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Iron in PDB 5eaw: Crystal Structure of DNA2 Nuclease-Helicase

Enzymatic activity of Crystal Structure of DNA2 Nuclease-Helicase

All present enzymatic activity of Crystal Structure of DNA2 Nuclease-Helicase:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of DNA2 Nuclease-Helicase, PDB code: 5eaw 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 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.900, 148.600, 170.500, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of DNA2 Nuclease-Helicase (pdb code 5eaw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of DNA2 Nuclease-Helicase, PDB code: 5eaw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5eaw

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Iron binding site 1 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


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 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:58.8
occ:1.00
 FE1 A:SF41101 0.0 58.8 1.0
S2 A:SF41101 2.1 51.4 1.0
S3 A:SF41101 2.1 57.4 1.0
S4 A:SF41101 2.1 57.5 1.0
SG A:CYS137 2.2 54.2 1.0
FE3 A:SF41101 2.9 63.9 1.0
FE4 A:SF41101 2.9 64.4 1.0
FE2 A:SF41101 3.1 61.2 1.0
CB A:CYS137 3.5 51.8 1.0
N A:ARG140 3.7 41.4 1.0
CB A:ARG140 3.7 45.4 1.0
S1 A:SF41101 3.8 59.6 1.0
CB A:ARG139 4.1 37.3 1.0
CA A:ARG140 4.1 44.8 1.0
CG1 A:ILE388 4.3 56.9 1.0
CD A:ARG139 4.4 40.9 1.0
CG A:ARG139 4.5 38.8 1.0
CG A:ARG140 4.6 46.1 1.0
C A:ARG139 4.6 39.8 1.0
CD1 A:ILE388 4.6 51.7 1.0
CG2 A:ILE388 4.8 59.6 1.0
CA A:ARG139 4.9 38.4 1.0
CA A:CYS137 4.9 51.7 1.0
SG A:CYS397 4.9 60.7 1.0
SG A:CYS403 5.0 49.1 1.0

Iron binding site 2 out of 8 in 5eaw

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Iron binding site 2 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


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 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:61.2
occ:1.00
 FE2 A:SF41101 0.0 61.2 1.0
S1 A:SF41101 2.1 59.6 1.0
S3 A:SF41101 2.1 57.4 1.0
S4 A:SF41101 2.1 57.5 1.0
SG A:CYS403 2.3 49.1 1.0
FE4 A:SF41101 2.9 64.4 1.0
FE3 A:SF41101 3.0 63.9 1.0
CB A:CYS403 3.0 47.2 1.0
FE1 A:SF41101 3.1 58.8 1.0
S2 A:SF41101 3.7 51.4 1.0
CE A:MET423 3.8 75.5 1.0
CD A:ARG139 4.2 40.9 1.0
NE A:ARG139 4.2 40.2 1.0
CA A:CYS403 4.5 46.6 1.0
CG2 A:ILE387 4.6 57.8 1.0
CA A:ILE400 4.7 53.8 1.0
CG1 A:ILE387 4.8 60.9 1.0
CG A:ARG139 4.8 38.8 1.0
SG A:CYS397 5.0 60.7 1.0
N A:ILE400 5.0 53.8 1.0
CD1 A:LEU143 5.0 32.6 1.0

Iron binding site 3 out of 8 in 5eaw

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Iron binding site 3 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


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 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:63.9
occ:1.00
 FE3 A:SF41101 0.0 63.9 1.0
S4 A:SF41101 2.1 57.5 1.0
S1 A:SF41101 2.1 59.6 1.0
S2 A:SF41101 2.2 51.4 1.0
SG A:CYS397 2.2 60.7 1.0
FE4 A:SF41101 2.9 64.4 1.0
FE1 A:SF41101 2.9 58.8 1.0
FE2 A:SF41101 3.0 61.2 1.0
CB A:CYS397 3.4 71.5 1.0
S3 A:SF41101 3.6 57.4 1.0
CG A:ARG140 3.7 46.1 1.0
CB A:ARG140 3.9 45.4 1.0
N A:ILE400 4.2 53.8 1.0
CB A:GLN399 4.3 53.4 1.0
CA A:ARG140 4.5 44.8 1.0
C A:GLN399 4.5 55.2 1.0
CA A:ILE400 4.7 53.8 1.0
CA A:CYS397 4.7 74.3 1.0
SG A:CYS137 4.7 54.2 1.0
CB A:CYS403 4.9 47.2 1.0
N A:ARG140 4.9 41.4 1.0
CA A:GLN399 4.9 57.5 1.0

Iron binding site 4 out of 8 in 5eaw

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Iron binding site 4 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


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 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:64.4
occ:1.00
 FE4 A:SF41101 0.0 64.4 1.0
S3 A:SF41101 2.1 57.4 1.0
S1 A:SF41101 2.1 59.6 1.0
S2 A:SF41101 2.1 51.4 1.0
SG A:CYS394 2.6 73.1 1.0
FE2 A:SF41101 2.9 61.2 1.0
FE3 A:SF41101 2.9 63.9 1.0
FE1 A:SF41101 2.9 58.8 1.0
CB A:CYS394 3.4 73.0 1.0
CA A:CYS394 3.4 76.4 1.0
S4 A:SF41101 3.6 57.5 1.0
CG1 A:ILE388 4.1 56.9 1.0
CE A:MET423 4.1 75.5 1.0
N A:CYS394 4.1 78.3 1.0
CD1 A:ILE388 4.3 51.7 1.0
SG A:CYS397 4.5 60.7 1.0
C A:CYS394 4.6 79.2 1.0
O A:CYS394 4.8 75.4 1.0
SG A:CYS137 4.8 54.2 1.0
CB A:CYS397 4.8 71.5 1.0
CG2 A:ILE387 5.0 57.8 1.0

Iron binding site 5 out of 8 in 5eaw

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Iron binding site 5 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of DNA2 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:67.0
occ:1.00
 FE1 B:SF41101 0.0 67.0 1.0
SG B:CYS137 2.0 59.0 1.0
S2 B:SF41101 2.1 63.0 1.0
S3 B:SF41101 2.1 60.8 1.0
S4 B:SF41101 2.2 57.1 1.0
FE3 B:SF41101 2.9 67.9 1.0
FE4 B:SF41101 3.0 72.3 1.0
FE2 B:SF41101 3.0 71.7 1.0
CB B:CYS137 3.3 57.1 1.0
N B:ARG140 3.7 50.7 1.0
CB B:ARG140 3.7 50.1 1.0
S1 B:SF41101 3.7 61.6 1.0
CB B:ARG139 4.1 50.4 1.0
CA B:ARG140 4.2 49.4 1.0
CG1 B:ILE388 4.2 66.4 1.0
CD B:ARG139 4.5 52.5 1.0
CG B:ARG140 4.6 50.1 1.0
CG B:ARG139 4.6 50.6 1.0
CD1 B:ILE388 4.6 64.5 1.0
C B:ARG139 4.7 53.0 1.0
CA B:CYS137 4.7 55.9 1.0
CG2 B:ILE388 4.7 64.2 1.0
CA B:ARG139 4.8 53.0 1.0
N B:ILE388 5.0 70.4 1.0
SG B:CYS397 5.0 68.2 1.0

Iron binding site 6 out of 8 in 5eaw

Go back to Iron Binding Sites List in 5eaw
Iron binding site 6 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of DNA2 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:71.7
occ:1.00
 FE2 B:SF41101 0.0 71.7 1.0
S1 B:SF41101 2.1 61.6 1.0
S3 B:SF41101 2.1 60.8 1.0
S4 B:SF41101 2.1 57.1 1.0
SG B:CYS403 2.4 62.7 1.0
FE4 B:SF41101 2.9 72.3 1.0
FE3 B:SF41101 2.9 67.9 1.0
FE1 B:SF41101 3.0 67.0 1.0
CB B:CYS403 3.2 57.6 1.0
S2 B:SF41101 3.7 63.0 1.0
CE B:MET423 3.9 79.0 1.0
CD B:ARG139 3.9 52.5 1.0
NE B:ARG139 4.0 56.8 1.0
CG2 B:ILE387 4.4 69.4 1.0
CG1 B:ILE387 4.6 62.3 1.0
CG B:ARG139 4.6 50.6 1.0
CA B:CYS403 4.6 55.0 1.0
SG B:CYS137 4.9 59.0 1.0
SG B:CYS394 4.9 87.5 1.0
CB B:ILE387 4.9 65.9 1.0

Iron binding site 7 out of 8 in 5eaw

Go back to Iron Binding Sites List in 5eaw
Iron binding site 7 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of DNA2 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:67.9
occ:1.00
 FE3 B:SF41101 0.0 67.9 1.0
S4 B:SF41101 2.1 57.1 1.0
S2 B:SF41101 2.1 63.0 1.0
S1 B:SF41101 2.2 61.6 1.0
SG B:CYS397 2.3 68.2 1.0
FE2 B:SF41101 2.9 71.7 1.0
FE1 B:SF41101 2.9 67.0 1.0
FE4 B:SF41101 3.0 72.3 1.0
CB B:CYS397 3.5 71.8 1.0
S3 B:SF41101 3.7 60.8 1.0
CG B:ARG140 3.8 50.1 1.0
CB B:ARG140 3.9 50.1 1.0
N B:ILE400 4.3 53.2 1.0
CB B:GLN399 4.5 55.3 1.0
CA B:ARG140 4.6 49.4 1.0
C B:GLN399 4.6 52.9 1.0
SG B:CYS137 4.7 59.0 1.0
CA B:ILE400 4.7 53.1 1.0
CB B:CYS403 4.8 57.6 1.0
CA B:CYS397 4.9 76.5 1.0
N B:ARG140 4.9 50.7 1.0
SG B:CYS403 5.0 62.7 1.0

Iron binding site 8 out of 8 in 5eaw

Go back to Iron Binding Sites List in 5eaw
Iron binding site 8 out of 8 in the Crystal Structure of DNA2 Nuclease-Helicase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of DNA2 Nuclease-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:72.3
occ:1.00
 FE4 B:SF41101 0.0 72.3 1.0
S3 B:SF41101 2.1 60.8 1.0
S1 B:SF41101 2.1 61.6 1.0
S2 B:SF41101 2.1 63.0 1.0
SG B:CYS394 2.4 87.5 1.0
FE2 B:SF41101 2.9 71.7 1.0
FE1 B:SF41101 3.0 67.0 1.0
FE3 B:SF41101 3.0 67.9 1.0
CB B:CYS394 3.4 76.9 1.0
CA B:CYS394 3.6 80.6 1.0
S4 B:SF41101 3.7 57.1 1.0
CG1 B:ILE388 3.8 66.4 1.0
CE B:MET423 3.9 79.0 1.0
CD1 B:ILE388 4.2 64.5 1.0
N B:CYS394 4.2 80.0 1.0
CG2 B:ILE387 4.6 69.4 1.0
SG B:CYS137 4.7 59.0 1.0
SD B:MET423 4.8 80.3 1.0
SG B:CYS397 4.8 68.2 1.0
C B:CYS394 4.9 82.2 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: Mon Aug 5 23:37:46 2024

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