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Iron in PDB 6q0c: Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg

Enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg

All present enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg:
3.2.2.31;

Protein crystallography data

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg, PDB code: 6q0c was solved by V.L.O'shea Murray, 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) 41.30 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.860, 86.140, 141.170, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.1

Other elements in 6q0c:

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg (pdb code 6q0c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg, PDB code: 6q0c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6q0c

Go back to Iron Binding Sites List in 6q0c
Iron binding site 1 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:49.1
occ:1.00
 FE1 A:SF4401 0.0 49.1 1.0
S3 A:SF4401 2.3 50.8 1.0
S2 A:SF4401 2.3 40.5 1.0
S4 A:SF4401 2.3 42.3 1.0
SG A:CYS208 2.4 51.5 1.0
HB2 A:CYS208 2.6 45.2 1.0
FE2 A:SF4401 2.7 47.5 1.0
FE3 A:SF4401 2.7 45.5 1.0
FE4 A:SF4401 2.7 47.0 1.0
CB A:CYS208 2.8 37.6 1.0
HB3 A:CYS208 2.8 45.2 1.0
HA A:CYS205 3.3 60.1 1.0
HB2 A:CYS198 3.8 48.1 1.0
S1 A:SF4401 3.9 42.2 1.0
HA A:GLN211 3.9 79.1 1.0
HG23 A:VAL210 4.0 67.6 1.0
HG12 A:VAL197 4.0 54.9 1.0
CA A:CYS205 4.2 50.1 1.0
HB3 A:CYS205 4.2 58.6 1.0
CA A:CYS208 4.3 50.8 1.0
HB2 A:CYS214 4.4 74.4 1.0
HB2 A:GLN211 4.5 74.2 1.0
HA A:CYS208 4.6 60.9 1.0
CB A:CYS205 4.6 48.8 1.0
HG22 A:VAL210 4.6 67.6 1.0
CB A:CYS198 4.6 40.1 1.0
HD21 A:LEU193 4.7 55.9 1.0
HD11 A:LEU193 4.7 50.6 1.0
CA A:GLN211 4.7 66.0 1.0
N A:GLN211 4.7 61.2 1.0
H A:VAL210 4.7 72.3 1.0
HG11 A:VAL197 4.7 54.9 1.0
HD23 A:LEU154 4.8 64.8 1.0
CG2 A:VAL210 4.8 56.4 1.0
O A:CYS205 4.8 50.9 1.0
SG A:CYS205 4.8 42.9 1.0
H A:CYS208 4.8 59.6 1.0
CG1 A:VAL197 4.8 45.7 1.0
H A:GLN211 4.9 73.4 1.0
HA A:CYS198 4.9 47.1 1.0
C A:VAL210 4.9 64.0 1.0
HD21 A:LEU154 4.9 64.8 1.0
SG A:CYS198 5.0 40.2 1.0
HB3 A:CYS214 5.0 74.4 1.0

Iron binding site 2 out of 4 in 6q0c

Go back to Iron Binding Sites List in 6q0c
Iron binding site 2 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:47.5
occ:1.00
 FE2 A:SF4401 0.0 47.5 1.0
SG A:CYS205 2.2 42.9 1.0
S3 A:SF4401 2.3 50.8 1.0
S4 A:SF4401 2.3 42.3 1.0
S1 A:SF4401 2.3 42.2 1.0
HB3 A:CYS205 2.6 58.6 1.0
HA A:CYS205 2.7 60.1 1.0
FE1 A:SF4401 2.7 49.1 1.0
CB A:CYS205 2.7 48.8 1.0
FE4 A:SF4401 2.7 47.0 1.0
FE3 A:SF4401 2.7 45.5 1.0
CA A:CYS205 3.2 50.1 1.0
HB2 A:PRO203 3.5 53.1 1.0
HB2 A:CYS205 3.7 58.6 1.0
N A:CYS205 3.8 43.5 1.0
H A:CYS205 3.8 52.3 1.0
S2 A:SF4401 3.9 40.5 1.0
HB2 A:PHE217 3.9 77.8 1.0
HB2 A:CYS208 4.2 45.2 1.0
HB3 A:CYS208 4.3 45.2 1.0
HG2 A:PRO203 4.3 50.0 1.0
HB1 A:ALA222 4.4 66.7 1.0
HB2 A:ALA222 4.4 66.7 1.0
CB A:PRO203 4.4 44.2 1.0
C A:CYS205 4.5 45.7 1.0
HD1 A:PHE217 4.5 69.7 1.0
CB A:CYS208 4.6 37.6 1.0
CG A:PRO203 4.7 41.6 1.0
SG A:CYS214 4.7 60.8 1.0
HG3 A:PRO203 4.7 50.0 1.0
HD3 A:ARG153 4.8 49.5 1.0
HB3 A:PRO203 4.8 53.1 1.0
O A:CYS205 4.8 50.9 1.0
CB A:ALA222 4.8 55.6 1.0
C A:SER204 4.8 46.3 1.0
HB2 A:CYS198 4.8 48.1 1.0
HA A:CYS198 4.8 47.1 1.0
CB A:PHE217 4.9 64.8 1.0
HG3 A:GLN211 5.0 78.2 1.0
SG A:CYS208 5.0 51.5 1.0

Iron binding site 3 out of 4 in 6q0c

Go back to Iron Binding Sites List in 6q0c
Iron binding site 3 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:45.5
occ:1.00
 FE3 A:SF4401 0.0 45.5 1.0
S2 A:SF4401 2.3 40.5 1.0
S1 A:SF4401 2.3 42.2 1.0
S4 A:SF4401 2.3 42.3 1.0
SG A:CYS198 2.5 40.2 1.0
HB2 A:CYS198 2.6 48.1 1.0
FE4 A:SF4401 2.7 47.0 1.0
FE1 A:SF4401 2.7 49.1 1.0
FE2 A:SF4401 2.7 47.5 1.0
CB A:CYS198 3.0 40.1 1.0
HD3 A:ARG153 3.3 49.5 1.0
HA A:CYS198 3.5 47.1 1.0
HH11 A:ARG153 3.6 50.2 1.0
HB2 A:PRO203 3.8 53.1 1.0
CA A:CYS198 3.8 39.3 1.0
HB3 A:CYS198 3.9 48.1 1.0
S3 A:SF4401 3.9 50.8 1.0
HD2 A:ARG153 4.1 49.5 1.0
CD A:ARG153 4.1 41.2 1.0
HB2 A:ARG153 4.2 50.4 1.0
HB3 A:PRO203 4.3 53.1 1.0
HB3 A:ARG153 4.3 50.4 1.0
NH1 A:ARG153 4.4 41.8 1.0
CB A:PRO203 4.5 44.2 1.0
SG A:CYS205 4.6 42.9 1.0
HA A:VAL150 4.6 46.6 1.0
CB A:ARG153 4.6 42.0 1.0
HG22 A:VAL150 4.7 41.3 1.0
HA A:CYS205 4.7 60.1 1.0
HB2 A:CYS208 4.7 45.2 1.0
N A:CYS198 4.8 43.2 1.0
HG12 A:VAL197 4.8 54.9 1.0
HH12 A:ARG153 4.8 50.2 1.0
HG3 A:PRO203 4.8 50.0 1.0
HD23 A:LEU154 4.9 64.8 1.0
SG A:CYS214 4.9 60.8 1.0
SG A:CYS208 4.9 51.5 1.0
HB1 A:ALA222 4.9 66.7 1.0
H A:CYS198 4.9 51.8 1.0
C A:CYS198 5.0 36.1 1.0

Iron binding site 4 out of 4 in 6q0c

Go back to Iron Binding Sites List in 6q0c
Iron binding site 4 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:47.0
occ:1.00
 FE4 A:SF4401 0.0 47.0 1.0
S1 A:SF4401 2.3 42.2 1.0
S2 A:SF4401 2.3 40.5 1.0
S3 A:SF4401 2.3 50.8 1.0
SG A:CYS214 2.4 60.8 1.0
FE3 A:SF4401 2.7 45.5 1.0
FE2 A:SF4401 2.7 47.5 1.0
FE1 A:SF4401 2.7 49.1 1.0
HB2 A:CYS214 2.9 74.4 1.0
CB A:CYS214 3.1 62.0 1.0
HB3 A:CYS214 3.3 74.4 1.0
HD23 A:LEU154 3.3 64.8 1.0
HB2 A:PHE217 3.7 77.8 1.0
S4 A:SF4401 3.9 42.3 1.0
HB3 A:ARG153 3.9 50.4 1.0
HA A:GLN211 4.1 79.1 1.0
CD2 A:LEU154 4.2 54.0 1.0
H A:PHE217 4.3 67.8 1.0
HD21 A:LEU154 4.3 64.8 1.0
HB2 A:ARG153 4.4 50.4 1.0
HB3 A:ALA216 4.5 63.5 1.0
HB3 A:CYS205 4.5 58.6 1.0
HA A:LEU154 4.5 65.5 1.0
CA A:CYS214 4.5 65.0 1.0
HD3 A:ARG153 4.6 49.5 1.0
CB A:ARG153 4.6 42.0 1.0
CB A:PHE217 4.6 64.8 1.0
HD22 A:LEU154 4.6 64.8 1.0
HA A:CYS214 4.7 78.0 1.0
HB3 A:PHE217 4.8 77.8 1.0
SG A:CYS208 4.8 51.5 1.0
SG A:CYS205 4.8 42.9 1.0
HG23 A:VAL210 4.8 67.6 1.0
HA A:CYS205 4.8 60.1 1.0
N A:PHE217 4.9 56.5 1.0
HG A:LEU154 4.9 63.9 1.0
SG A:CYS198 5.0 40.2 1.0

Reference:

L.P.Russelburg, V.L.O'shea Murray, M.Demir, K.R.Knutsen, S.L.Sehgal, S.Cao, S.S.David, M.P.Horvath. Structural Basis For Finding Og Lesions and Avoiding Undamaged G By the Dna Glycosylase Muty To Be Published.
Page generated: Wed Aug 7 06:48:04 2024

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