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Sodium in PDB 5cqk: Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B

Protein crystallography data

The structure of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B, PDB code: 5cqk was solved by K.Shi, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.92 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.630, 54.040, 66.420, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.3

Other elements in 5cqk:

The structure of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B (pdb code 5cqk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B, PDB code: 5cqk:

Sodium binding site 1 out of 1 in 5cqk

Go back to Sodium Binding Sites List in 5cqk
Sodium binding site 1 out of 1 in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B


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 the Cancer Genomic Dna Mutator APOBEC3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:39.8
occ:1.00
H5 A:PGE405 1.7 44.5 1.0
H42 A:PGE404 2.0 57.6 1.0
C5 A:PGE405 2.5 37.1 1.0
OD1 A:ASP260 2.5 30.8 1.0
H52 A:PGE405 2.6 44.5 1.0
O2 A:PGE404 2.8 46.6 1.0
C4 A:PGE404 2.8 48.0 1.0
O1 A:PGE404 2.8 41.9 1.0
H2 A:PGE404 2.9 56.0 1.0
H4 A:PGE405 3.0 46.1 1.0
O4 A:PGE405 3.0 37.4 1.0
C3 A:PGE404 3.1 46.1 1.0
C2 A:PGE404 3.1 46.7 1.0
H3 A:PGE404 3.1 55.4 1.0
HA A:ASP260 3.2 26.4 1.0
C1 A:PGE404 3.3 45.1 1.0
H42 A:PGE405 3.4 46.1 1.0
C6 A:PGE405 3.4 34.0 1.0
C4 A:PGE405 3.4 38.5 1.0
H1 A:PGE404 3.4 54.1 1.0
O3 A:PGE405 3.4 43.8 1.0
HO1 A:PGE404 3.5 50.3 1.0
H4 A:PGE404 3.5 57.6 1.0
CG A:ASP260 3.5 27.6 1.0
HH21 A:ARG252 3.5 36.7 1.0
H52 A:PGE404 3.6 60.2 1.0
O3 A:PGE404 3.6 52.1 1.0
HO4 A:PGE405 3.6 44.8 1.0
HH22 A:ARG252 4.0 36.7 1.0
C5 A:PGE404 4.0 50.1 1.0
NH2 A:ARG252 4.0 30.6 1.0
H6 A:PGE405 4.0 40.8 1.0
H62 A:PGE405 4.0 40.8 1.0
H5 A:PGE404 4.0 60.2 1.0
CA A:ASP260 4.1 22.0 1.0
H32 A:PGE404 4.1 55.4 1.0
H22 A:PGE404 4.1 56.0 1.0
CB A:ASP260 4.2 22.5 1.0
H12 A:PGE404 4.3 54.1 1.0
HB3 A:ASP260 4.3 27.0 1.0
OD2 A:ASP260 4.3 23.7 1.0
N A:ASP260 4.7 18.2 1.0
C3 A:PGE405 4.9 39.8 1.0
H A:ASP260 5.0 21.8 1.0

Reference:

K.Shi, M.A.Carpenter, K.Kurahashi, R.S.Harris, H.Aihara. Crystal Structure of the Dna Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem. V. 290 28120 2015.
ISSN: ESSN 1083-351X
PubMed: 26416889
DOI: 10.1074/JBC.M115.679951
Page generated: Tue Dec 15 10:46:47 2020

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