Zinc in PDB 5jw2: Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct

The structure of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct, PDB code: 5jw2 was solved by C.Hou, J.Rohr, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.380, 49.380, 128.295, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 28.8

The binding sites of Zinc atom in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct (pdb code 5jw2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct, PDB code: 5jw2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:13.7 occ:1.00 O15 A:6O7102 1.9 12.2 1.0 O15 A:6O7101 1.9 17.3 1.0 O14 A:6O7102 2.0 13.0 1.0 O A:HOH202 2.0 12.7 1.0 O14 A:6O7101 2.0 16.4 1.0 O A:HOH201 2.0 12.2 1.0 C20 A:6O7102 2.9 12.7 1.0 C20 A:6O7101 3.0 18.3 1.0 C41 A:6O7102 3.0 11.7 1.0 C41 A:6O7101 3.1 19.1 1.0 C19 A:6O7102 3.4 12.2 1.0 C19 A:6O7101 3.5 18.9 1.0 O23 A:6O7101 3.9 21.8 1.0 O4' A:DG7 3.9 8.4 1.0 O23 A:6O7102 4.1 10.5 1.0 N3 A:DG6 4.2 6.0 1.0 C42 A:6O7102 4.2 11.1 1.0 C42 A:6O7101 4.3 20.8 1.0 C21 A:6O7102 4.3 13.0 1.0 C21 A:6O7101 4.3 18.7 1.0 O4 A:6O7101 4.5 17.3 1.0 N2 A:DG6 4.5 6.1 1.0 O2 B:DC6 4.6 12.3 1.0 C22 A:6O7102 4.6 13.8 1.0 C4' A:DG7 4.6 8.4 1.0 C1' A:DG6 4.6 5.8 1.0 C22 A:6O7101 4.6 16.1 1.0 O4 A:6O7102 4.6 13.2 1.0 C60 A:6O7101 4.6 22.1 1.0 C2' A:DG6 4.6 5.8 1.0 C60 A:6O7102 4.7 10.5 1.0 C17 A:6O7102 4.7 12.2 1.0 C23 A:6O7102 4.7 14.1 1.0 O4' B:DT7 4.8 10.7 1.0 C23 A:6O7101 4.8 15.5 1.0 C17 A:6O7101 4.8 19.9 1.0 C2 A:DG6 4.9 6.1 1.0 C5' A:DG7 5.0 7.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:5.8 occ:0.80 O A:HOH204 2.0 5.7 1.0 O A:HOH203 2.0 5.7 1.0 O A:HOH209 2.0 5.7 1.0 O A:HOH205 2.0 5.8 1.0 N7 A:DG6 2.1 5.8 1.0 C5 A:DG6 2.9 5.9 1.0 C8 A:DG6 3.1 5.8 1.0 O6 A:DG6 3.3 5.9 1.0 C6 A:DG6 3.4 6.0 1.0 O6 A:DG7 3.7 8.0 1.0 C4 A:DG6 4.1 5.9 1.0 N9 A:DG6 4.1 5.8 1.0 C6 A:DG7 4.6 8.1 1.0 N1 A:DG6 4.7 6.0 1.0 OP2 A:DG6 4.8 4.0 1.0 C6 A:DG5 4.8 3.1 1.0 N7 A:DG7 4.8 8.1 1.0 C5 A:DG5 4.8 3.1 1.0 O6 A:DG5 4.9 3.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:3.0 occ:0.20 O A:HOH208 2.0 3.0 1.0 O A:HOH206 2.0 3.0 1.0 N7 A:DG5 2.1 3.1 1.0 C5 A:DG5 3.0 3.1 1.0 C8 A:DG5 3.1 3.1 1.0 O6 A:DG5 3.2 3.1 1.0 C6 A:DG5 3.5 3.1 1.0 O A:HOH203 3.6 5.7 1.0 O A:HOH205 3.7 5.8 1.0 N7 A:DA4 4.2 2.9 1.0 C4 A:DG5 4.2 3.1 1.0 N9 A:DG5 4.3 3.1 1.0 C5 A:DA4 4.6 2.9 1.0 OP2 A:DG5 4.8 3.0 1.0 N6 A:DA4 4.8 2.9 1.0 C8 A:DA4 4.8 2.9 1.0 N1 A:DG5 4.8 3.1 1.0 C6 A:DA4 4.9 2.9 1.0 O A:HOH209 5.0 5.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:14.2 occ:1.00 O15 B:6O7101 1.9 13.9 1.0 O14 B:6O7101 1.9 13.9 1.0 O15 A:6O7103 2.0 15.2 1.0 O B:HOH202 2.0 12.7 1.0 O B:HOH201 2.0 13.1 1.0 O14 A:6O7103 2.0 15.4 1.0 C20 B:6O7101 2.7 13.6 1.0 C41 B:6O7101 2.7 13.6 1.0 C19 B:6O7101 3.0 13.5 1.0 C20 A:6O7103 3.0 16.2 1.0 C41 A:6O7103 3.1 15.6 1.0 C19 A:6O7103 3.5 15.9 1.0 O2 A:DC11 3.7 7.8 1.0 N3 B:DG1 4.0 6.0 1.0 O23 A:6O7103 4.0 15.5 1.0 C42 B:6O7101 4.0 13.7 1.0 C2' A:DC11 4.1 7.9 1.0 C21 B:6O7101 4.1 13.5 1.0 O23 B:6O7101 4.2 13.7 1.0 C42 A:6O7103 4.3 15.6 1.0 C17 B:6O7101 4.3 13.6 1.0 C21 A:6O7103 4.4 16.7 1.0 O4 A:6O7103 4.5 17.1 1.0 C1' B:DG1 4.5 6.2 1.0 N2 B:DG1 4.5 6.0 1.0 C1' A:DC11 4.5 8.0 1.0 O4 B:6O7101 4.6 12.9 1.0 O4' A:DC12 4.6 4.5 1.0 C60 B:6O7101 4.6 13.7 1.0 C60 A:6O7103 4.7 15.6 1.0 C22 A:6O7103 4.7 17.3 1.0 C2 B:DG1 4.7 6.0 1.0 C2' B:DG1 4.7 6.3 1.0 O4' B:DA2 4.7 9.4 1.0 C2 A:DC11 4.8 7.8 1.0 C17 A:6O7103 4.9 16.2 1.0 C23 A:6O7103 4.9 17.3 1.0 C22 B:6O7101 4.9 12.4 1.0 C4 B:DG1 5.0 6.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggatccct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:4.0 occ:1.00 O B:HOH210 2.0 4.0 1.0 O B:HOH204 2.0 4.0 1.0 O B:HOH203 2.0 4.0 1.0 O B:HOH207 2.0 3.9 1.0 N7 B:DG0 2.1 3.9 1.0 O6 B:DG0 2.9 3.9 1.0 C5 B:DG0 2.9 3.9 1.0 C6 B:DG0 3.2 3.9 1.0 C8 B:DG0 3.2 3.9 1.0 N7 B:DG-1 3.9 3.1 1.0 C4 B:DG0 4.1 3.9 1.0 N9 B:DG0 4.3 3.9 1.0 O6 B:DG-1 4.6 3.1 1.0 N1 B:DG0 4.6 3.9 1.0 C5 B:DG-1 4.6 3.1 1.0 C8 B:DG-1 4.6 3.1 1.0 OP2 B:DG-1 4.7 2.9 1.0 C6 B:DG-1 4.9 3.1 1.0

C.Hou, S.Weidenbach, K.E.Cano, Z.Wang, P.Mitra, D.N.Ivanov, J.Rohr, O.V.Tsodikov. Structures of Mithramycin Analogues Bound to Dna and Implications For Targeting Transcription Factor FLI1. Nucleic Acids Res. V. 44 8990 2016.
ISSN: ESSN 1362-4962
PubMed: 27587584
DOI: 10.1093/NAR/GKW761