Atomistry » Sodium » PDB 7opz-7pfg » 7p0j
Atomistry »
  Sodium »
    PDB 7opz-7pfg »
      7p0j »

Sodium in PDB 7p0j: Crystal Structure of S.Pombe MDB1 Brct Domains

Protein crystallography data

The structure of Crystal Structure of S.Pombe MDB1 Brct Domains, PDB code: 7p0j was solved by M.Day, A.W.Oliver, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.82 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.18, 44.12, 49.86, 90, 92.37, 90
R / Rfree (%) 17 / 19.7

Other elements in 7p0j:

The structure of Crystal Structure of S.Pombe MDB1 Brct Domains also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of S.Pombe MDB1 Brct Domains (pdb code 7p0j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of S.Pombe MDB1 Brct Domains, PDB code: 7p0j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7p0j

Go back to Sodium Binding Sites List in 7p0j
Sodium binding site 1 out of 2 in the Crystal Structure of S.Pombe MDB1 Brct Domains


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 S.Pombe MDB1 Brct Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:12.9
occ:0.49
HO7 A:CIT601 1.9 17.1 1.0
O5 A:CIT601 2.3 14.9 1.0
O7 A:CIT601 2.3 14.3 1.0
O3 A:CIT601 2.4 19.1 1.0
C6 A:CIT601 2.9 15.4 1.0
C3 A:CIT601 3.0 14.7 1.0
HA A:SER393 3.2 15.6 0.7
HA A:SER393 3.2 15.7 0.3
H A:SER393 3.3 16.4 0.3
H A:SER393 3.3 16.4 0.7
C5 A:CIT601 3.4 18.7 1.0
HH12 A:ARG430 3.6 17.5 1.0
C4 A:CIT601 3.7 14.2 1.0
N A:SER393 3.9 13.6 1.0
CA A:SER393 4.0 13.0 0.7
CA A:SER393 4.0 13.1 0.3
O A:HOH722 4.0 25.3 0.9
O6 A:CIT601 4.1 14.7 1.0
H41 A:CIT601 4.2 17.1 1.0
NH1 A:ARG430 4.3 14.6 1.0
C2 A:CIT601 4.4 16.3 1.0
O2 A:CIT601 4.4 26.8 1.0
HH11 A:ARG430 4.5 17.5 1.0
O4 A:CIT601 4.5 21.0 1.0
H42 A:CIT601 4.6 17.1 1.0
HB2 A:SER393 4.6 17.8 0.7
H A:PHE394 4.7 15.5 1.0
H21 A:CIT601 4.7 19.6 1.0
CB A:SER393 4.8 14.8 0.7
OG A:SER393 4.8 15.8 0.3
C1 A:CIT601 4.8 23.8 1.0
OG A:SER393 4.9 15.2 0.7
HA A:SER392 4.9 14.6 1.0
CB A:SER393 5.0 14.8 0.3
C A:SER393 5.0 12.8 1.0

Sodium binding site 2 out of 2 in 7p0j

Go back to Sodium Binding Sites List in 7p0j
Sodium binding site 2 out of 2 in the Crystal Structure of S.Pombe MDB1 Brct Domains


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 S.Pombe MDB1 Brct Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:39.9
occ:1.00
O A:HOH818 2.1 20.2 0.7
OG A:SER552 2.6 20.5 0.8
O A:HOH864 2.7 17.3 0.6
O A:SER552 2.8 17.9 1.0
HB3 A:SER552 2.9 21.2 0.2
C A:SER552 3.5 15.9 1.0
O A:HOH879 3.6 27.9 0.7
O A:HOH774 3.7 23.2 0.6
CB A:SER552 3.7 17.7 0.2
CB A:SER552 3.7 17.8 0.8
HA A:SER552 3.8 17.4 0.2
HA A:SER552 3.8 17.2 0.8
CA A:SER552 3.9 14.5 0.2
CA A:SER552 3.9 14.3 0.8
HB3 A:SER552 4.1 21.4 0.8
HA A:ALA553 4.3 17.6 1.0
HA2 A:GLY555 4.3 21.6 1.0
HB2 A:SER552 4.4 21.2 0.2
HB2 A:SER552 4.4 21.4 0.8
OG A:SER552 4.4 16.0 0.2
N A:ALA553 4.4 14.2 1.0
H A:GLY555 4.5 18.9 1.0
O A:LEU556 4.6 17.1 1.0
HG A:SER552 4.6 19.2 0.2
O A:HOH713 4.7 17.8 0.7
O A:HOH849 4.7 23.1 0.7
CA A:ALA553 4.9 14.7 1.0

Reference:

M.Day, A.W.Oliver, L.H.Pearl. The Role of TOPBP1 in Phosphorylation-Dependent Assembly of Dna Damage Response Systems To Be Published.
Page generated: Tue Oct 8 18:24:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy