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Sodium in PDB 1zm8: Apo Crystal Structure of Nuclease A From Anabaena Sp.

Protein crystallography data

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8 was solved by M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.87 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.690, 66.682, 81.730, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.6

Other elements in 1zm8:

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp. also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo Crystal Structure of Nuclease A From Anabaena Sp. (pdb code 1zm8). 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 Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8:

Sodium binding site 1 out of 1 in 1zm8

Go back to Sodium Binding Sites List in 1zm8
Sodium binding site 1 out of 1 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na280

b:47.4
occ:1.00
O A:LEU234 2.1 44.4 1.0
OD1 A:ASN236 2.3 49.0 1.0
OD2 A:ASP153 2.3 51.3 1.0
C A:LEU234 3.2 44.6 1.0
CG A:ASP153 3.2 49.9 1.0
OD1 A:ASP153 3.4 52.7 1.0
CG A:ASN236 3.5 47.2 1.0
N A:LEU234 3.6 47.6 1.0
CA A:LEU234 3.9 45.7 1.0
N A:ASN236 4.0 42.2 1.0
N A:ASN235 4.2 43.2 1.0
ND2 A:ASN236 4.2 50.2 1.0
C A:ASN235 4.3 43.4 1.0
ND2 A:ASN157 4.3 42.2 1.0
CA A:ASN236 4.4 42.9 1.0
CB A:LEU234 4.5 45.6 1.0
CA A:ASN235 4.5 42.9 1.0
CB A:ASN236 4.5 43.1 1.0
CB A:ASP153 4.6 47.2 1.0
C A:GLU233 4.7 49.0 1.0
O A:ASN235 4.8 42.9 1.0
CB A:ASN157 5.0 39.7 1.0

Reference:

M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen. Structural Insights Into the Mechanism of Nuclease A, A Beta Beta Alpha Metal Nuclease From Anabaena. J.Biol.Chem. V. 280 27990 2005.
ISSN: ISSN 0021-9258
PubMed: 15897201
DOI: 10.1074/JBC.M501798200
Page generated: Tue Dec 15 05:44:35 2020

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