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Calcium in PDB 8dwe: Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine

Enzymatic activity of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine

All present enzymatic activity of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine:
3.2.2.31;

Protein crystallography data

The structure of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine, PDB code: 8dwe was solved by L.P.Russelburg, M.Demir, S.S.David, M.P.Horvath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.12 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.63, 137.96, 74.49, 90, 101, 90
R / Rfree (%) 19.2 / 23.4

Other elements in 8dwe:

The structure of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine (pdb code 8dwe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine, PDB code: 8dwe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8dwe

Go back to Calcium Binding Sites List in 8dwe
Calcium binding site 1 out of 4 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:41.9
occ:1.00
 O A:SER118 2.2 49.3 1.0
O A:VAL123 2.4 42.0 1.0
O A:HOH522 2.4 37.5 1.0
O A:HOH552 2.5 45.2 1.0
OG A:SER118 2.6 37.9 1.0
O C:HOH119 2.6 39.5 1.0
C A:SER118 3.2 47.4 1.0
HA2 A:GLY124 3.3 42.7 1.0
CB A:SER118 3.5 41.3 1.0
HA A:SER118 3.6 53.2 1.0
C A:VAL123 3.6 43.6 1.0
CA A:SER118 3.7 46.1 1.0
HB3 A:SER118 3.8 47.5 1.0
CA A:GLY124 4.2 35.2 1.0
HA A:ARG119 4.2 55.4 1.0
HG12 A:VAL123 4.2 47.6 1.0
HB A:VAL123 4.3 46.8 1.0
OP2 C:DC21 4.3 42.4 1.0
N A:ARG119 4.3 39.5 1.0
HB2 A:SER118 4.3 47.5 1.0
N A:GLY124 4.4 34.7 1.0
O A:LEU120 4.6 40.0 1.0
OP1 C:DC21 4.6 40.4 1.0
O A:HOH538 4.7 44.0 1.0
CA A:ARG119 4.7 45.6 1.0
H A:VAL123 4.7 46.1 1.0
CA A:VAL123 4.7 36.3 1.0
CB A:VAL123 4.8 39.7 1.0
HA3 A:GLY124 4.8 42.7 1.0
C A:GLY124 4.9 32.3 1.0
HD3 A:PRO125 4.9 43.3 1.0
P C:DC21 5.0 41.6 1.0
CG1 A:VAL123 5.0 40.2 1.0
HG21 A:VAL128 5.0 53.2 1.0

Calcium binding site 2 out of 4 in 8dwe

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Calcium binding site 2 out of 4 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:78.9
occ:0.69
 HG1 A:THR259 2.0 83.7 1.0
OD2 A:ASP257 2.4 68.3 1.0
O A:HOH528 2.4 57.6 1.0
OD1 A:ASP257 2.7 76.2 1.0
O A:THR259 2.7 61.9 1.0
OG1 A:THR259 2.7 68.9 1.0
CG A:ASP257 2.9 70.4 1.0
C A:THR259 3.7 55.8 1.0
CB A:THR259 3.9 62.4 1.0
H A:THR259 3.9 68.0 1.0
HB A:THR259 4.1 76.6 1.0
CA A:THR259 4.2 56.9 1.0
O A:HOH523 4.3 51.3 1.0
HA3 A:GLY260 4.3 67.3 1.0
CB A:ASP257 4.4 64.6 1.0
N A:THR259 4.5 54.9 1.0
HB2 A:ASP257 4.5 74.0 1.0
O A:HOH543 4.6 54.6 1.0
N A:GLY260 4.7 60.3 1.0
O A:HOH520 4.8 57.2 1.0
HB3 A:ASP257 4.8 74.0 1.0
CA A:GLY260 5.0 59.3 1.0

Calcium binding site 3 out of 4 in 8dwe

Go back to Calcium Binding Sites List in 8dwe
Calcium binding site 3 out of 4 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:42.2
occ:1.00
 O D:SER118 2.4 45.9 1.0
O D:VAL123 2.4 35.5 1.0
OG D:SER118 2.4 40.8 1.0
O D:HOH528 2.5 35.8 1.0
O F:HOH107 2.6 40.7 1.0
O D:HOH558 2.6 47.2 1.0
C D:SER118 3.3 47.8 1.0
HA2 D:GLY124 3.4 47.7 1.0
CB D:SER118 3.5 43.0 1.0
C D:VAL123 3.6 38.7 1.0
HA D:SER118 3.6 58.5 1.0
CA D:SER118 3.7 50.1 1.0
HB3 D:SER118 3.7 49.9 1.0
HB D:VAL123 4.1 44.9 1.0
CA D:GLY124 4.2 40.1 1.0
OP2 F:DC21 4.2 37.3 1.0
HB2 D:SER118 4.3 49.9 1.0
HA D:ARG119 4.3 55.6 1.0
HG12 D:VAL123 4.4 49.3 1.0
N D:GLY124 4.4 35.2 1.0
N D:ARG119 4.5 40.3 1.0
CA D:VAL123 4.6 33.0 1.0
H D:VAL123 4.6 43.0 1.0
OP1 F:DC21 4.7 38.8 1.0
O D:HOH559 4.7 48.7 1.0
CB D:VAL123 4.7 37.7 1.0
O D:LEU120 4.8 38.1 1.0
CA D:ARG119 4.9 47.5 1.0
C D:GLY124 4.9 38.2 1.0
HG23 D:VAL128 4.9 53.0 1.0
HG21 D:VAL128 4.9 53.0 1.0
HA3 D:GLY124 4.9 47.7 1.0
N D:VAL123 5.0 36.1 1.0
P F:DC21 5.0 39.8 1.0

Calcium binding site 4 out of 4 in 8dwe

Go back to Calcium Binding Sites List in 8dwe
Calcium binding site 4 out of 4 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca404

b:92.1
occ:1.00
 O D:THR259 2.7 62.3 1.0
HB2 D:ASP257 2.8 74.7 1.0
OG1 D:THR259 2.9 69.4 1.0
OD2 D:ASP257 3.1 82.5 1.0
HG1 D:THR259 3.3 79.2 1.0
HB3 D:ASP257 3.4 74.7 1.0
CB D:ASP257 3.4 67.5 1.0
CG D:ASP257 3.6 82.8 1.0
C D:THR259 3.7 61.9 1.0
H D:THR259 3.8 75.0 1.0
CB D:THR259 4.1 63.2 1.0
O D:HOH552 4.1 56.5 1.0
CA D:THR259 4.3 65.7 1.0
HA3 D:GLY260 4.3 66.0 1.0
N D:THR259 4.4 64.9 1.0
HG23 D:THR259 4.6 76.2 1.0
HB D:THR259 4.8 72.7 1.0
CA D:ASP257 4.8 61.4 1.0
N D:GLY260 4.8 60.4 1.0
OD1 D:ASP257 4.8 89.8 1.0
H D:ASP257 5.0 69.1 1.0
CG2 D:THR259 5.0 66.6 1.0

Reference:

L.P.Russelburg, M.Demir, K.Cedeno, S.S.David, M.P.Horvath. Structural Basis For Base Engagement and Stereochemistry Revealed By Alteration of Catalytic Residue GLU43 in Dna Repair Glycosylase Muty To Be Published.
Page generated: Thu Dec 28 01:38:04 2023

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