Sodium in PDB 8dw4: Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium

Enzymatic activity of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium

All present enzymatic activity of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium:
3.2.2.31;

Protein crystallography data

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium, PDB code: 8dw4 was solved by M.Demir, L.P.Russelburg, M.P.Horvath, S.S.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.45 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.64, 85.55, 141.17, 90, 90, 90
R / Rfree (%) 23.1 / 24.9

Other elements in 8dw4:

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium (pdb code 8dw4). 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 Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium, PDB code: 8dw4:

Sodium binding site 1 out of 1 in 8dw4

Go back to Sodium Binding Sites List in 8dw4
Sodium binding site 1 out of 1 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:42.6
occ:1.00
 O C:HOH108 2.0 44.2 1.0
O A:HOH517 2.3 45.8 1.0
O A:SER118 2.5 52.9 1.0
O A:VAL123 2.6 37.2 1.0
O A:LEU120 2.9 45.3 1.0
OP1 C:DC21 2.9 34.9 1.0
H A:VAL123 3.6 43.5 1.0
OP2 C:DC21 3.7 37.0 1.0
C A:SER118 3.7 56.0 1.0
C A:VAL123 3.7 35.8 1.0
P C:DC21 3.8 35.9 1.0
HB A:VAL123 3.9 47.5 1.0
C A:LEU120 3.9 47.2 1.0
HG A:SER118 4.0 63.1 1.0
HA A:LYS121 4.1 48.5 1.0
HA A:SER118 4.2 58.3 1.0
C A:ARG119 4.2 56.9 1.0
N A:VAL123 4.2 34.0 1.0
HA A:ARG119 4.3 58.6 1.0
O A:ARG119 4.3 54.8 1.0
HA2 A:GLY124 4.3 46.9 1.0
N A:LEU120 4.4 52.9 1.0
CA A:VAL123 4.4 34.8 1.0
CA A:SER118 4.5 57.0 1.0
N A:ARG119 4.5 61.0 1.0
CA A:ARG119 4.6 61.7 1.0
H A:GLY122 4.6 45.9 1.0
CB A:VAL123 4.6 38.5 1.0
H A:LEU120 4.6 53.9 1.0
OG A:SER118 4.7 60.0 1.0
CA A:LYS121 4.7 43.9 1.0
O3' C:DT20 4.7 34.9 1.0
N A:LYS121 4.8 46.0 1.0
N A:GLY124 4.8 39.5 1.0
CA A:LEU120 4.8 50.9 1.0
N A:GLY122 4.8 34.6 1.0
HG12 A:VAL123 5.0 49.0 1.0
C A:LYS121 5.0 41.5 1.0

Reference:

M.Demir, L.P.Russelburg, J.Lin, C.H.Trasvina-Arenas, B.Huang, P.K.Yuen, M.P.Horvath, S.S.David. Structural Snapshots of Base Excision Mechanism By Dna Glycosylase Muty Reveal Retention of Stereochemistry For Abasic Site Product Formation To Be Published.
Page generated: Fri Apr 7 18:45:03 2023

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