Zinc in PDB 5jw0: Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct

The structure of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct, PDB code: 5jw0 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)	40.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.564, 50.564, 125.243, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 28.9

The binding sites of Zinc atom in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct (pdb code 5jw0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct, PDB code: 5jw0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


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 Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:37.6 occ:1.00 O15 A:6O7102 2.0 34.6 1.0 O A:HOH204 2.0 32.3 1.0 O15 A:6O7101 2.0 42.3 1.0 O14 A:6O7102 2.0 32.7 1.0 O A:HOH205 2.0 39.0 1.0 O14 A:6O7101 2.0 46.6 1.0 C20 A:6O7102 3.1 34.5 1.0 C41 A:6O7102 3.1 31.7 1.0 C20 A:6O7101 3.1 42.4 1.0 C41 A:6O7101 3.1 44.9 1.0 C19 A:6O7102 3.5 32.8 1.0 C19 A:6O7101 3.6 43.0 1.0 O23 A:6O7102 3.8 33.5 1.0 O23 A:6O7101 3.9 52.1 1.0 C42 A:6O7102 4.2 32.2 1.0 O4' A:DG7 4.3 37.6 1.0 C42 A:6O7101 4.3 48.5 1.0 N3 A:DG6 4.3 41.7 1.0 C21 A:6O7102 4.4 35.3 1.0 C21 A:6O7101 4.4 44.1 1.0 O2 B:DC6 4.4 39.4 1.0 O4' B:DT7 4.5 47.3 1.0 C60 A:6O7102 4.5 33.0 1.0 C22 A:6O7102 4.6 39.3 1.0 C60 A:6O7101 4.6 51.4 1.0 C22 A:6O7101 4.7 37.9 1.0 O4 A:6O7101 4.7 41.3 1.0 N2 A:DG6 4.7 43.9 1.0 O4 A:6O7102 4.7 34.9 1.0 C1' A:DG6 4.8 41.7 1.0 C4' A:DG7 4.8 37.8 1.0 C2' A:DG6 4.8 43.6 1.0 C17 A:6O7102 4.9 34.4 1.0 C17 A:6O7101 5.0 47.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


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 Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:65.9 occ:0.80 O A:HOH207 2.0 52.2 1.0 O A:HOH206 2.0 41.6 1.0 N7 A:DG6 2.1 49.7 1.0 C8 A:DG6 2.8 45.5 1.0 C5 A:DG6 3.1 40.8 1.0 O6 A:DG6 3.7 41.0 1.0 C6 A:DG6 3.7 43.8 1.0 N9 A:DG6 4.0 46.1 1.0 C4 A:DG6 4.1 41.7 1.0 O6 A:DG7 4.2 35.8 1.0 C5 A:DG5 4.7 40.3 1.0 C6 A:DG5 4.8 38.9 1.0 N7 A:DG5 4.9 42.6 1.0 N7 A:DG7 5.0 39.4 1.0 OP2 A:DG6 5.0 39.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


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 Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:41.7 occ:1.00 O15 A:6O7103 2.0 44.7 1.0 O15 B:6O7101 2.0 35.1 1.0 O A:HOH203 2.0 40.2 1.0 O A:HOH201 2.0 40.1 1.0 O14 A:6O7103 2.0 39.0 1.0 O14 B:6O7101 2.0 38.7 1.0 C20 A:6O7103 3.0 37.6 1.0 C20 B:6O7101 3.0 40.5 1.0 C41 A:6O7103 3.1 38.9 1.0 C41 B:6O7101 3.1 38.8 1.0 C19 A:6O7103 3.4 35.6 1.0 C19 B:6O7101 3.5 37.1 1.0 O2 A:DC11 4.0 37.0 1.0 O23 B:6O7101 4.0 45.4 1.0 O23 A:6O7103 4.1 36.1 1.0 O4' A:DC12 4.2 33.1 1.0 C42 A:6O7103 4.3 40.1 1.0 C42 B:6O7101 4.3 42.8 1.0 C21 A:6O7103 4.3 39.4 1.0 C21 B:6O7101 4.4 42.6 1.0 O4' B:DT2 4.5 39.9 1.0 N3 B:DG1 4.5 47.9 1.0 C22 A:6O7103 4.6 40.1 1.0 C60 A:6O7103 4.7 39.9 1.0 O4 B:6O7101 4.7 42.4 1.0 C60 B:6O7101 4.7 40.0 1.0 O4 A:6O7103 4.7 36.1 1.0 C22 B:6O7101 4.7 48.6 1.0 N2 B:DG0 4.7 52.3 1.0 C1' B:DG1 4.7 42.8 1.0 C2' B:DG1 4.8 40.9 1.0 C4' A:DC12 4.8 37.5 1.0 C1' A:DC11 4.8 38.6 1.0 C23 A:6O7103 4.8 41.4 1.0 C17 A:6O7103 4.8 38.0 1.0 C17 B:6O7101 4.9 40.5 1.0 C2' A:DC11 4.9 39.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


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 Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:26.8 occ:0.20 N7 A:DA9 2.1 32.1 1.0 C8 A:DA9 3.0 36.2 1.0 C5 A:DA9 3.2 34.5 1.0 N6 A:DA9 3.5 33.1 1.0 C5 A:DT8 3.5 40.9 1.0 C6 A:DT8 3.6 38.8 1.0 C7 A:DT8 3.7 39.2 1.0 C6 A:DA9 3.7 34.8 1.0 N4 A:DC10 3.7 43.7 1.0 C4 A:DC10 4.1 42.6 1.0 C4 A:DT8 4.1 39.4 1.0 C5 A:DC10 4.2 43.8 1.0 N1 A:DT8 4.2 39.9 1.0 N9 A:DA9 4.3 37.1 1.0 C4 A:DA9 4.3 34.0 1.0 N3 A:DT8 4.6 41.3 1.0 O4 A:DT8 4.6 35.6 1.0 C2' A:DT8 4.6 47.0 1.0 C2 A:DT8 4.7 42.6 1.0 N3 A:DC10 4.9 44.0 1.0 C1' A:DT8 5.0 47.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


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 Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:36.1 occ:0.20 O A:HOH202 2.0 47.5 1.0 N7 A:DG5 2.1 42.6 1.0 C8 A:DG5 3.1 41.3 1.0 C5 A:DG5 3.1 40.3 1.0 O6 A:DG5 3.4 36.0 1.0 C6 A:DG5 3.6 38.9 1.0 O A:HOH206 3.7 41.6 1.0 N7 A:DA4 3.8 37.5 1.0 C5 A:DA4 4.2 38.2 1.0 N9 A:DG5 4.3 44.1 1.0 N6 A:DA4 4.3 45.8 1.0 OP2 A:DA4 4.3 65.0 1.0 C4 A:DG5 4.3 42.7 1.0 C6 A:DA4 4.4 41.1 1.0 C8 A:DA4 4.5 38.0 1.0 C4 A:DA4 4.9 38.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mithramycin Analogue Mtm Sa-Phe in Complex with A 10-Mer Dna Agggtaccct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:53.6 occ:1.00 O B:HOH201 2.0 39.6 1.0 O B:HOH202 2.0 55.1 1.0 O B:HOH203 2.0 52.1 1.0 N7 B:DG0 2.1 46.4 1.0 C8 B:DG0 3.0 46.6 1.0 C5 B:DG0 3.2 44.5 1.0 O6 B:DG0 3.7 39.6 1.0 C6 B:DG0 3.8 47.6 1.0 N7 B:DG-1 3.9 42.3 1.0 N9 B:DG0 4.2 43.0 1.0 C4 B:DG0 4.4 45.2 1.0 O6 B:DG-1 4.5 38.6 1.0 C5 B:DG-1 4.6 42.7 1.0 C8 B:DG-1 4.7 41.1 1.0 C6 B:DG-1 4.8 43.4 1.0 OP2 B:DG-1 4.9 35.6 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