Calcium in PDB 8dw7: Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)

Enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)

All present enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G):
3.2.2.31;

Protein crystallography data

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G), PDB code: 8dw7 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) 72.80 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.89, 137.21, 74.16, 90, 101, 90
R / Rfree (%) 20.3 / 23.4

Other elements in 8dw7:

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) (pdb code 8dw7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G), PDB code: 8dw7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8dw7

Go back to Calcium Binding Sites List in 8dw7
Calcium binding site 1 out of 2 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


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 the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:40.4
occ:1.00
 O A:VAL123 2.3 41.0 1.0
O A:SER118 2.3 46.1 1.0
O A:HOH548 2.4 44.1 1.0
OG A:SER118 2.6 42.7 1.0
O C:HOH108 2.6 37.3 1.0
O C:HOH107 2.6 34.6 1.0
C A:SER118 3.2 47.5 1.0
HA2 A:GLY124 3.3 33.9 1.0
HA A:SER118 3.4 41.4 1.0
CB A:SER118 3.5 46.1 1.0
C A:VAL123 3.5 40.1 1.0
CA A:SER118 3.6 45.8 1.0
HB3 A:SER118 3.8 42.5 1.0
HB A:VAL123 4.1 36.4 1.0
CA A:GLY124 4.2 36.5 1.0
HG12 A:VAL123 4.3 37.1 1.0
OP2 C:DC21 4.3 38.6 1.0
N A:GLY124 4.3 35.7 1.0
HA A:ARG119 4.3 44.4 1.0
HB2 A:SER118 4.3 42.5 1.0
N A:ARG119 4.4 44.2 1.0
H A:VAL123 4.6 34.4 1.0
O A:LEU120 4.6 38.8 1.0
CA A:VAL123 4.6 40.0 1.0
OP1 C:DC21 4.6 37.6 1.0
CB A:VAL123 4.7 41.3 1.0
CA A:ARG119 4.8 47.5 1.0
HA3 A:GLY124 4.8 33.9 1.0
C A:GLY124 4.9 38.1 1.0
O A:HOH550 4.9 50.9 1.0
P C:DC21 4.9 38.5 1.0
HD3 A:PRO125 5.0 35.9 1.0
N A:VAL123 5.0 39.9 1.0
CG1 A:VAL123 5.0 41.3 1.0

Calcium binding site 2 out of 2 in 8dw7

Go back to Calcium Binding Sites List in 8dw7
Calcium binding site 2 out of 2 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


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 the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:38.8
occ:1.00
 O D:VAL123 2.3 37.0 1.0
O D:SER118 2.4 43.9 1.0
OG D:SER118 2.4 42.3 1.0
O D:HOH529 2.4 41.2 1.0
O D:HOH516 2.4 37.6 1.0
O F:HOH108 2.5 39.5 1.0
C D:SER118 3.2 45.0 1.0
HA2 D:GLY124 3.3 34.4 1.0
HA D:SER118 3.4 41.2 1.0
CB D:SER118 3.4 40.7 1.0
C D:VAL123 3.6 37.5 1.0
CA D:SER118 3.6 44.2 1.0
HB3 D:SER118 3.8 35.4 1.0
HB D:VAL123 4.0 35.9 1.0
HB2 D:SER118 4.2 35.4 1.0
CA D:GLY124 4.2 35.3 1.0
OP2 F:DC21 4.2 36.7 1.0
HA D:ARG119 4.3 41.8 1.0
N D:GLY124 4.3 34.6 1.0
HG12 D:VAL123 4.4 36.7 1.0
N D:ARG119 4.4 41.5 1.0
H D:VAL123 4.5 36.1 1.0
CA D:VAL123 4.6 37.0 1.0
O D:LEU120 4.6 38.9 1.0
CB D:VAL123 4.7 38.5 1.0
OP1 F:DC21 4.7 36.3 1.0
CA D:ARG119 4.8 44.7 1.0
O D:HOH554 4.8 48.8 1.0
HA3 D:GLY124 4.9 34.4 1.0
N D:VAL123 4.9 38.4 1.0
C D:GLY124 4.9 36.1 1.0
P F:DC21 5.0 38.8 1.0
HG21 D:VAL128 5.0 40.6 1.0
HG23 D:VAL128 5.0 40.6 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: Tue Apr 4 19:35:43 2023

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