 B:5ZL608 3.6 83.3 1.0 CB B:ASP70 3.7 64.6 1.0 CA B:GLY17 3.8 35.4 1.0 N B:GLY17 3.8 47.6 1.0 O2A B:DAT606 3.9 62.6 1.0 NZ B:LYS38 4.1 41.4 1.0 MG B:MG605 4.1 53.0 1.0 O32 B:5ZL608 4.2 77.5 1.0 O3A B:DAT606 4.3 59.3 1.0 O2B B:DAT606 4.4 61.3 1.0 O12 B:5ZL608 4.4 67.4 1.0 O1B B:DAT606 4.5 55.4 1.0 CE B:LYS38 4.5 38.2 1.0 O31 B:5ZL608 4.6 66.2 1.0 CA B:ASP70 4.7 59.8 1.0 PA B:DAT606 4.8 56.8 1.0 CD B:LYS38 4.8 45.0 1.0 C B:LYS16 4.8 37.5 1.0 CG B:GLU145 4.8 33.0 1.0

Magnesium binding site 8 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:53.0 occ:1.00 O32 B:5ZL608 2.0 77.5 1.0 O2B B:DAT606 2.6 61.3 1.0 P30 B:5ZL608 3.2 83.3 1.0 O33 B:5ZL608 3.3 64.4 1.0 O3B B:DAT606 3.5 66.6 1.0 PB B:DAT606 3.5 58.8 1.0 O B:SER12 3.7 67.9 1.0 MG B:MG604 4.1 48.7 1.0 O12 B:5ZL608 4.1 67.4 1.0 O31 B:5ZL608 4.3 66.2 1.0 O2A B:DAT606 4.4 62.6 1.0 O1B B:DAT606 4.5 55.4 1.0 O B:HIS55 4.7 80.9 1.0 O3A B:DAT606 4.7 59.3 1.0 C B:SER12 4.8 64.0 1.0 C28 B:5ZL608 4.9 63.1 1.0 OD2 B:ASP70 4.9 75.7 1.0 O5' B:DAT606 4.9 60.0 1.0 C29 B:5ZL608 4.9 67.6 1.0 PA B:DAT606 5.0 56.8 1.0

Magnesium binding site 9 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:93.1 occ:1.00 O1G C:DGT607 3.0 109.7 1.0 O2A C:DGT607 3.0 108.0 1.0 N2 C:DGT607 3.4 102.3 1.0 O1B C:DGT607 3.4 109.0 1.0 O3A C:DGT607 3.8 108.4 1.0 PA C:DGT607 4.0 108.0 1.0 PB C:DGT607 4.1 115.2 1.0 PG C:DGT607 4.1 112.5 1.0 O3G C:DGT607 4.4 108.7 1.0 O3B C:DGT607 4.4 108.3 1.0 C2 C:DGT607 4.7 106.4 1.0 C5' C:DGT607 4.8 108.3 1.0 O5' C:DGT607 4.9 106.0 1.0

Magnesium binding site 10 out of 16 in the Dmctps Tetramer with Datp Dutp Dgtp and Don


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Dmctps Tetramer with Datp Dutp Dgtp and Don within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:48.4 occ:1.00 OD2 C:ASP70 2.1 73.7 1.0 O3B C:DAT606 2.1 65.2 1.0 O33 C:5ZL608 2.2 63.0 1.0 OD1 C:ASP70 2.2 70.6 1.0 CG C:ASP70 2.3 68.9 1.0 OE2 C:GLU145 2.5 41.5 1.0 CD C:GLU145 3.4 45.6 1.0 OE1 C:GLU145 3.5 56.4 1.0 PB C:DAT606 3.6 57.2 1.0 P30 C:5ZL608 3.6 79.9 1.0 CB C:ASP70 3.7 63.0 1.0 CA C:GLY17 3.8 37.9 1.0 N C:GLY17 3.8 49.1 1.0 O2A C:DAT606 3.9 62.3 1.0 NZ C:LYS38 4.1 39.4 1.0 MG C:MG605 4.1 52.4 1.0 O32 C:5ZL608 4.2 77.0 1.0 O3A C:DAT606 4.3 58.5 1.0 O2B C:DAT606 4.4 59.4 1.0 O12 C:5ZL608 4.4 67.4 1.0 O1B C:DAT606 4.5 53.7 1.0 CE C:LYS38 4.5 36.4 1.0 O31 C:5ZL608 4.6 63.8 1.0 CA C:ASP70 4.7 58.4 1.0 PA C:DAT606 4.8 54.3 1.0 CG C:GLU145 4.8 32.1 1.0 CD C:LYS38 4.8 44.5 1.0 C C:LYS16 4.8 37.9 1.0

C.J.Guo, Z.Zhang, J.L.Lu, J.Zhong, Y.F.Wu, S.Y.Guo, J.L.Liu. Structural Basis of Bifunctional Ctp/Dctp Synthase. J.Mol.Biol. V. 436 68750 2024.
ISSN: ESSN 1089-8638
PubMed: 39173734
DOI: 10.1016/J.JMB.2024.168750