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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 21:57:53 2024

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