Atomistry » Calcium » PDB 8db7-8dzt » 8dwf
Atomistry »
  Calcium »
    PDB 8db7-8dzt »
      8dwf »

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

Go back to Calcium Binding Sites List in 8dwf
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

Go back to Calcium Binding Sites List in 8dwf
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: Fri Jul 19 08:03:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy