Atomistry » Iron » PDB 3ae6-3arj » 3agu
Atomistry »
  Iron »
    PDB 3ae6-3arj »
      3agu »

Iron in PDB 3agu: Hemerythrin-Like Domain of Dcrh (Semimet-R)

Protein crystallography data

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R), PDB code: 3agu was solved by A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, Y.Shiro, T.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.81
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.425, 44.903, 48.076, 95.21, 103.98, 89.95
R / Rfree (%) 24.7 / 29.2

Other elements in 3agu:

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Hemerythrin-Like Domain of Dcrh (Semimet-R) (pdb code 3agu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Hemerythrin-Like Domain of Dcrh (Semimet-R), PDB code: 3agu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3agu

Go back to Iron Binding Sites List in 3agu
Iron binding site 1 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:8.9
occ:1.00
FE2 A:CFO201 0.0 8.9 1.0
O A:CFO201 2.0 5.7 1.0
OD2 A:ASP123 2.2 7.3 1.0
NE2 A:HIS59 2.2 8.4 1.0
CL A:CFO201 2.4 11.2 1.0
OE2 A:GLU63 2.4 5.8 1.0
NE2 A:HIS23 2.4 9.2 1.0
CG A:ASP123 3.1 8.4 1.0
CE1 A:HIS59 3.2 7.6 1.0
CD A:GLU63 3.2 7.3 1.0
CD2 A:HIS59 3.2 6.4 1.0
CD2 A:HIS23 3.3 7.3 1.0
FE1 A:CFO201 3.3 6.9 1.0
OD1 A:ASP123 3.4 9.8 1.0
CE1 A:HIS23 3.4 9.5 1.0
OE1 A:GLU63 3.5 6.6 1.0
CD2 A:HIS118 3.9 9.0 1.0
NE2 A:HIS118 4.2 9.9 1.0
ND1 A:HIS59 4.3 6.5 1.0
CG A:HIS59 4.4 8.2 1.0
CB A:ASP123 4.4 9.9 1.0
OH A:TYR126 4.4 8.6 1.0
CG A:GLU63 4.5 8.0 1.0
CG A:HIS23 4.5 8.2 1.0
ND1 A:HIS23 4.5 7.9 1.0
CG1 A:ILE119 4.6 8.2 1.0
CE1 A:PHE60 4.7 8.9 1.0
NE2 A:HIS82 4.8 9.8 1.0
CD1 A:PHE60 4.9 8.0 1.0

Iron binding site 2 out of 4 in 3agu

Go back to Iron Binding Sites List in 3agu
Iron binding site 2 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:6.9
occ:1.00
FE1 A:CFO201 0.0 6.9 1.0
O A:CFO201 2.0 5.7 1.0
OE1 A:GLU63 2.2 6.6 1.0
NE2 A:HIS118 2.2 9.9 1.0
NE2 A:HIS78 2.2 5.8 1.0
NE2 A:HIS82 2.3 9.8 1.0
OD1 A:ASP123 2.3 9.8 1.0
CE1 A:HIS82 3.1 8.2 1.0
CD A:GLU63 3.1 7.3 1.0
CD2 A:HIS118 3.1 9.0 1.0
CE1 A:HIS78 3.2 6.1 1.0
CE1 A:HIS118 3.2 9.2 1.0
CD2 A:HIS78 3.2 8.2 1.0
CG A:ASP123 3.2 8.4 1.0
CD2 A:HIS82 3.3 9.7 1.0
FE2 A:CFO201 3.3 8.9 1.0
OE2 A:GLU63 3.4 5.8 1.0
OD2 A:ASP123 3.5 7.3 1.0
ND1 A:HIS82 4.3 11.1 1.0
CG A:HIS118 4.3 9.8 1.0
ND1 A:HIS118 4.3 9.6 1.0
ND1 A:HIS78 4.3 9.4 1.0
CG A:HIS78 4.4 9.2 1.0
CG A:HIS82 4.4 9.6 1.0
CG A:GLU63 4.5 8.0 1.0
CE2 A:TYR126 4.6 7.7 1.0
CB A:ASP123 4.6 9.9 1.0
CL A:CFO201 4.7 11.2 1.0
CD1 A:PHE60 4.8 8.0 1.0
CB A:GLU63 4.8 10.0 1.0
NE2 A:HIS59 4.8 8.4 1.0
CE1 A:PHE60 4.8 8.9 1.0
CA A:ASP123 4.9 9.8 1.0
N A:ASP123 4.9 10.6 1.0

Iron binding site 3 out of 4 in 3agu

Go back to Iron Binding Sites List in 3agu
Iron binding site 3 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:9.3
occ:1.00
FE2 B:CFO201 0.0 9.3 1.0
O B:CFO201 2.0 7.1 1.0
OD2 B:ASP123 2.0 6.7 1.0
NE2 B:HIS59 2.3 8.1 1.0
NE2 B:HIS23 2.3 9.2 1.0
CL B:CFO201 2.4 10.5 1.0
OE2 B:GLU63 2.4 5.3 1.0
CG B:ASP123 3.0 8.7 1.0
CE1 B:HIS59 3.2 7.0 1.0
CD2 B:HIS23 3.2 7.5 1.0
CD B:GLU63 3.3 7.2 1.0
FE1 B:CFO201 3.3 7.8 1.0
CD2 B:HIS59 3.3 6.5 1.0
OD1 B:ASP123 3.3 9.1 1.0
CE1 B:HIS23 3.4 9.2 1.0
OE1 B:GLU63 3.6 6.5 1.0
CD2 B:HIS118 4.0 8.9 1.0
NE2 B:HIS118 4.3 10.8 1.0
CB B:ASP123 4.3 9.8 1.0
ND1 B:HIS59 4.4 6.4 1.0
CG B:HIS23 4.4 8.6 1.0
OH B:TYR126 4.4 8.1 1.0
ND1 B:HIS23 4.5 8.2 1.0
CG B:HIS59 4.5 7.8 1.0
CG B:GLU63 4.5 7.8 1.0
CG1 B:ILE119 4.6 8.6 1.0
CE1 B:PHE60 4.7 8.2 1.0
NE2 B:HIS82 4.8 8.7 1.0
CD1 B:PHE60 4.9 7.9 1.0

Iron binding site 4 out of 4 in 3agu

Go back to Iron Binding Sites List in 3agu
Iron binding site 4 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:7.8
occ:1.00
FE1 B:CFO201 0.0 7.8 1.0
O B:CFO201 2.0 7.1 1.0
OE1 B:GLU63 2.1 6.5 1.0
OD1 B:ASP123 2.2 9.1 1.0
NE2 B:HIS118 2.2 10.8 1.0
NE2 B:HIS82 2.3 8.7 1.0
NE2 B:HIS78 2.3 6.0 1.0
CD B:GLU63 3.1 7.2 1.0
CE1 B:HIS82 3.1 7.7 1.0
CD2 B:HIS118 3.1 8.9 1.0
CG B:ASP123 3.2 8.7 1.0
CD2 B:HIS78 3.2 8.2 1.0
CE1 B:HIS118 3.3 9.0 1.0
CE1 B:HIS78 3.3 5.8 1.0
FE2 B:CFO201 3.3 9.3 1.0
CD2 B:HIS82 3.3 9.3 1.0
OE2 B:GLU63 3.4 5.3 1.0
OD2 B:ASP123 3.4 6.7 1.0
ND1 B:HIS82 4.3 10.3 1.0
CG B:HIS118 4.3 9.7 1.0
ND1 B:HIS118 4.3 9.6 1.0
ND1 B:HIS78 4.4 9.4 1.0
CG B:HIS78 4.4 8.3 1.0
CG B:HIS82 4.4 8.8 1.0
CG B:GLU63 4.5 7.8 1.0
CE2 B:TYR126 4.5 6.8 1.0
CB B:ASP123 4.6 9.8 1.0
CL B:CFO201 4.7 10.5 1.0
CD1 B:PHE60 4.7 7.9 1.0
CB B:GLU63 4.8 9.4 1.0
CE1 B:PHE60 4.8 8.2 1.0
NE2 B:HIS59 4.8 8.1 1.0
CA B:ASP123 4.9 9.7 1.0
N B:ASP123 5.0 11.0 1.0

Reference:

A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, Y.Shiro, T.Hayashi. Characteristics of Diiron Site with Large Cavity in Hemerythrin-Like Domain of Dcrh To Be Published.
Page generated: Sun Dec 13 15:00:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy