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Calcium in PDB 8dwf: Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine

Enzymatic activity of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine

All present enzymatic activity of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine:
3.2.2.31;

Protein crystallography data

The structure of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine, PDB code: 8dwf 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) 73.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.08, 137.9, 74.52, 90, 101.44, 90
R / Rfree (%) 20.7 / 25.3

Other elements in 8dwf:

The structure of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine (pdb code 8dwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine, PDB code: 8dwf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8dwf

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Calcium binding site 1 out of 4 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:52.6
occ:1.00
 O A:SER118 2.2 46.8 1.0
O A:VAL123 2.4 46.8 1.0
O C:HOH105 2.5 47.0 1.0
OG A:SER118 2.6 46.6 1.0
HA2 A:GLY124 3.1 42.3 1.0
C A:SER118 3.2 48.7 1.0
HA A:SER118 3.4 62.3 1.0
CB A:SER118 3.6 46.1 1.0
C A:VAL123 3.6 45.7 1.0
CA A:SER118 3.6 50.9 1.0
HB3 A:SER118 3.8 56.7 1.0
CA A:GLY124 3.9 35.5 1.0
OP2 C:DC21 4.1 41.9 1.0
N A:GLY124 4.2 38.9 1.0
HG12 A:VAL123 4.2 52.6 1.0
HA A:ARG119 4.4 58.8 1.0
HB A:VAL123 4.4 50.3 1.0
HB2 A:SER118 4.4 56.7 1.0
N A:ARG119 4.4 46.2 1.0
HA3 A:GLY124 4.6 42.3 1.0
OP1 C:DC21 4.7 52.7 1.0
C A:GLY124 4.7 36.9 1.0
O A:LEU120 4.8 37.9 1.0
CA A:VAL123 4.8 45.8 1.0
HD3 A:PRO125 4.8 48.6 1.0
CA A:ARG119 4.9 47.9 1.0
HG21 A:VAL128 4.9 62.2 1.0
CB A:VAL123 4.9 45.3 1.0
H A:VAL123 4.9 52.0 1.0
P C:DC21 5.0 45.4 1.0

Calcium binding site 2 out of 4 in 8dwf

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Calcium binding site 2 out of 4 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:84.9
occ:1.00
 OD2 A:ASP257 2.5 66.9 1.0
HG1 A:THR259 2.6 90.2 1.0
O A:HOH525 2.6 52.5 1.0
O A:THR259 2.6 67.7 1.0
HB2 A:ASP257 2.7 81.1 1.0
HB3 A:ASP257 3.0 81.1 1.0
CB A:ASP257 3.1 61.3 1.0
CG A:ASP257 3.2 76.1 1.0
OG1 A:THR259 3.3 69.6 1.0
C A:THR259 3.8 54.8 1.0
H A:THR259 4.0 80.4 1.0
O A:HOH503 4.1 54.0 1.0
HA3 A:GLY260 4.2 74.5 1.0
OD1 A:ASP257 4.4 88.1 1.0
CB A:THR259 4.4 67.1 1.0
CA A:THR259 4.6 60.8 1.0
CA A:ASP257 4.6 55.9 1.0
N A:THR259 4.6 61.2 1.0
HB A:THR259 4.7 87.6 1.0
N A:GLY260 4.9 51.0 1.0
H A:ASP257 4.9 80.8 1.0
CA A:GLY260 4.9 60.1 1.0

Calcium binding site 3 out of 4 in 8dwf

Go back to Calcium Binding Sites List in 8dwf
Calcium binding site 3 out of 4 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:54.6
occ:1.00
 O D:VAL123 2.2 55.5 1.0
O D:SER118 2.3 52.4 1.0
O F:HOH102 2.5 47.6 1.0
O D:HOH512 2.7 41.1 1.0
OG D:SER118 2.8 43.5 1.0
HA2 D:GLY124 3.2 40.5 1.0
HG D:SER118 3.2 50.9 1.0
O F:HOH110 3.2 51.2 1.0
C D:SER118 3.3 54.0 1.0
C D:VAL123 3.4 48.8 1.0
HA D:SER118 3.6 66.8 1.0
CB D:SER118 3.7 55.8 1.0
OP2 F:DC21 3.8 52.2 1.0
CA D:SER118 3.8 57.3 1.0
HB3 D:SER118 3.9 65.3 1.0
OP1 F:DC21 4.0 51.2 1.0
CA D:GLY124 4.0 31.8 1.0
N D:GLY124 4.1 40.6 1.0
HB D:VAL123 4.2 60.4 1.0
HA D:ARG119 4.3 55.2 1.0
H D:VAL123 4.4 51.2 1.0
HG12 D:VAL123 4.4 54.7 1.0
CA D:VAL123 4.5 50.5 1.0
P F:DC21 4.5 49.3 1.0
N D:ARG119 4.5 40.4 1.0
HB2 D:SER118 4.5 65.3 1.0
HA3 D:GLY124 4.6 40.5 1.0
N D:VAL123 4.7 46.0 1.0
CB D:VAL123 4.7 53.7 1.0
O D:LEU120 4.7 32.9 1.0
C D:GLY124 4.8 39.0 1.0
CA D:ARG119 4.9 42.9 1.0
H D:GLY124 4.9 51.0 1.0
HD3 D:PRO125 5.0 42.3 1.0

Calcium binding site 4 out of 4 in 8dwf

Go back to Calcium Binding Sites List in 8dwf
Calcium binding site 4 out of 4 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:66.1
occ:0.50
 HB2 D:ASP257 2.0 91.7 1.0
OD2 D:ASP257 2.5 65.8 1.0
CB D:ASP257 2.6 74.5 1.0
O D:THR259 2.6 70.0 1.0
HG1 D:THR259 2.6 113.0 1.0
HB3 D:ASP257 2.6 91.7 1.0
CG D:ASP257 2.7 84.9 1.0
OG1 D:THR259 3.3 84.3 1.0
H D:THR259 3.6 96.8 1.0
C D:THR259 3.7 67.6 1.0
OD1 D:ASP257 3.7 93.3 1.0
O D:HOH515 4.0 53.7 1.0
CA D:ASP257 4.0 67.3 1.0
H D:ASP257 4.2 86.1 1.0
N D:THR259 4.3 70.1 1.0
CA D:THR259 4.3 70.5 1.0
CB D:THR259 4.3 75.8 1.0
HA3 D:GLY260 4.4 79.6 1.0
HA D:ASP257 4.6 83.3 1.0
HB D:THR259 4.6 103.4 1.0
N D:ASP257 4.6 69.5 1.0
C D:ASP257 4.6 66.9 1.0
N D:GLY260 4.8 68.6 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 01:38:14 2023

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