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Iron in PDB 8dzk: DBR1 in Complex with 5-Mer Cleavage Product

Protein crystallography data

The structure of DBR1 in Complex with 5-Mer Cleavage Product, PDB code: 8dzk was solved by N.E.Clark, A.B.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.12 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.272, 143.341, 214.006, 90, 90, 90
R / Rfree (%) 17.8 / 20.9

Other elements in 8dzk:

The structure of DBR1 in Complex with 5-Mer Cleavage Product also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the DBR1 in Complex with 5-Mer Cleavage Product (pdb code 8dzk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the DBR1 in Complex with 5-Mer Cleavage Product, PDB code: 8dzk:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 8dzk

Go back to Iron Binding Sites List in 8dzk
Iron binding site 1 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:39.9
occ:1.00
OD1 A:ASN90 2.0 42.0 1.0
NE2 A:HIS180 2.0 39.8 1.0
OD2 A:ASP45 2.2 43.8 1.0
ND1 A:HIS230 2.3 43.7 1.0
O1P F:G46511 2.5 54.9 0.8
O3P F:G46511 2.5 53.5 0.8
CE1 A:HIS180 3.0 40.5 1.0
P F:G46511 3.0 48.8 0.8
CG A:ASP45 3.0 45.4 1.0
CD2 A:HIS180 3.0 36.0 1.0
CE1 A:HIS230 3.1 46.2 1.0
CG A:ASN90 3.1 44.3 1.0
OD1 A:ASP45 3.1 44.6 1.0
CG A:HIS230 3.4 44.3 1.0
ND2 A:ASN90 3.6 44.1 1.0
ZN A:ZN402 3.7 63.8 1.0
CA A:HIS230 3.8 46.9 1.0
CB A:HIS230 3.8 42.8 1.0
ND1 A:HIS180 4.1 37.7 1.0
CG A:HIS180 4.2 39.3 1.0
O5' F:G46511 4.2 58.2 0.8
N A:ASN90 4.3 40.2 1.0
NE2 A:HIS230 4.3 46.0 1.0
O A:HIS230 4.4 54.0 1.0
CB A:ASN90 4.4 39.8 1.0
CB A:ASP45 4.4 41.5 1.0
CD2 A:HIS230 4.4 47.9 1.0
SG A:CYS14 4.5 55.3 1.0
C5' F:G46511 4.5 57.3 0.8
S2P F:G46511 4.5 65.4 0.8
C A:HIS230 4.7 50.2 1.0
N A:HIS230 4.8 45.6 1.0
CD2 A:HIS91 4.9 51.0 1.0
CA A:ASN90 4.9 39.3 1.0

Iron binding site 2 out of 5 in 8dzk

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Iron binding site 2 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:41.8
occ:1.00
OD1 B:ASN90 2.0 46.1 1.0
O3P G:G46511 2.1 55.0 0.8
NE2 B:HIS180 2.1 39.3 1.0
OD2 B:ASP45 2.3 44.5 1.0
ND1 B:HIS230 2.3 49.4 1.0
O1P G:G46511 2.7 62.2 0.8
P G:G46511 2.9 51.8 0.8
CG B:ASP45 3.1 44.1 1.0
CE1 B:HIS180 3.1 39.5 1.0
CD2 B:HIS180 3.1 36.8 1.0
CG B:ASN90 3.1 47.9 1.0
CE1 B:HIS230 3.1 56.5 1.0
OD1 B:ASP45 3.2 44.6 1.0
CG B:HIS230 3.4 46.7 1.0
ND2 B:ASN90 3.6 51.3 1.0
ZN B:ZN402 3.7 63.1 1.0
CB B:HIS230 3.7 41.4 1.0
CA B:HIS230 3.8 44.7 1.0
O5' G:G46511 3.9 68.2 0.8
ND1 B:HIS180 4.2 39.6 1.0
CG B:HIS180 4.2 39.2 1.0
N B:ASN90 4.3 40.8 1.0
NE2 B:HIS230 4.3 54.5 1.0
O B:HIS230 4.4 52.4 1.0
CB B:ASN90 4.4 43.9 1.0
CD2 B:HIS230 4.4 51.6 1.0
CB B:ASP45 4.5 44.0 1.0
SG B:CYS14 4.5 51.9 1.0
S2P G:G46511 4.6 72.8 0.8
C B:HIS230 4.7 49.4 1.0
C5' G:G46511 4.8 69.8 0.8
N B:HIS230 4.9 39.6 1.0
CA B:ASN90 4.9 47.6 1.0
CD2 B:HIS91 4.9 60.1 1.0

Iron binding site 3 out of 5 in 8dzk

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Iron binding site 3 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:45.6
occ:1.00
OD1 C:ASN90 1.9 46.5 1.0
NE2 C:HIS180 2.1 47.3 1.0
OD2 C:ASP45 2.2 49.2 1.0
ND1 C:HIS230 2.3 49.2 1.0
O3P N:G46511 2.5 60.1 0.8
O1P N:G46511 2.7 59.2 0.8
CD2 C:HIS180 3.0 44.8 1.0
CG C:ASP45 3.0 50.2 1.0
CG C:ASN90 3.1 47.3 1.0
CE1 C:HIS230 3.1 54.1 1.0
CE1 C:HIS180 3.1 47.1 1.0
P N:G46511 3.2 53.5 0.8
OD1 C:ASP45 3.3 46.1 1.0
CG C:HIS230 3.4 49.5 1.0
ND2 C:ASN90 3.6 53.5 1.0
ZN C:ZN402 3.7 70.0 1.0
CA C:HIS230 3.8 51.4 1.0
CB C:HIS230 3.8 44.0 1.0
O5' N:G46511 4.1 63.9 0.8
CG C:HIS180 4.2 46.9 1.0
ND1 C:HIS180 4.2 41.9 1.0
N C:ASN90 4.2 43.4 1.0
NE2 C:HIS230 4.3 54.0 1.0
O C:HIS230 4.3 52.2 1.0
CB C:ASN90 4.3 44.5 1.0
CB C:ASP45 4.4 47.1 1.0
CD2 C:HIS230 4.4 49.9 1.0
SG C:CYS14 4.5 55.6 1.0
C C:HIS230 4.6 53.8 1.0
C5' N:G46511 4.7 68.3 0.8
N C:HIS230 4.8 48.0 1.0
S2P N:G46511 4.8 79.5 0.8
CA C:ASN90 4.8 47.5 1.0
CG2 C:ILE132 5.0 44.2 1.0

Iron binding site 4 out of 5 in 8dzk

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Iron binding site 4 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:54.4
occ:1.00
OD1 D:ASN90 2.0 54.5 1.0
NE2 D:HIS180 2.1 48.5 1.0
O1P O:G46511 2.2 66.7 0.9
OD2 D:ASP45 2.2 59.1 1.0
ND1 D:HIS230 2.3 56.1 1.0
O3P O:G46511 3.0 77.2 0.9
CD2 D:HIS180 3.0 46.7 1.0
CG D:ASP45 3.0 54.3 1.0
OD1 D:ASP45 3.1 53.1 1.0
CE1 D:HIS230 3.2 62.9 1.0
CG D:ASN90 3.2 59.5 1.0
P O:G46511 3.2 70.7 0.9
CE1 D:HIS180 3.2 51.7 1.0
CG D:HIS230 3.4 57.4 1.0
ZN D:ZN402 3.7 77.3 1.0
CB D:HIS230 3.7 53.7 1.0
ND2 D:ASN90 3.8 63.5 1.0
CA D:HIS230 3.8 59.0 1.0
O5' O:G46511 4.0 86.9 0.9
CG D:HIS180 4.2 48.0 1.0
ND1 D:HIS180 4.2 51.4 1.0
N D:ASN90 4.3 44.7 1.0
NE2 D:HIS230 4.3 65.0 1.0
CB D:ASN90 4.3 52.7 1.0
CB D:ASP45 4.4 55.8 1.0
SG D:CYS14 4.4 64.9 1.0
CD2 D:HIS230 4.4 58.6 1.0
O D:HIS230 4.5 69.6 1.0
C D:HIS230 4.7 67.7 1.0
C5' O:G46511 4.7 87.0 0.9
N D:HIS230 4.8 57.4 1.0
CA D:ASN90 4.9 50.3 1.0
S2P O:G46511 4.9 98.6 0.9
CG2 D:ILE132 5.0 49.9 1.0

Iron binding site 5 out of 5 in 8dzk

Go back to Iron Binding Sites List in 8dzk
Iron binding site 5 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:45.7
occ:1.00
NE2 E:HIS180 2.0 40.8 1.0
OD1 E:ASN90 2.0 41.6 1.0
OD2 E:ASP45 2.2 47.0 1.0
O3P P:G46511 2.2 54.9 0.7
ND1 E:HIS230 2.4 45.5 1.0
CE1 E:HIS180 2.8 39.6 1.0
O1P P:G46511 2.8 64.2 0.7
CG E:ASP45 3.0 44.2 1.0
CD2 E:HIS180 3.1 38.0 1.0
P P:G46511 3.1 58.4 0.7
CG E:ASN90 3.1 48.9 1.0
OD1 E:ASP45 3.1 43.2 1.0
CE1 E:HIS230 3.3 51.2 1.0
CG E:HIS230 3.4 45.0 1.0
ZN E:ZN402 3.6 55.9 1.0
ND2 E:ASN90 3.6 52.2 1.0
CB E:HIS230 3.8 43.7 1.0
CA E:HIS230 3.8 46.1 1.0
O5' P:G46511 3.9 71.6 0.7
ND1 E:HIS180 4.0 39.2 1.0
CG E:HIS180 4.1 40.0 1.0
N E:ASN90 4.2 36.9 1.0
SG E:CYS14 4.3 50.4 1.0
O E:HIS230 4.3 50.9 1.0
CB E:ASN90 4.4 40.0 1.0
CB E:ASP45 4.4 42.5 1.0
NE2 E:HIS230 4.4 49.1 1.0
C5' P:G46511 4.5 70.2 0.7
CD2 E:HIS230 4.5 49.9 1.0
C E:HIS230 4.6 48.9 1.0
N E:HIS230 4.8 45.4 1.0
S2P P:G46511 4.8 81.2 0.7
CA E:ASN90 4.9 43.3 1.0

Reference:

N.E.Clark, A.B.Taylor. DBR1 in Complex with 5-Mer Cleavage Product To Be Published.
Page generated: Sat Aug 10 00:42:19 2024

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