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Calcium in PDB 9bs2: Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution

Enzymatic activity of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution

All present enzymatic activity of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution:
3.2.2.31;

Protein crystallography data

The structure of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution, PDB code: 9bs2 was solved by C.H.Trasvina-Arenas, N.Tamayo, W.J.Lin, M.Demir, A.J.Fisher, 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) 43.00 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.5, 86, 140.64, 90, 90, 90
R / Rfree (%) 20.6 / 23

Other elements in 9bs2:

The structure of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution (pdb code 9bs2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution, PDB code: 9bs2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 9bs2

Go back to Calcium Binding Sites List in 9bs2
Calcium binding site 1 out of 3 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution


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 R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:26.0
occ:1.00
 O C:HOH108 2.3 29.4 1.0
OD1 A:ASN146 2.3 21.2 1.0
O A:HOH576 2.3 23.4 1.0
O C:HOH111 2.4 28.8 1.0
O A:HOH590 2.4 30.2 1.0
O C:HOH110 2.4 19.9 1.0
O A:GLY194 2.8 25.5 1.0
HA A:ALA195 3.2 26.1 1.0
H5'' C:DA17 3.4 32.2 1.0
CG A:ASN146 3.4 19.9 1.0
HD3 A:PRO200 3.4 37.5 1.0
C A:GLY194 3.6 21.0 1.0
HA A:ASN146 3.6 22.7 1.0
OP1 C:DA17 3.9 34.0 1.0
HD21 A:ASN146 4.0 25.4 1.0
HA A:THR199 4.0 37.0 1.0
CA A:ALA195 4.0 21.7 1.0
N A:ALA195 4.1 23.1 1.0
ND2 A:ASN146 4.1 21.2 1.0
C5' C:DA17 4.3 26.9 1.0
HA3 A:GLY194 4.3 32.8 1.0
CD A:PRO200 4.4 31.3 1.0
CB A:ASN146 4.4 20.9 1.0
CA A:ASN146 4.4 18.9 1.0
OP2 C:3DR18 4.4 25.1 1.0
CA A:GLY194 4.5 27.3 1.0
HG3 A:PRO200 4.5 38.0 1.0
OE1 A:GLN149 4.5 33.3 1.0
O5' C:DA17 4.6 40.0 1.0
O A:HOH665 4.6 40.0 1.0
HB3 A:ASN146 4.6 25.0 1.0
HG22 A:THR199 4.6 36.5 1.0
H3' C:DA17 4.7 31.7 1.0
O A:CYS198 4.7 30.7 1.0
HD2 A:PRO200 4.7 37.5 1.0
HA2 A:GLY194 4.7 32.8 1.0
H5' C:DA17 4.8 32.2 1.0
H A:ALA195 4.8 27.7 1.0
C A:ALA195 4.8 21.9 1.0
O A:ALA195 4.9 24.6 1.0
CG A:PRO200 4.9 31.7 1.0
N A:ASN146 4.9 20.5 1.0
HD22 A:ASN146 4.9 25.4 1.0
O A:HOH633 4.9 22.3 1.0
HG2 A:PRO200 5.0 38.0 1.0
P C:DA17 5.0 40.3 1.0
HB2 A:ALA195 5.0 24.7 1.0
O A:HOH597 5.0 30.8 1.0

Calcium binding site 2 out of 3 in 9bs2

Go back to Calcium Binding Sites List in 9bs2
Calcium binding site 2 out of 3 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution


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 R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:29.4
occ:1.00
 O C:HOH106 2.2 41.7 1.0
O A:HOH575 2.2 36.7 1.0
O A:HOH638 2.3 32.6 1.0
O A:VAL123 2.3 26.8 1.0
O A:SER118 2.4 31.7 1.0
OG A:SER118 2.5 36.7 1.0
O A:HOH578 2.5 25.6 1.0
HA2 A:GLY124 3.3 24.8 1.0
C A:SER118 3.3 39.2 1.0
HA A:SER118 3.4 34.9 1.0
C A:VAL123 3.5 35.1 1.0
CB A:SER118 3.6 41.5 1.0
CA A:SER118 3.7 29.1 1.0
HB3 A:SER118 4.0 49.8 1.0
HB A:VAL123 4.1 35.1 1.0
CA A:GLY124 4.1 20.7 1.0
OP2 C:DC21 4.2 28.0 1.0
N A:GLY124 4.3 23.3 1.0
HB2 A:SER118 4.3 49.8 1.0
HG12 A:VAL123 4.4 35.7 1.0
N A:ARG119 4.5 30.3 1.0
O A:HOH640 4.6 41.1 1.0
O A:LEU120 4.6 29.7 1.0
H A:VAL123 4.6 29.7 1.0
CA A:VAL123 4.6 23.5 1.0
HA A:ARG119 4.6 51.0 1.0
O C:HOH136 4.6 39.0 1.0
CB A:VAL123 4.7 29.3 1.0
HA3 A:GLY124 4.8 24.8 1.0
HG23 A:VAL128 4.8 41.7 1.0
C A:GLY124 4.8 26.9 1.0
OP1 C:DC21 4.8 29.1 1.0
N A:VAL123 4.9 24.8 1.0
HD3 A:PRO125 4.9 32.5 1.0
P C:DC21 5.0 25.4 1.0
CA A:ARG119 5.0 42.5 1.0

Calcium binding site 3 out of 3 in 9bs2

Go back to Calcium Binding Sites List in 9bs2
Calcium binding site 3 out of 3 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution


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 R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:59.1
occ:0.50
 OG1 A:THR259 2.1 61.6 1.0
OD1 A:ASP257 2.3 61.5 1.0
O A:HOH659 2.5 51.1 1.0
CG A:ASP257 2.9 61.1 1.0
O A:THR259 3.0 63.1 1.0
OD2 A:ASP257 3.0 69.6 1.0
CB A:THR259 3.5 62.4 1.0
HG23 A:THR259 3.9 68.5 1.0
C A:THR259 3.9 52.2 1.0
H A:THR259 4.1 60.1 1.0
HB A:THR259 4.1 74.8 1.0
CG2 A:THR259 4.2 57.1 1.0
CB A:ASP257 4.2 54.0 1.0
CA A:THR259 4.2 61.7 1.0
HB2 A:ASP257 4.2 64.7 1.0
HG21 A:THR259 4.3 68.5 1.0
O A:HOH535 4.5 37.2 1.0
N A:THR259 4.6 50.1 1.0
O A:HOH562 4.7 41.0 1.0
HB3 A:ASP257 4.7 64.7 1.0
HA3 A:GLY260 4.8 48.4 1.0

Reference:

C.H.Trasvina-Arenas, U.C.Dissanayake, N.Tamayo, S.M.Hashemian, W.J.Lin, M.Demir, N.Hoyos-Gonzalez, A.J.Fisher, G.A.Cisneros, M.P.Horvath, S.S.David. Structural and Functional Profiling of Mutyh Cancer-Associated Variants Reveal An Allosteric Role For Its [4FE-4S] Cluster Cofactor To Be Published.
Page generated: Wed Nov 13 07:23:37 2024

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