Zinc in PDB 5jvw: Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.

The structure of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct., PDB code: 5jvw 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 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.567, 50.658, 92.064, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.7

The structure of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. (pdb code 5jvw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct., PDB code: 5jvw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:22.3 occ:1.00 O A:HOH243 2.0 21.0 1.0 O A:HOH230 2.0 21.7 1.0 O A:HOH224 2.0 19.5 1.0 O A:HOH218 2.0 21.0 1.0 O A:HOH217 2.0 22.2 1.0 N7 A:DG4 2.1 17.7 1.0 C8 A:DG4 2.9 16.7 1.0 C5 A:DG4 3.3 15.9 1.0 O6 A:DG4 3.8 16.1 1.0 C6 A:DG4 3.9 15.8 1.0 N7 A:DG5 4.1 14.5 1.0 O A:HOH212 4.2 21.5 1.0 N9 A:DG4 4.2 16.2 1.0 OP2 A:DG4 4.3 18.0 1.0 C4 A:DG4 4.3 15.9 1.0 N7 A:DA3 4.5 15.9 1.0 O A:HOH228 4.6 31.6 1.0 C8 A:DG5 4.6 14.3 1.0 C5 A:DA3 4.6 15.7 1.0 C8 A:DA3 4.9 16.0 1.0 C6 A:DA3 4.9 15.1 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:15.7 occ:1.00 O14 B:6O6101 2.0 14.0 1.0 O15 B:6O6101 2.0 14.7 1.0 O A:HOH201 2.0 14.4 1.0 O C:HOH208 2.0 14.2 1.0 O15 C:6O6101 2.0 15.2 1.0 O14 C:6O6101 2.0 15.0 1.0 C20 B:6O6101 2.9 13.9 1.0 C41 B:6O6101 3.0 13.8 1.0 C20 C:6O6101 3.1 14.9 1.0 C41 C:6O6101 3.1 14.8 1.0 C19 B:6O6101 3.4 14.0 1.0 C19 C:6O6101 3.6 15.0 1.0 O2 A:DC6 4.0 13.4 1.0 O23 B:6O6101 4.0 12.4 1.0 O23 C:6O6101 4.1 13.9 1.0 O2 B:DC6 4.1 12.4 1.0 O4' A:DC7 4.2 16.5 1.0 C21 B:6O6101 4.2 13.8 1.0 C42 B:6O6101 4.3 13.7 1.0 C42 C:6O6101 4.3 14.8 1.0 C21 C:6O6101 4.4 14.8 1.0 O4' B:DC7 4.4 13.2 1.0 O4 B:6O6101 4.6 13.9 1.0 C22 C:6O6101 4.6 14.7 1.0 N2 B:DG5 4.6 16.6 1.0 O4 C:6O6101 4.6 14.9 1.0 C22 B:6O6101 4.7 13.8 1.0 C60 B:6O6101 4.7 13.2 1.0 C4' A:DC7 4.7 16.4 1.0 C60 C:6O6101 4.7 14.6 1.0 N2 A:DG5 4.7 13.9 1.0 C2' A:DC6 4.7 13.7 1.0 C17 B:6O6101 4.8 13.9 1.0 C1' A:DC6 4.8 13.5 1.0 C1' B:DC6 4.8 12.1 1.0 C2' B:DC6 4.9 12.0 1.0 C4' B:DC7 4.9 13.2 1.0 C17 C:6O6101 4.9 14.8 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:17.0 occ:1.00 O A:HOH233 2.0 15.7 1.0 O A:HOH226 2.0 15.1 1.0 O A:HOH242 2.0 15.5 1.0 O A:HOH221 2.0 16.8 1.0 N7 A:DA1 2.1 16.4 1.0 C8 A:DA1 2.9 16.6 1.0 C5 A:DA1 3.2 16.3 1.0 N6 A:DA1 3.6 16.0 1.0 C6 A:DA1 3.9 16.3 1.0 O A:HOH223 4.0 21.9 1.0 N9 A:DA1 4.2 16.8 1.0 O B:HOH259 4.2 21.5 1.0 O B:HOH207 4.3 14.6 1.0 C4 A:DA1 4.3 16.7 1.0 O A:HOH241 4.4 27.1 1.0 O A:HOH206 4.6 26.6 1.0 O6 A:DG2 4.6 16.5 1.0 O5' A:DA1 4.7 17.1 1.0 N7 A:DG2 4.8 17.4 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:32.8 occ:1.00 O B:HOH243 2.0 28.9 1.0 O B:HOH232 2.0 28.7 1.0 O B:HOH248 2.0 30.7 1.0 O B:HOH252 2.0 29.4 1.0 N7 B:DG4 2.1 18.7 1.0 C8 B:DG4 3.0 17.1 1.0 C5 B:DG4 3.2 15.8 1.0 ZN B:ZN105 3.3 53.7 1.0 O6 B:DG4 3.7 14.0 1.0 C6 B:DG4 3.8 14.9 1.0 N7 B:DA3 4.0 15.2 1.0 N9 B:DG4 4.2 16.6 1.0 N7 B:DG5 4.3 23.5 1.0 OP2 B:DG4 4.3 15.8 1.0 C4 B:DG4 4.4 16.0 1.0 C8 B:DA3 4.4 15.4 1.0 C5 B:DA3 4.4 15.6 1.0 C8 B:DG5 4.7 18.8 1.0 OP2 B:DA3 4.8 13.9 1.0 O B:HOH255 4.8 28.9 1.0 C6 B:DA3 4.9 15.3 1.0 NA B:NA106 4.9 24.6 1.0 N6 B:DA3 5.0 15.3 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:11.9 occ:1.00 O B:HOH219 2.0 12.0 1.0 O D:HOH212 2.0 11.3 1.0 O B:HOH246 2.0 11.4 1.0 O B:HOH261 2.0 11.4 1.0 O B:HOH223 2.0 11.6 1.0 N7 B:DA1 2.1 11.6 1.0 C8 B:DA1 2.9 11.8 1.0 C5 B:DA1 3.3 11.4 1.0 N6 B:DA1 3.8 11.3 1.0 C6 B:DA1 4.0 11.3 1.0 O B:HOH214 4.1 11.1 1.0 O A:HOH247 4.1 24.2 1.0 N9 B:DA1 4.2 11.9 1.0 C4 B:DA1 4.4 11.6 1.0 OP1 D:DC7 4.4 13.4 1.0 C12 B:6O6102 4.5 10.5 1.0 O B:HOH204 4.6 14.5 1.0 O A:HOH211 4.6 22.1 1.0 O6 B:DG2 4.6 12.4 1.0 N1 B:6O6102 4.7 10.7 1.0 N7 B:DG2 4.8 12.6 1.0 O5' B:DA1 4.8 12.8 1.0 C7 B:6O6102 4.8 10.6 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


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-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:53.7 occ:1.00 N7 B:DG5 2.1 23.5 1.0 O B:HOH248 2.4 30.7 1.0 C8 B:DG5 3.0 18.8 1.0 O B:HOH255 3.1 28.9 1.0 C5 B:DG5 3.2 18.7 1.0 O B:HOH243 3.2 28.9 1.0 ZN B:ZN103 3.3 32.8 1.0 O6 B:DG5 3.5 17.6 1.0 C6 B:DG5 3.7 18.3 1.0 N7 B:DG4 4.0 18.7 1.0 O6 B:DG4 4.0 14.0 1.0 NA B:NA106 4.1 24.6 1.0 N9 B:DG5 4.2 17.3 1.0 O B:HOH258 4.3 21.3 1.0 C4 B:DG5 4.3 17.9 1.0 C5 B:DG4 4.4 15.8 1.0 C6 B:DG4 4.4 14.9 1.0 O B:HOH252 4.6 29.4 1.0 C8 B:DG4 4.8 17.1 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:36.4 occ:1.00 N7 C:DG4 2.1 25.2 1.0 C8 C:DG4 2.9 23.6 1.0 C5 C:DG4 3.3 22.8 1.0 ZN C:ZN106 3.7 65.2 1.0 O6 C:DG4 3.8 21.9 1.0 C6 C:DG4 3.9 21.9 1.0 OP2 C:DG4 4.2 24.0 1.0 N7 C:DA3 4.2 32.0 1.0 N9 C:DG4 4.2 23.1 1.0 O C:HOH221 4.2 32.0 1.0 N7 C:DG5 4.3 16.0 1.0 C4 C:DG4 4.4 22.8 1.0 C8 C:DA3 4.4 28.3 1.0 C5 C:DA3 4.7 26.7 1.0 C8 C:DG5 4.8 16.2 1.0 OP2 C:DA3 4.8 24.1 1.0 O5' C:DG4 5.0 23.2 1.0

Zinc binding site 8 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn104 b:16.4 occ:1.00 O C:HOH243 2.0 15.3 1.0 O C:HOH230 2.0 15.8 1.0 O C:HOH232 2.0 16.0 1.0 O C:HOH219 2.0 15.6 1.0 O C:HOH237 2.0 15.7 1.0 N7 C:DA1 2.1 17.0 1.0 C8 C:DA1 2.9 16.9 1.0 C5 C:DA1 3.2 17.4 1.0 ZN C:ZN107 3.7 69.1 1.0 N6 C:DA1 3.7 17.9 1.0 C6 C:DA1 3.9 17.6 1.0 O A:HOH204 3.9 13.2 1.0 N9 C:DA1 4.2 16.9 1.0 C12 C:6O6101 4.3 15.6 1.0 C4 C:DA1 4.3 17.3 1.0 O A:HOH210 4.4 13.1 1.0 O D:HOH202 4.4 20.0 1.0 OP1 A:DC7 4.5 13.4 1.0 O C:HOH255 4.6 23.7 1.0 N7 C:DG2 4.7 32.9 1.0 O6 C:DG2 4.7 24.3 1.0 C7 C:6O6101 4.8 15.5 1.0 C11 C:6O6101 4.9 15.4 1.0 N1 C:6O6101 5.0 15.1 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn105 b:16.9 occ:1.00 O15 B:6O6102 1.9 13.6 1.0 O15 C:6O6102 1.9 16.2 1.0 O C:HOH215 2.0 15.7 1.0 O B:HOH201 2.0 15.2 1.0 O14 C:6O6102 2.0 15.9 1.0 O14 B:6O6102 2.0 14.7 1.0 C20 C:6O6102 2.9 15.3 1.0 C41 C:6O6102 3.0 15.8 1.0 C41 B:6O6102 3.0 12.9 1.0 C20 B:6O6102 3.1 13.6 1.0 C19 C:6O6102 3.4 15.7 1.0 C19 B:6O6102 3.5 13.1 1.0 O23 C:6O6102 3.8 14.9 1.0 O23 B:6O6102 4.1 12.2 1.0 O2 C:DC6 4.1 14.9 1.0 C42 C:6O6102 4.2 15.9 1.0 O4' C:DC7 4.2 14.7 1.0 C42 B:6O6102 4.2 12.5 1.0 C21 C:6O6102 4.3 15.2 1.0 O4' D:DC7 4.3 14.9 1.0 O2 D:DC6 4.3 15.9 1.0 C21 B:6O6102 4.4 13.7 1.0 C60 C:6O6102 4.5 15.8 1.0 O4 C:6O6102 4.6 14.8 1.0 C22 B:6O6102 4.6 15.8 1.0 C4' C:DC7 4.6 14.9 1.0 C22 C:6O6102 4.6 14.3 1.0 C60 B:6O6102 4.6 12.3 1.0 N2 D:DG5 4.7 13.5 1.0 O4 B:6O6102 4.7 14.6 1.0 C1' C:DC6 4.7 15.3 1.0 C17 C:6O6102 4.8 15.5 1.0 C2' C:DC6 4.8 15.4 1.0 N2 C:DG5 4.8 15.3 1.0 C17 B:6O6102 4.8 12.9 1.0 C23 B:6O6102 4.9 16.5 1.0 C4' D:DC7 4.9 15.3 1.0 C5' C:DC7 4.9 15.0 1.0

Zinc binding site 10 out of 13 in the Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Mithramycin Analogue Mtm Sa-Trp in Complex with A 10-Mer Dna Agaggcctct. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn106 b:65.2 occ:1.00 N7 C:DA3 2.1 32.0 1.0 C8 C:DA3 2.6 28.3 1.0 OP2 C:DA3 2.9 24.1 1.0 C5 C:DA3 3.4 26.7 1.0 ZN C:ZN103 3.7 36.4 1.0 O5' C:DA3 3.9 23.5 1.0 N9 C:DA3 3.9 26.9 1.0 P C:DA3 4.0 25.1 1.0 C8 C:DG2 4.1 28.0 1.0 C3' C:DG2 4.1 23.7 1.0 N6 C:DA3 4.2 24.1 1.0 N7 C:DG2 4.2 32.9 1.0 C6 C:DA3 4.2 25.5 1.0 C4 C:DA3 4.3 26.8 1.0 N7 C:DG4 4.3 25.2 1.0 N9 C:DG2 4.4 26.4 1.0 C2' C:DG2 4.5 24.3 1.0 C5 C:DG2 4.5 27.4 1.0 O3' C:DG2 4.6 24.0 1.0 C4 C:DG2 4.7 26.3 1.0 ZN C:ZN107 4.7 69.1 1.0 O6 C:DG4 4.9 21.9 1.0 O5' C:DG2 4.9 20.7 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