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Sodium in PDB 191d: Crystal Structure of Intercalated Four-Stranded D(C3T)

Protein crystallography data

The structure of Crystal Structure of Intercalated Four-Stranded D(C3T), PDB code: 191d was solved by C.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 28.281, 44.341, 50.472, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Intercalated Four-Stranded D(C3T) (pdb code 191d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Intercalated Four-Stranded D(C3T), PDB code: 191d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 191d

Go back to Sodium Binding Sites List in 191d
Sodium binding site 1 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


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 Intercalated Four-Stranded D(C3T) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na19

b:28.2
occ:1.00
OP2 A:DC2 2.7 8.8 1.0
O A:HOH44 3.4 8.6 1.0
P A:DC2 3.6 11.4 1.0
C3' A:DC1 3.6 12.6 1.0
O3' A:DC1 3.7 11.2 1.0
C5' A:DC1 3.7 13.2 1.0
OP1 A:DC2 4.1 11.2 1.0
C4' A:DC1 4.3 13.6 1.0
O A:HOH64 4.5 22.1 1.0
C2' A:DC1 4.8 13.5 1.0
C6 A:DC1 4.8 8.8 1.0
O5' A:DC2 5.0 9.9 1.0

Sodium binding site 2 out of 3 in 191d

Go back to Sodium Binding Sites List in 191d
Sodium binding site 2 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


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 Intercalated Four-Stranded D(C3T) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na17

b:28.7
occ:1.00
O D:HOH69 2.8 10.7 1.0
OP1 B:DT8 2.9 13.6 1.0
O5' B:DT8 3.4 11.7 1.0
C2' B:DT8 3.6 14.5 1.0
P B:DT8 3.7 12.7 1.0
C3' B:DC7 3.9 13.4 1.0
H41 D:DC13 4.0 0.0 0.0
C2' B:DC7 4.0 12.7 1.0
C3' B:DT8 4.2 13.0 1.0
O3' B:DC7 4.4 13.0 1.0
C6 B:DT8 4.4 13.9 1.0
C6 B:DC7 4.5 13.5 1.0
O D:HOH46 4.6 11.8 1.0
C5' B:DT8 4.7 12.5 1.0
C1' B:DT8 4.7 13.0 1.0
N1 B:DT8 4.7 13.5 1.0
N4 D:DC13 4.9 8.4 1.0
C4' B:DT8 4.9 14.0 1.0
OP2 B:DT8 5.0 14.1 1.0

Sodium binding site 3 out of 3 in 191d

Go back to Sodium Binding Sites List in 191d
Sodium binding site 3 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


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 Intercalated Four-Stranded D(C3T) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na18

b:37.2
occ:1.00
O C:HOH35 3.1 44.2 1.0
O C:HOH42 3.1 34.6 1.0
O C:HOH23 3.5 15.3 1.0
OP2 C:DC11 3.6 12.4 1.0
OP2 C:DC10 3.9 29.2 1.0
HO3' C:DT12 4.2 0.0 0.0
O3' C:DT12 4.3 11.1 1.0
OP1 C:DC10 4.3 30.4 1.0
O A:HOH75 4.3 15.4 1.0
P C:DC10 4.5 28.6 1.0
O5' C:DC10 4.8 26.0 1.0

Reference:

C.H.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich. Crystal Structure of Intercalated Four-Stranded D(C3T) at 1.4 Angstroms Resolution. Proc.Natl.Acad.Sci.Usa V. 91 11636 1994.
ISSN: ISSN 0027-8424
PubMed: 7972115
DOI: 10.1073/PNAS.91.24.11636
Page generated: Tue Dec 15 05:21:32 2020

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