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Iron in PDB 4yph: Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced

Protein crystallography data

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced, PDB code: 4yph was solved by L.Wang, S.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.37 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.636, 83.757, 142.735, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 25.9

Other elements in 4yph:

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced (pdb code 4yph). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced, PDB code: 4yph:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4yph

Go back to Iron Binding Sites List in 4yph
Iron binding site 1 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:44.0
occ:1.00
FE1 A:SF4401 0.0 44.0 1.0
S4 A:SF4401 2.2 40.6 1.0
S3 A:SF4401 2.2 43.1 1.0
S2 A:SF4401 2.2 47.5 1.0
SG A:CYS205 2.5 50.1 1.0
FE3 A:SF4401 2.9 43.1 1.0
FE2 A:SF4401 2.9 48.3 1.0
FE4 A:SF4401 2.9 48.3 1.0
CB A:CYS205 3.2 46.8 1.0
CA A:CYS205 3.4 46.9 1.0
S1 A:SF4401 3.8 40.8 1.0
N A:CYS205 4.0 45.0 1.0
CB A:PRO203 4.2 40.0 1.0
CB A:ALA222 4.5 46.2 1.0
CG A:PRO203 4.5 40.9 1.0
CB A:CYS208 4.6 39.5 1.0
CB A:PHE217 4.7 47.4 1.0
C A:CYS205 4.7 50.8 1.0
CD1 A:PHE217 4.8 46.9 1.0
C A:SER204 4.9 45.4 1.0
SG A:CYS214 4.9 53.8 1.0
O A:CYS205 5.0 53.3 1.0
SG A:CYS198 5.0 36.7 1.0

Iron binding site 2 out of 4 in 4yph

Go back to Iron Binding Sites List in 4yph
Iron binding site 2 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:48.3
occ:1.00
FE2 A:SF4401 0.0 48.3 1.0
S3 A:SF4401 2.1 43.1 1.0
S1 A:SF4401 2.2 40.8 1.0
S4 A:SF4401 2.2 40.6 1.0
SG A:CYS198 2.4 36.7 1.0
FE3 A:SF4401 2.9 43.1 1.0
FE4 A:SF4401 2.9 48.3 1.0
FE1 A:SF4401 2.9 44.0 1.0
CB A:CYS198 3.1 32.9 1.0
S2 A:SF4401 3.8 47.5 1.0
CA A:CYS198 3.8 31.4 1.0
CD A:ARG153 4.1 42.9 1.0
CB A:ARG153 4.3 46.3 1.0
NH1 A:ARG153 4.4 33.5 1.0
CB A:PRO203 4.6 40.0 1.0
CG A:ARG153 4.7 46.3 1.0
N A:CYS198 4.8 39.0 1.0
C A:CYS198 4.9 34.4 1.0
SG A:CYS208 5.0 51.3 1.0

Iron binding site 3 out of 4 in 4yph

Go back to Iron Binding Sites List in 4yph
Iron binding site 3 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:43.1
occ:1.00
FE3 A:SF4401 0.0 43.1 1.0
S2 A:SF4401 2.2 47.5 1.0
S4 A:SF4401 2.2 40.6 1.0
S1 A:SF4401 2.2 40.8 1.0
SG A:CYS208 2.4 51.3 1.0
CB A:CYS208 2.8 39.5 1.0
FE1 A:SF4401 2.9 44.0 1.0
FE2 A:SF4401 2.9 48.3 1.0
FE4 A:SF4401 2.9 48.3 1.0
S3 A:SF4401 3.7 43.1 1.0
CA A:CYS208 4.3 48.0 1.0
CG2 A:VAL210 4.5 42.2 1.0
CA A:CYS205 4.6 46.9 1.0
N A:GLN211 4.6 46.5 1.0
CA A:GLN211 4.6 49.2 1.0
CB A:CYS198 4.8 32.9 1.0
CG1 A:VAL197 4.8 34.1 1.0
SG A:CYS198 4.9 36.7 1.0
C A:VAL210 4.9 49.6 1.0
C A:CYS208 5.0 42.2 1.0
CB A:CYS214 5.0 46.8 1.0

Iron binding site 4 out of 4 in 4yph

Go back to Iron Binding Sites List in 4yph
Iron binding site 4 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:48.3
occ:1.00
FE4 A:SF4401 0.0 48.3 1.0
S3 A:SF4401 2.2 43.1 1.0
S1 A:SF4401 2.2 40.8 1.0
S2 A:SF4401 2.2 47.5 1.0
SG A:CYS214 2.4 53.8 1.0
FE3 A:SF4401 2.9 43.1 1.0
FE2 A:SF4401 2.9 48.3 1.0
FE1 A:SF4401 2.9 44.0 1.0
CB A:CYS214 2.9 46.8 1.0
S4 A:SF4401 3.8 40.6 1.0
CB A:PHE217 4.3 47.4 1.0
CB A:ARG153 4.4 46.3 1.0
CA A:CYS214 4.4 56.4 1.0
CD2 A:LEU154 4.4 44.7 1.0
N A:PHE217 4.8 53.9 1.0
C A:ARG153 4.9 44.1 1.0
CG A:LEU154 5.0 43.2 1.0

Reference:

L.Wang, S.-J.Lee, G.Verdine. Structural Basis For Avoidance of Promutagenic Dna Repair By Muty Adenine Dna Glycosylase. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.657866
Page generated: Mon Aug 5 16:40:01 2024

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