Atomistry » Iron » PDB 6txa-6uoj » 6u7t
Atomistry »
  Iron »
    PDB 6txa-6uoj »
      6u7t »

Iron in PDB 6u7t: Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)

Enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)

All present enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G):
3.2.2.31;

Protein crystallography data

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 6u7t was solved by V.L.O'shea Murray, S.Cao, 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) 41.33 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.800, 86.490, 140.580, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 27

Other elements in 6u7t:

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

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 D(8-Oxo-G) (pdb code 6u7t). 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 D(8-Oxo-G), PDB code: 6u7t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 1 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


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 D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:45.4
occ:1.00
FE1 A:SF4401 0.0 45.4 1.0
S3 A:SF4401 2.2 50.6 1.0
S2 A:SF4401 2.3 37.2 1.0
S4 A:SF4401 2.3 43.7 1.0
SG A:CYS208 2.3 55.5 1.0
FE2 A:SF4401 2.7 46.0 1.0
FE4 A:SF4401 2.7 49.8 1.0
FE3 A:SF4401 2.7 37.2 0.7
HB2 A:CYS208 2.8 52.4 1.0
CB A:CYS208 3.0 43.7 1.0
HB3 A:CYS208 3.1 52.4 1.0
HA A:CYS205 3.5 52.5 1.0
HB2 A:CYS198 3.8 41.1 1.0
S1 A:SF4401 3.8 49.8 1.0
HG23 A:VAL210 3.9 65.0 1.0
HA A:GLN211 4.0 68.0 1.0
HB2 A:CYS214 4.2 65.8 1.0
HG22 A:VAL210 4.2 65.0 1.0
HG12 A:VAL197 4.2 53.4 1.0
HG11 A:VAL197 4.3 53.4 1.0
HB3 A:CYS205 4.3 60.3 1.0
CA A:CYS205 4.4 43.8 1.0
CA A:CYS208 4.5 50.7 1.0
CG2 A:VAL210 4.5 54.1 1.0
HD11 A:LEU193 4.5 49.7 1.0
CB A:CYS198 4.6 34.2 1.0
H A:VAL210 4.6 67.3 1.0
HB3 A:CYS214 4.6 65.8 1.0
HB3 A:GLN211 4.6 70.0 1.0
SG A:CYS198 4.6 43.6 1.0
HA A:CYS208 4.7 60.8 1.0
CB A:CYS205 4.7 50.2 1.0
CA A:GLN211 4.7 56.7 1.0
CB A:CYS214 4.7 54.9 1.0
HA A:CYS198 4.7 44.0 1.0
O A:VAL210 4.8 59.3 1.0
CG1 A:VAL197 4.8 44.5 1.0
N A:GLN211 4.8 55.0 1.0
C A:VAL210 4.8 54.1 1.0
O A:CYS205 4.8 39.5 1.0
SG A:CYS205 4.9 40.5 1.0
HD2 A:PRO209 4.9 54.1 1.0
SG A:CYS214 4.9 53.6 1.0
HD21 A:LEU193 5.0 50.2 1.0

Iron binding site 2 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 2 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


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 D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:46.0
occ:1.00
FE2 A:SF4401 0.0 46.0 1.0
S3 A:SF4401 2.2 50.6 1.0
S4 A:SF4401 2.3 43.7 1.0
SG A:CYS205 2.3 40.5 1.0
S1 A:SF4401 2.3 49.8 1.0
HB3 A:CYS205 2.5 60.3 1.0
HA A:CYS205 2.7 52.5 1.0
FE1 A:SF4401 2.7 45.4 1.0
CB A:CYS205 2.7 50.2 1.0
FE4 A:SF4401 2.8 49.8 1.0
FE3 A:SF4401 2.8 37.2 0.7
CA A:CYS205 3.2 43.8 1.0
HB2 A:CYS205 3.7 60.3 1.0
HB2 A:PHE217 3.7 65.1 1.0
HB2 A:PRO203 3.8 42.4 1.0
S2 A:SF4401 3.9 37.2 1.0
N A:CYS205 4.0 45.6 1.0
HB2 A:CYS208 4.0 52.4 1.0
HB3 A:CYS208 4.2 52.4 1.0
H A:CYS205 4.2 54.7 1.0
HG2 A:PRO203 4.2 44.2 1.0
SG A:CYS214 4.2 53.6 1.0
C A:CYS205 4.4 45.1 1.0
CB A:CYS208 4.4 43.7 1.0
HB1 A:ALA222 4.4 54.9 1.0
HB2 A:ALA222 4.5 54.9 1.0
HB3 A:CYS214 4.5 65.8 1.0
HA A:GLN211 4.6 68.0 1.0
O A:CYS205 4.6 39.5 1.0
CB A:PRO203 4.6 35.3 1.0
CB A:PHE217 4.7 54.2 1.0
HB2 A:CYS214 4.7 65.8 1.0
SG A:CYS208 4.7 55.5 1.0
CG A:PRO203 4.7 36.8 1.0
HG3 A:PRO203 4.8 44.2 1.0
CB A:CYS214 4.8 54.9 1.0
C A:SER204 4.8 46.6 1.0
HD1 A:PHE217 4.9 74.5 1.0
CB A:ALA222 4.9 45.8 1.0
HD3 A:ARG153 4.9 43.9 1.0
HA A:CYS198 4.9 44.0 1.0
SG A:CYS198 5.0 43.6 1.0

Iron binding site 3 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 3 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


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 D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:37.2
occ:0.69
FE3 A:SF4401 0.0 37.2 0.7
S2 A:SF4401 2.2 37.2 1.0
S1 A:SF4401 2.3 49.8 1.0
SG A:CYS198 2.3 43.6 1.0
S4 A:SF4401 2.3 43.7 1.0
FE4 A:SF4401 2.6 49.8 1.0
FE1 A:SF4401 2.7 45.4 1.0
FE2 A:SF4401 2.8 46.0 1.0
HB2 A:CYS198 2.9 41.1 1.0
HD3 A:ARG153 3.1 43.9 1.0
CB A:CYS198 3.1 34.2 1.0
HA A:CYS198 3.4 44.0 1.0
HH11 A:ARG153 3.6 46.8 1.0
HB2 A:PRO203 3.8 42.4 1.0
CA A:CYS198 3.8 36.7 1.0
S3 A:SF4401 3.8 50.6 1.0
HB3 A:CYS198 4.0 41.1 1.0
CD A:ARG153 4.0 36.6 1.0
HB3 A:ARG153 4.0 49.8 1.0
HD2 A:ARG153 4.1 43.9 1.0
HB2 A:ARG153 4.2 49.8 1.0
NH1 A:ARG153 4.3 39.0 1.0
HB3 A:PRO203 4.4 42.4 1.0
CB A:ARG153 4.5 41.5 1.0
CB A:PRO203 4.5 35.3 1.0
HG3 A:PRO203 4.5 44.2 1.0
SG A:CYS205 4.6 40.5 1.0
SG A:CYS214 4.7 53.6 1.0
HA A:VAL150 4.7 44.5 1.0
HH12 A:ARG153 4.7 46.8 1.0
CG A:ARG153 4.7 38.7 1.0
HB1 A:ALA222 4.7 54.9 1.0
HA A:CYS205 4.8 52.5 1.0
C A:CYS198 4.8 33.6 1.0
N A:CYS198 4.8 34.5 1.0
HB2 A:CYS208 4.9 52.4 1.0
SG A:CYS208 4.9 55.5 1.0
HG2 A:PRO203 4.9 44.2 1.0
CG A:PRO203 4.9 36.8 1.0
NE A:ARG153 4.9 39.2 1.0
HG2 A:ARG153 4.9 46.5 1.0
HB2 A:CYS214 4.9 65.8 1.0
HG13 A:VAL150 5.0 48.9 1.0
HG12 A:VAL197 5.0 53.4 1.0

Iron binding site 4 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 4 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)


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 D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:49.8
occ:1.00
FE4 A:SF4401 0.0 49.8 1.0
S1 A:SF4401 2.2 49.8 1.0
S2 A:SF4401 2.3 37.2 1.0
S3 A:SF4401 2.3 50.6 1.0
SG A:CYS214 2.3 53.6 1.0
HB2 A:CYS214 2.4 65.8 1.0
FE3 A:SF4401 2.6 37.2 0.7
FE1 A:SF4401 2.7 45.4 1.0
CB A:CYS214 2.7 54.9 1.0
FE2 A:SF4401 2.8 46.0 1.0
HB3 A:CYS214 3.0 65.8 1.0
HD23 A:LEU154 3.5 54.0 1.0
HB3 A:ARG153 3.6 49.8 1.0
S4 A:SF4401 3.9 43.7 1.0
HB2 A:PHE217 4.0 65.1 1.0
CA A:CYS214 4.2 57.9 1.0
HA A:CYS214 4.3 69.5 1.0
HA A:GLN211 4.3 68.0 1.0
CD2 A:LEU154 4.3 45.0 1.0
HD3 A:ARG153 4.4 43.9 1.0
H A:PHE217 4.4 58.5 1.0
CB A:ARG153 4.4 41.5 1.0
HD21 A:LEU154 4.4 54.0 1.0
HB2 A:ARG153 4.4 49.8 1.0
HG A:LEU154 4.5 56.1 1.0
HA A:LEU154 4.6 55.3 1.0
HB3 A:ALA216 4.6 55.3 1.0
HG23 A:VAL210 4.7 65.0 1.0
SG A:CYS198 4.7 43.6 1.0
HB3 A:CYS205 4.7 60.3 1.0
SG A:CYS208 4.8 55.5 1.0
SG A:CYS205 4.9 40.5 1.0
CB A:PHE217 4.9 54.2 1.0
O A:VAL210 5.0 59.3 1.0
H A:CYS214 5.0 67.5 1.0
HB3 A:PHE217 5.0 65.1 1.0

Reference:

R.D.Woods, V.L.O'shea, A.Chu, S.Cao, J.L.Richards, M.P.Horvath, S.S.David. Structure and Stereochemistry of the Base Excision Repair Glycosylase Muty Reveal A Mechanism Similar to Retaining Glycosidases. Nucleic Acids Res. V. 44 801 2016.
ISSN: ESSN 1362-4962
PubMed: 26673696
DOI: 10.1093/NAR/GKV1469
Page generated: Sun Dec 13 17:15:09 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy