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Iron in PDB 5eax: Crystal Structure of DNA2 in Complex with An Ssdna

Enzymatic activity of Crystal Structure of DNA2 in Complex with An Ssdna

All present enzymatic activity of Crystal Structure of DNA2 in Complex with An Ssdna:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of DNA2 in Complex with An Ssdna, PDB code: 5eax 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) 29.99 / 3.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.234, 149.211, 172.900, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of DNA2 in Complex with An Ssdna (pdb code 5eax). 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 in Complex with An Ssdna, PDB code: 5eax:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 1 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:70.0
occ:1.00
 FE1 A:SF41101 0.0 70.0 1.0
S2 A:SF41101 2.1 70.2 1.0
S3 A:SF41101 2.1 70.3 1.0
S4 A:SF41101 2.1 68.8 1.0
SG A:CYS137 2.3 67.5 1.0
FE4 A:SF41101 3.0 77.0 1.0
FE3 A:SF41101 3.0 70.2 1.0
FE2 A:SF41101 3.1 67.1 1.0
CB A:CYS137 3.6 64.6 1.0
S1 A:SF41101 3.8 69.3 1.0
CB A:ARG140 3.8 58.9 1.0
N A:ARG140 3.8 56.9 1.0
CD A:ARG139 4.2 53.5 1.0
CB A:ARG139 4.2 53.5 1.0
CA A:ARG140 4.2 57.8 1.0
CG1 A:ILE388 4.3 75.9 1.0
CG A:ARG139 4.4 53.5 1.0
CG A:ARG140 4.7 60.2 1.0
C A:ARG139 4.7 55.2 1.0
CD1 A:ILE388 4.8 75.8 1.0
CG2 A:ILE388 4.8 76.4 1.0
N A:ILE388 4.8 77.9 1.0
SG A:CYS394 4.9 81.4 1.0
SG A:CYS403 4.9 61.3 1.0
CA A:CYS137 4.9 63.2 1.0
CA A:ARG139 5.0 54.4 1.0

Iron binding site 2 out of 8 in 5eax

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Iron binding site 2 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:67.1
occ:1.00
 FE2 A:SF41101 0.0 67.1 1.0
S1 A:SF41101 2.1 69.3 1.0
S3 A:SF41101 2.1 70.3 1.0
S4 A:SF41101 2.1 68.8 1.0
SG A:CYS403 2.3 61.3 1.0
CB A:CYS403 2.9 56.6 1.0
FE4 A:SF41101 2.9 77.0 1.0
FE3 A:SF41101 2.9 70.2 1.0
FE1 A:SF41101 3.1 70.0 1.0
S2 A:SF41101 3.7 70.2 1.0
CE A:MET423 3.8 96.5 1.0
NE A:ARG139 4.1 52.2 1.0
CD A:ARG139 4.1 53.5 1.0
CA A:CYS403 4.3 53.6 1.0
CG2 A:ILE387 4.6 71.0 1.0
CA A:ILE400 4.8 64.9 1.0
CG A:ARG139 4.9 53.5 1.0
SG A:CYS394 4.9 81.4 1.0
SG A:CYS397 4.9 74.6 1.0

Iron binding site 3 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 3 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:70.2
occ:1.00
 FE3 A:SF41101 0.0 70.2 1.0
S4 A:SF41101 2.1 68.8 1.0
S2 A:SF41101 2.1 70.2 1.0
S1 A:SF41101 2.1 69.3 1.0
SG A:CYS397 2.3 74.6 1.0
FE4 A:SF41101 2.9 77.0 1.0
FE2 A:SF41101 2.9 67.1 1.0
FE1 A:SF41101 3.0 70.0 1.0
CB A:CYS397 3.4 79.8 1.0
S3 A:SF41101 3.6 70.3 1.0
CG A:ARG140 3.8 60.2 1.0
CB A:ARG140 4.0 58.9 1.0
N A:ILE400 4.3 66.2 1.0
CB A:GLN399 4.5 68.7 1.0
CA A:ARG140 4.6 57.8 1.0
C A:GLN399 4.6 67.5 1.0
CA A:ILE400 4.7 64.9 1.0
CA A:CYS397 4.8 83.5 1.0
CB A:CYS403 4.8 56.6 1.0
SG A:CYS137 4.8 67.5 1.0

Iron binding site 4 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 4 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:77.0
occ:1.00
 FE4 A:SF41101 0.0 77.0 1.0
S3 A:SF41101 2.1 70.3 1.0
S1 A:SF41101 2.1 69.3 1.0
S2 A:SF41101 2.2 70.2 1.0
SG A:CYS394 2.3 81.4 1.0
FE2 A:SF41101 2.9 67.1 1.0
FE3 A:SF41101 2.9 70.2 1.0
FE1 A:SF41101 3.0 70.0 1.0
CB A:CYS394 3.3 84.8 1.0
CA A:CYS394 3.5 88.7 1.0
S4 A:SF41101 3.6 68.8 1.0
CE A:MET423 4.0 96.5 1.0
CG1 A:ILE388 4.1 75.9 1.0
N A:CYS394 4.2 90.3 1.0
CD1 A:ILE388 4.4 75.8 1.0
SG A:CYS397 4.7 74.6 1.0
SD A:MET423 4.7 98.8 1.0
C A:CYS394 4.7 91.7 1.0
CG2 A:ILE387 4.8 71.0 1.0
CB A:CYS397 4.9 79.8 1.0
O A:CYS394 4.9 90.3 1.0
SG A:CYS137 5.0 67.5 1.0

Iron binding site 5 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 5 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 in Complex with An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:69.8
occ:1.00
 FE1 B:SF41101 0.0 69.8 1.0
S2 B:SF41101 2.1 72.1 1.0
S3 B:SF41101 2.1 72.0 1.0
S4 B:SF41101 2.1 71.6 1.0
SG B:CYS137 2.3 65.0 1.0
FE4 B:SF41101 3.0 79.6 1.0
FE3 B:SF41101 3.0 74.2 1.0
FE2 B:SF41101 3.1 72.5 1.0
CB B:CYS137 3.6 63.3 1.0
S1 B:SF41101 3.8 73.4 1.0
N B:ARG140 3.8 60.2 1.0
CB B:ARG140 3.9 63.0 1.0
CB B:ARG139 4.0 58.2 1.0
CD B:ARG139 4.0 58.0 1.0
CG1 B:ILE388 4.2 82.7 1.0
CG B:ARG139 4.2 58.3 1.0
CA B:ARG140 4.3 61.1 1.0
C B:ARG139 4.6 58.9 1.0
CG2 B:ILE388 4.6 82.2 1.0
N B:ILE388 4.6 81.0 1.0
CA B:ARG139 4.8 58.5 1.0
CD1 B:ILE388 4.8 82.8 1.0
CG B:ARG140 4.8 64.7 1.0
CA B:CYS137 4.9 62.9 1.0
CB B:ILE388 4.9 83.4 1.0
NE B:ARG139 5.0 58.2 1.0
SG B:CYS403 5.0 65.8 1.0

Iron binding site 6 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 6 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 in Complex with An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:72.5
occ:1.00
 FE2 B:SF41101 0.0 72.5 1.0
S1 B:SF41101 2.1 73.4 1.0
S4 B:SF41101 2.1 71.6 1.0
S3 B:SF41101 2.1 72.0 1.0
SG B:CYS403 2.3 65.8 1.0
FE4 B:SF41101 2.9 79.6 1.0
CB B:CYS403 2.9 60.9 1.0
FE3 B:SF41101 3.0 74.2 1.0
FE1 B:SF41101 3.1 69.8 1.0
S2 B:SF41101 3.7 72.1 1.0
CE B:MET423 3.9 94.1 1.0
NE B:ARG139 3.9 58.2 1.0
CD B:ARG139 3.9 58.0 1.0
CA B:CYS403 4.4 58.1 1.0
CG2 B:ILE387 4.6 74.5 1.0
CG B:ARG139 4.7 58.3 1.0
SG B:CYS397 4.9 76.1 1.0
CA B:ILE400 5.0 60.5 1.0
SG B:CYS394 5.0 84.5 1.0

Iron binding site 7 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 7 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 in Complex with An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:74.2
occ:1.00
 FE3 B:SF41101 0.0 74.2 1.0
S4 B:SF41101 2.1 71.6 1.0
S2 B:SF41101 2.1 72.1 1.0
S1 B:SF41101 2.1 73.4 1.0
SG B:CYS397 2.3 76.1 1.0
FE2 B:SF41101 3.0 72.5 1.0
FE4 B:SF41101 3.0 79.6 1.0
FE1 B:SF41101 3.0 69.8 1.0
CB B:CYS397 3.5 80.4 1.0
CG B:ARG140 3.7 64.7 1.0
S3 B:SF41101 3.7 72.0 1.0
CB B:ARG140 3.8 63.0 1.0
CA B:ARG140 4.4 61.1 1.0
N B:ILE400 4.6 62.1 1.0
CB B:GLN399 4.6 66.6 1.0
SG B:CYS137 4.7 65.0 1.0
CB B:CYS403 4.8 60.9 1.0
C B:GLN399 4.8 64.3 1.0
CA B:ILE400 4.9 60.5 1.0
CA B:CYS397 4.9 83.4 1.0
N B:ARG140 4.9 60.2 1.0

Iron binding site 8 out of 8 in 5eax

Go back to Iron Binding Sites List in 5eax
Iron binding site 8 out of 8 in the Crystal Structure of DNA2 in Complex with An Ssdna


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 in Complex with An Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1101

b:79.6
occ:1.00
 FE4 B:SF41101 0.0 79.6 1.0
S3 B:SF41101 2.1 72.0 1.0
S1 B:SF41101 2.1 73.4 1.0
S2 B:SF41101 2.2 72.1 1.0
SG B:CYS394 2.3 84.5 1.0
FE2 B:SF41101 2.9 72.5 1.0
FE1 B:SF41101 3.0 69.8 1.0
FE3 B:SF41101 3.0 74.2 1.0
CB B:CYS394 3.5 88.6 1.0
S4 B:SF41101 3.6 71.6 1.0
CA B:CYS394 3.7 93.8 1.0
CG1 B:ILE388 3.8 82.7 1.0
CE B:MET423 4.0 94.1 1.0
CD1 B:ILE388 4.2 82.8 1.0
N B:CYS394 4.3 96.0 1.0
CG2 B:ILE387 4.6 74.5 1.0
SD B:MET423 4.7 95.5 1.0
SG B:CYS397 4.8 76.1 1.0
SG B:CYS137 4.9 65.0 1.0
N B:ILE388 5.0 81.0 1.0
C B:CYS394 5.0 96.6 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: Tue Aug 5 20:58:51 2025

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