Atomistry » Sodium » PDB 5jiq-5kc1 » 5jvw
Atomistry »
  Sodium »
    PDB 5jiq-5kc1 »
      5jvw »

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

Protein crystallography data

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

Other elements in 5jvw:

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:

Zinc (Zn) 13 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 1 out of 7 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 Sodium with other atoms in the Na 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:Na104

b:36.3
occ:1.00
 OP2 A:DA3 2.4 18.2 1.0
P A:DA3 3.6 18.3 1.0
OP1 A:DG2 3.6 20.1 1.0
OP1 A:DA3 3.9 19.1 1.0
O5' A:DG2 4.3 19.1 1.0
P A:DG2 4.3 19.6 1.0
O3' A:DG2 4.3 17.8 1.0
C5' A:DG2 4.5 18.6 1.0
OP2 A:DG2 4.6 19.1 1.0
C3' A:DG2 4.8 18.0 1.0
O5' A:DA3 4.8 17.9 1.0

Sodium binding site 2 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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
B:Na106

b:24.6
occ:1.00
 O B:HOH258 2.5 21.3 1.0
OP2 B:DG5 2.5 15.2 1.0
O B:HOH243 3.3 28.9 1.0
C5' B:DG5 3.7 14.6 1.0
P B:DG5 3.8 16.0 1.0
C8 B:DG5 3.8 18.8 1.0
O5' B:DG5 4.0 15.0 1.0
ZN B:ZN105 4.1 53.7 1.0
C3' B:DG4 4.2 16.0 1.0
N7 B:DG5 4.4 23.5 1.0
C8 B:DG4 4.4 17.1 1.0
O4' B:DG5 4.4 14.9 1.0
O3' B:DG4 4.5 15.9 1.0
C4' B:DG5 4.6 14.4 1.0
N7 B:DG4 4.7 18.7 1.0
O5' B:DG4 4.7 15.8 1.0
C2' B:DG4 4.8 16.1 1.0
ZN B:ZN103 4.9 32.8 1.0
N9 B:DG5 4.9 17.3 1.0
N9 B:DG4 5.0 16.6 1.0

Sodium binding site 3 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na 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
C:Na108

b:22.9
occ:1.00
 OP1 C:DC7 2.6 15.4 1.0
O C:HOH240 3.2 19.7 1.0
P C:DC7 3.6 15.0 1.0
O5' C:DC7 3.7 15.2 1.0
O C:HOH224 3.8 16.2 1.0
C5' C:DC7 3.9 15.0 1.0
C3' C:DC7 3.9 14.9 1.0
N1 C:6O6102 4.0 16.0 1.0
C6 C:6O6102 4.0 15.9 1.0
OP2 C:DT8 4.0 15.3 1.0
O C:HOH209 4.1 14.2 1.0
OP2 C:DC7 4.3 14.7 1.0
C2' C:DC7 4.5 14.8 1.0
C4' C:DC7 4.5 14.9 1.0
O2 C:6O6102 4.8 15.3 1.0
O3' C:DC7 4.9 15.4 1.0
O3' C:DC6 4.9 15.6 1.0

Sodium binding site 4 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na 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
C:Na109

b:32.6
occ:1.00
 OP1 C:DT8 2.3 16.1 1.0
O C:HOH218 2.6 20.1 1.0
O2 C:6O6102 3.0 15.3 1.0
P C:DT8 3.3 15.9 1.0
OP2 C:DT8 3.6 15.3 1.0
C2 C:6O6102 3.9 15.2 1.0
O3' C:DC7 3.9 15.4 1.0
C1 C:6O6102 4.0 15.2 1.0
O4 C:6O6102 4.2 14.8 1.0
C23 C:6O6102 4.5 14.0 1.0
O5 C:6O6102 4.6 14.3 1.0
O5' C:DT8 4.6 16.0 1.0
C22 C:6O6102 4.7 14.3 1.0
C C:6O6102 4.7 15.3 1.0
C3' C:DC7 4.8 14.9 1.0

Sodium binding site 5 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na 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
D:Na103

b:16.2
occ:1.00
 OP1 D:DA3 2.5 12.5 1.0
O D:HOH231 2.8 32.3 1.0
P D:DA3 3.7 12.0 1.0
O5' D:DA3 4.0 11.4 1.0
C5' D:DA3 4.1 11.1 1.0
OP2 D:DA3 4.4 12.1 1.0
O D:HOH207 4.7 13.4 1.0
OP2 D:DG4 4.7 11.6 1.0
O3' D:DA3 4.9 11.5 1.0
O3' D:DG2 5.0 12.0 1.0

Sodium binding site 6 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na 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
D:Na104

b:25.0
occ:1.00
 OP2 D:DG5 2.8 12.8 1.0
C8 D:DG5 3.7 14.0 1.0
C5' D:DG5 4.0 13.6 1.0
C8 D:DG4 4.0 15.3 1.0
P D:DG5 4.0 13.0 1.0
C3' D:DG4 4.1 13.3 1.0
N7 D:DG5 4.2 14.0 1.0
ZN D:ZN101 4.2 24.8 1.0
O D:HOH215 4.3 24.4 1.0
N7 D:DG4 4.3 16.6 1.0
O5' D:DG5 4.3 13.3 1.0
O5' D:DG4 4.5 12.2 1.0
O3' D:DG4 4.5 13.2 1.0
O4' D:DG5 4.6 14.1 1.0
OP2 D:DG4 4.6 11.6 1.0
N9 D:DG4 4.7 14.6 1.0
C2' D:DG4 4.7 13.6 1.0
C4' D:DG5 4.9 13.8 1.0
N9 D:DG5 4.9 13.9 1.0

Sodium binding site 7 out of 7 in 5jvw

Go back to Sodium Binding Sites List in 5jvw
Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na 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
D:Na105

b:29.1
occ:1.00
 OP2 D:DG2 2.4 14.3 1.0
O D:HOH236 2.7 24.5 1.0
O D:HOH226 3.0 27.1 1.0
O5' D:DA1 3.3 16.4 1.0
C5' D:DA1 3.5 15.1 1.0
P D:DG2 3.6 14.3 1.0
O3' D:DA1 3.9 14.2 1.0
C3' D:DA1 3.9 14.1 1.0
O D:HOH209 4.0 23.1 1.0
C4' D:DA1 4.1 14.5 1.0
O D:HOH223 4.4 11.3 1.0
OP1 D:DG2 4.5 14.1 1.0
O D:HOH205 4.6 18.6 1.0
O5' D:DG2 4.8 13.3 1.0

Reference:

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
Page generated: Tue Dec 15 11:08:33 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy