Iron in PDB 5ean: Crystal Structure of DNA2 in Complex with A 5' Overhang Dna

Enzymatic activity of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna

All present enzymatic activity of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean was solved by C.Zhou, S.Pourmal, N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.36
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.153, 118.488, 149.260, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.6

Other elements in 5ean:

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna (pdb code 5ean). 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 DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ean

Go back to Iron Binding Sites List in 5ean
Iron binding site 1 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


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 DNA2 in Complex with A 5' Overhang Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:58.7
occ:1.00
FE1 A:SF41101 0.0 58.7 1.0
S2 A:SF41101 2.1 62.3 1.0
S3 A:SF41101 2.1 60.4 1.0
S4 A:SF41101 2.1 55.6 1.0
SG A:CYS137 2.3 57.9 1.0
FE3 A:SF41101 2.9 61.8 1.0
FE4 A:SF41101 2.9 67.2 1.0
FE2 A:SF41101 3.0 59.4 1.0
CB A:CYS137 3.4 58.5 1.0
S1 A:SF41101 3.7 61.9 1.0
N A:ARG140 3.9 53.6 1.0
CB A:ARG140 4.0 57.4 1.0
CG1 A:ILE388 4.1 69.7 1.0
CB A:ARG139 4.2 52.5 1.0
CD A:ARG139 4.4 53.9 1.0
CA A:ARG140 4.4 53.9 1.0
CG A:ARG139 4.6 52.0 1.0
CD1 A:ILE388 4.6 69.3 1.0
C A:ARG139 4.7 52.0 1.0
CA A:CYS137 4.8 58.6 1.0
CA A:ARG139 4.9 51.9 1.0
SG A:CYS394 5.0 74.9 1.0
SG A:CYS397 5.0 64.6 1.0

Iron binding site 2 out of 4 in 5ean

Go back to Iron Binding Sites List in 5ean
Iron binding site 2 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


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 DNA2 in Complex with A 5' Overhang Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:59.4
occ:1.00
FE2 A:SF41101 0.0 59.4 1.0
S1 A:SF41101 2.1 61.9 1.0
S4 A:SF41101 2.1 55.6 1.0
S3 A:SF41101 2.2 60.4 1.0
SG A:CYS403 2.3 55.1 1.0
FE3 A:SF41101 2.9 61.8 1.0
FE4 A:SF41101 2.9 67.2 1.0
FE1 A:SF41101 3.0 58.7 1.0
CB A:CYS403 3.1 52.2 1.0
S2 A:SF41101 3.7 62.3 1.0
CD A:ARG139 4.0 53.9 1.0
CE A:MET423 4.0 81.6 1.0
NE A:ARG139 4.1 53.9 1.0
CG1 A:ILE387 4.5 59.8 1.0
CA A:CYS403 4.5 50.1 1.0
CG A:ARG139 4.7 52.0 1.0
SG A:CYS394 5.0 74.9 1.0

Iron binding site 3 out of 4 in 5ean

Go back to Iron Binding Sites List in 5ean
Iron binding site 3 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


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 DNA2 in Complex with A 5' Overhang Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:61.8
occ:1.00
FE3 A:SF41101 0.0 61.8 1.0
S4 A:SF41101 2.1 55.6 1.0
S1 A:SF41101 2.1 61.9 1.0
S2 A:SF41101 2.1 62.3 1.0
SG A:CYS397 2.3 64.6 1.0
FE1 A:SF41101 2.9 58.7 1.0
FE2 A:SF41101 2.9 59.4 1.0
FE4 A:SF41101 3.0 67.2 1.0
CB A:CYS397 3.0 71.8 1.0
S3 A:SF41101 3.7 60.4 1.0
CB A:ARG140 4.2 57.4 1.0
CG A:ARG140 4.3 60.0 1.0
CA A:CYS397 4.5 74.6 1.0
CA A:ARG140 4.7 53.9 1.0
N A:ILE400 4.7 59.4 1.0
CA A:CYS394 4.7 76.9 1.0
CB A:GLN399 4.8 61.1 1.0
SG A:CYS137 4.8 57.9 1.0
C A:GLN399 4.8 59.4 1.0
CB A:CYS403 4.9 52.2 1.0
SG A:CYS403 5.0 55.1 1.0
CA A:ILE400 5.0 59.4 1.0

Iron binding site 4 out of 4 in 5ean

Go back to Iron Binding Sites List in 5ean
Iron binding site 4 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


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 DNA2 in Complex with A 5' Overhang Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:67.2
occ:1.00
FE4 A:SF41101 0.0 67.2 1.0
S3 A:SF41101 2.1 60.4 1.0
S2 A:SF41101 2.2 62.3 1.0
S1 A:SF41101 2.2 61.9 1.0
SG A:CYS394 2.3 74.9 1.0
FE1 A:SF41101 2.9 58.7 1.0
FE2 A:SF41101 2.9 59.4 1.0
FE3 A:SF41101 3.0 61.8 1.0
CB A:CYS394 3.2 76.4 1.0
CA A:CYS394 3.5 76.9 1.0
S4 A:SF41101 3.7 55.6 1.0
CG1 A:ILE388 4.0 69.7 1.0
N A:CYS394 4.1 78.5 1.0
CE A:MET423 4.1 81.6 1.0
CD1 A:ILE388 4.4 69.3 1.0
C A:CYS394 4.7 79.7 1.0
CB A:CYS397 4.8 71.8 1.0
SD A:MET423 4.9 91.3 1.0
C A:THR393 4.9 79.2 1.0
SG A:CYS137 4.9 57.9 1.0
O A:CYS394 4.9 78.6 1.0
SG A:CYS397 5.0 64.6 1.0

Reference:

C.Zhou, S.Pourmal, N.P.Pavletich. DNA2 Nuclease-Helicase Structure, Mechanism and Regulation By Rpa. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26491943
DOI: 10.7554/ELIFE.09832
Page generated: Sun Dec 13 16:00:26 2020

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