Magnesium in PDB 8d86: Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.

The structure of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin., PDB code: 8d86 was solved by A.R.Orun, C.D.Snow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.32 / 3.12
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.15, 132.731, 134.261, 90, 90, 90
R / Rfree (%)	19.3 / 23.4

The binding sites of Magnesium atom in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. (pdb code 8d86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin., PDB code: 8d86:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:75.2 occ:1.00 O A:HOH203 2.4 75.8 1.0 O A:HOH208 2.6 69.4 1.0 OP1 A:DC4 3.0 89.3 1.0 O A:HOH206 3.1 73.3 1.0 OP2 A:DC4 3.8 88.3 1.0 P A:DC4 3.9 94.3 1.0 O5' A:DC4 5.0 90.7 1.0

Magnesium binding site 2 out of 5 in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:91.3 occ:1.00 OP1 A:DG5 3.1 89.2 1.0 P A:DG5 4.3 85.0 1.0 OP2 A:DG5 4.5 85.2 1.0

Magnesium binding site 3 out of 5 in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:55.3 occ:1.00 OP1 B:DG27 2.0 61.7 1.0 O B:HOH203 2.3 71.8 1.0 P B:DG27 3.4 69.0 1.0 OP2 B:DG27 4.1 75.8 1.0 O3' B:DA26 4.3 59.3 1.0 O5' B:DG27 4.3 63.1 1.0 C5' B:DG27 4.6 63.9 1.0

Magnesium binding site 4 out of 5 in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:56.0 occ:1.00 O6 B:DG28 3.4 64.7 1.0 N7 B:DG28 3.5 62.9 1.0 N7 B:DG27 3.8 64.1 1.0 C6 B:DG28 4.1 64.1 1.0 C5 B:DG28 4.1 63.2 1.0 C8 B:DG27 4.2 64.7 1.0 C5 B:DG27 4.2 62.8 1.0 O4 B:DT29 4.3 68.3 1.0 C8 B:DG28 4.6 62.2 1.0 C6 B:DG27 4.7 62.7 1.0 O6 B:DG27 4.7 68.7 1.0 O A:HOH204 4.8 64.5 1.0 C7 B:DT29 4.8 66.3 1.0 N9 B:DG27 4.8 63.1 1.0 C4 B:DG27 4.9 66.2 1.0

Magnesium binding site 5 out of 5 in the Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Isoreticular, Interpenetrating Co-Crystal of Replication Initiator Protein REPE54 and Symmetrical Expanded Duplex (31MER) Containing the Cognate REPE54 Sequence and An Additional G-C Rich Sequence Co- Crystallized with A Guest Small Molecule, Netropsin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:79.2 occ:1.00 O C:HOH403 1.8 81.8 1.0 O A:HOH201 2.0 88.1 1.0 OE2 C:GLU77 2.3 101.3 1.0 O C:HOH402 2.3 88.8 1.0 O C:HOH404 2.6 73.7 1.0 OD1 C:ASP81 2.7 85.1 1.0 CD C:GLU77 3.4 98.5 1.0 CG C:ASP81 3.6 83.8 1.0 OD2 C:ASP81 3.7 87.1 1.0 OP2 A:DG21 3.9 98.6 1.0 CG C:GLU77 4.0 108.5 1.0 NH2 C:ARG33 4.1 84.9 1.0 OD2 C:ASP34 4.2 95.2 1.0 OP2 A:DT20 4.2 84.2 1.0 N7 A:DG21 4.3 87.6 1.0 OE1 C:GLU77 4.4 101.5 1.0 O5' A:DT20 4.7 80.4 1.0 C8 A:DG21 4.7 90.4 1.0 P A:DT20 4.9 89.2 1.0

A.R.Ward, E.T.Shields, S.Dmytriw, A.Vajapayajula, C.D.Snow. Designed Crystalline Assemblies of Protein and Dna Enable Site-Specific Installation of A Guest Protein, Dna, and Small Molecule. To Be Published.