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Calcium in PDB 8dvy: Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate

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

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

Protein crystallography data

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate, PDB code: 8dvy 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) 70.35 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.86, 85.48, 140.71, 90, 90, 90
R / Rfree (%) 24.7 / 27.4

Other elements in 8dvy:

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

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate (pdb code 8dvy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate, PDB code: 8dvy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8dvy

Go back to Calcium Binding Sites List in 8dvy
Calcium binding site 1 out of 3 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:52.6
occ:1.00
 O A:HOH512 2.0 47.7 1.0
O A:VAL123 2.3 51.4 1.0
O A:HOH510 2.3 47.6 1.0
O A:SER118 2.3 52.9 1.0
OG A:SER118 2.6 54.6 1.0
HA2 A:GLY124 3.3 52.3 1.0
C A:SER118 3.4 46.7 1.0
C A:VAL123 3.5 43.9 1.0
HA A:SER118 3.6 62.2 1.0
CB A:SER118 3.7 51.3 1.0
CA A:SER118 3.8 51.8 1.0
HB3 A:SER118 4.0 61.7 1.0
OP2 C:DC21 4.1 44.5 1.0
HB A:VAL123 4.1 53.9 1.0
CA A:GLY124 4.2 43.5 1.0
N A:GLY124 4.3 46.9 1.0
HG12 A:VAL123 4.4 58.8 1.0
HB2 A:SER118 4.4 61.7 1.0
O A:LEU120 4.4 42.1 1.0
H A:VAL123 4.5 54.3 1.0
N A:ARG119 4.6 51.7 1.0
OP1 C:DC21 4.6 44.1 1.0
CA A:VAL123 4.6 45.2 1.0
HA A:ARG119 4.6 62.2 1.0
HA3 A:GLY124 4.7 52.3 1.0
CB A:VAL123 4.7 44.8 1.0
P C:DC21 4.8 43.0 1.0
N A:VAL123 4.9 45.2 1.0
CA A:ARG119 5.0 51.8 1.0

Calcium binding site 2 out of 3 in 8dvy

Go back to Calcium Binding Sites List in 8dvy
Calcium binding site 2 out of 3 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:58.3
occ:0.50
 HB2 A:ASP257 2.5 74.5 1.0
O A:THR259 2.6 60.9 1.0
OD2 A:ASP257 2.7 69.4 1.0
OG1 A:THR259 2.7 64.1 1.0
HG1 A:THR259 3.0 77.1 1.0
CB A:ASP257 3.2 62.0 1.0
HB3 A:ASP257 3.3 74.5 1.0
CG A:ASP257 3.3 66.4 1.0
C A:THR259 3.6 60.0 1.0
H A:THR259 3.7 72.9 1.0
CB A:THR259 3.9 59.1 1.0
HB A:THR259 4.1 71.0 1.0
CA A:THR259 4.2 62.0 1.0
HA3 A:GLY260 4.3 67.9 1.0
N A:THR259 4.3 60.6 1.0
CA A:ASP257 4.5 59.7 1.0
OD1 A:ASP257 4.6 70.1 1.0
N A:GLY260 4.7 55.7 1.0
H A:ASP257 4.7 72.1 1.0
C A:ASP257 4.9 61.7 1.0
CA A:GLY260 5.0 56.5 1.0

Calcium binding site 3 out of 3 in 8dvy

Go back to Calcium Binding Sites List in 8dvy
Calcium binding site 3 out of 3 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:63.2
occ:0.50
 H4' C:AAB18 1.6 79.7 1.0
C4' C:AAB18 2.4 66.3 1.0
OG A:SER146 2.5 63.0 1.0
O A:HOH509 2.6 53.0 1.0
O4' C:AAB18 2.6 69.8 1.0
OD2 A:ASP144 2.7 59.9 1.0
HB2 A:SER146 2.8 65.1 1.0
O3' C:AAB18 3.1 67.9 1.0
H3' C:DA17 3.1 73.4 1.0
CB A:SER146 3.1 54.2 1.0
H A:SER146 3.2 62.0 1.0
C3' C:AAB18 3.2 63.4 1.0
O2P C:AAB18 3.3 79.5 1.0
C5' C:AAB18 3.6 63.4 1.0
O5' C:DA17 3.7 67.7 1.0
CG A:ASP144 3.7 55.3 1.0
C1' C:AAB18 3.8 64.0 1.0
O5' C:AAB18 3.8 72.1 1.0
HB3 A:SER146 3.9 65.1 1.0
H1' C:AAB18 3.9 77.0 1.0
N A:SER146 3.9 51.6 1.0
H5'1 C:AAB18 4.0 76.1 1.0
H3' C:AAB18 4.0 76.2 1.0
C3' C:DA17 4.0 61.1 1.0
OP2 C:DA17 4.0 55.9 1.0
CA A:SER146 4.1 50.1 1.0
P C:AAB18 4.1 85.0 1.0
C2' C:AAB18 4.2 64.2 1.0
P C:DG19 4.2 80.9 1.0
OD1 A:ASP144 4.4 56.4 1.0
H2' C:DA17 4.4 67.4 1.0
OP1 C:DG19 4.4 64.2 1.0
P C:DA17 4.4 60.8 1.0
HB2 A:ASP144 4.4 63.6 1.0
HA A:SER146 4.5 60.3 1.0
H5'2 C:AAB18 4.5 76.1 1.0
O3' C:DA17 4.5 63.1 1.0
HG23 A:ILE191 4.5 57.4 1.0
OP2 C:DG19 4.6 59.0 1.0
H2'2 C:AAB18 4.7 77.2 1.0
C2' C:DA17 4.7 56.1 1.0
CB A:ASP144 4.7 52.9 1.0
C5' C:DA17 4.8 64.6 1.0
H A:GLY145 4.8 66.9 1.0
H5'' C:DA17 4.9 77.6 1.0
H2'' C:DA17 4.9 67.4 1.0
O1' C:AAB18 5.0 61.9 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: Thu Jul 10 04:00:29 2025

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