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Sodium in PDB 2vla: Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna

Enzymatic activity of Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna

All present enzymatic activity of Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna:
3.1.21.4;

Protein crystallography data

The structure of Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna, PDB code: 2vla was solved by R.Sukackaite, S.Grazulis, M.Bochtler, V.Siksnys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.62 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.292, 167.513, 43.846, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna (pdb code 2vla). 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 Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna, PDB code: 2vla:

Sodium binding site 1 out of 1 in 2vla

Go back to Sodium Binding Sites List in 2vla
Sodium binding site 1 out of 1 in the Crystal Structure of Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna


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 Restriction Endonuclease Bpuji Recognition Domain in Complex with Cognate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1282

b:15.2
occ:1.00
 O A:GLY173 2.6 16.4 1.0
O5 A:PG61281 2.6 42.2 1.0
O3 A:PG61281 2.8 30.5 1.0
O4 A:PG61281 2.8 26.8 1.0
O2 A:PG61281 2.8 34.2 1.0
O1 A:PG61281 3.0 33.7 1.0
C12 A:PG61281 3.2 54.6 1.0
O6 A:PG61281 3.2 54.0 1.0
C11 A:PG61281 3.2 46.7 1.0
C10 A:PG61281 3.4 43.5 1.0
C6 A:PG61281 3.5 28.0 1.0
C7 A:PG61281 3.6 22.7 1.0
C8 A:PG61281 3.6 31.8 1.0
C5 A:PG61281 3.6 25.2 1.0
C9 A:PG61281 3.6 35.9 1.0
C A:GLY173 3.7 14.3 1.0
C4 A:PG61281 3.7 28.4 1.0
C3 A:PG61281 3.9 37.1 1.0
C1 A:PG61281 3.9 28.0 1.0
C2 A:PG61281 4.0 37.9 1.0
CA A:GLY173 4.3 12.4 1.0
O A:GLY248 4.8 17.1 1.0
N A:LYS174 4.8 12.9 1.0

Reference:

R.Sukackaite, S.Grazulis, M.Bochtler, V.Siksnys. The Recognition Domain of the Bpuji Restriction Endonuclease in Complex with Cognate Dna at 1.3-A Resolution. J.Mol.Biol. V. 378 1084 2008.
ISSN: ISSN 0022-2836
PubMed: 18433771
DOI: 10.1016/J.JMB.2008.03.041
Page generated: Sun Aug 17 11:48:22 2025

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