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Iron in PDB 3ord: Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata

Protein crystallography data

The structure of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata, PDB code: 3ord was solved by V.S.De Serrano, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.50 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.674, 67.805, 68.304, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 28.9

Other elements in 3ord:

The structure of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata also contains other interesting chemical elements:

Xenon (Xe) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata (pdb code 3ord). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata, PDB code: 3ord:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3ord

Go back to Iron Binding Sites List in 3ord
Iron binding site 1 out of 2 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe139

b:25.6
occ:1.00
FE A:HEM139 0.0 25.6 1.0
NC A:HEM139 2.0 23.8 1.0
ND A:HEM139 2.1 23.3 1.0
NA A:HEM139 2.1 22.1 1.0
NB A:HEM139 2.1 23.3 1.0
NE2 A:HIS89 2.2 37.0 1.0
O A:HOH254 2.7 28.5 1.0
C1D A:HEM139 3.0 24.6 1.0
C4C A:HEM139 3.0 23.6 1.0
C4A A:HEM139 3.1 22.9 1.0
C1C A:HEM139 3.1 24.1 1.0
C4D A:HEM139 3.1 24.8 1.0
C1A A:HEM139 3.1 23.5 1.0
C1B A:HEM139 3.1 22.5 1.0
C4B A:HEM139 3.2 22.2 1.0
CD2 A:HIS89 3.2 36.2 1.0
CE1 A:HIS89 3.2 36.0 1.0
CHD A:HEM139 3.4 23.8 1.0
CHB A:HEM139 3.4 22.5 1.0
CHA A:HEM139 3.5 23.3 1.0
CHC A:HEM139 3.5 21.4 1.0
C2D A:HEM139 4.3 26.3 1.0
C3C A:HEM139 4.3 23.8 1.0
C3A A:HEM139 4.3 23.3 1.0
C2C A:HEM139 4.3 23.3 1.0
C3D A:HEM139 4.3 27.0 1.0
ND1 A:HIS89 4.3 35.7 1.0
C2A A:HEM139 4.3 23.7 1.0
CG A:HIS89 4.3 35.9 1.0
C2B A:HEM139 4.3 19.7 1.0
C3B A:HEM139 4.4 20.3 1.0
CG2 A:VAL59 4.4 16.6 1.0
NE2 A:HIS55 4.6 22.8 0.3
CG1 A:VAL59 4.8 18.6 1.0
XE A:XE140 4.8 46.7 0.6

Iron binding site 2 out of 2 in 3ord

Go back to Iron Binding Sites List in 3ord
Iron binding site 2 out of 2 in the Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe139

b:25.2
occ:1.00
FE B:HEM139 0.0 25.2 1.0
NC B:HEM139 2.0 23.6 1.0
NB B:HEM139 2.1 24.0 1.0
NA B:HEM139 2.1 22.2 1.0
ND B:HEM139 2.1 24.5 1.0
NE2 B:HIS89 2.3 26.9 1.0
O B:HOH256 2.3 27.8 1.0
C1C B:HEM139 3.0 22.4 1.0
C4C B:HEM139 3.0 25.2 1.0
C4B B:HEM139 3.1 22.9 1.0
C1D B:HEM139 3.1 24.7 1.0
C4D B:HEM139 3.1 24.6 1.0
C4A B:HEM139 3.1 23.4 1.0
C1A B:HEM139 3.1 22.8 1.0
C1B B:HEM139 3.1 22.2 1.0
CD2 B:HIS89 3.2 25.1 1.0
CE1 B:HIS89 3.3 26.3 1.0
CHC B:HEM139 3.4 23.5 1.0
CHD B:HEM139 3.4 23.9 1.0
CHA B:HEM139 3.4 21.3 1.0
CHB B:HEM139 3.5 23.9 1.0
C2C B:HEM139 4.3 23.3 1.0
C3C B:HEM139 4.3 23.5 1.0
C3B B:HEM139 4.3 22.0 1.0
C2B B:HEM139 4.3 23.0 1.0
C2D B:HEM139 4.3 25.9 1.0
C3A B:HEM139 4.3 20.9 1.0
C3D B:HEM139 4.3 26.7 1.0
C2A B:HEM139 4.3 22.5 1.0
ND1 B:HIS89 4.4 26.2 1.0
CG B:HIS89 4.4 27.8 1.0
CG2 B:VAL59 4.6 14.5 1.0
NE2 B:HIS55 4.7 24.1 1.0
XE B:XE140 4.7 51.8 0.3
CE B:MET86 4.9 25.7 1.0

Reference:

V.De Serrano, S.Franzen. Structural Evidence For Stabilization of Inhibitor Binding By A Protein Cavity in the Dehaloperoxidase-Hemoglobin From Amphitrite Ornata. Biopolymers V. 98 27 2012.
ISSN: ISSN 0006-3525
PubMed: 23325557
DOI: 10.1002/BIP.21674
Page generated: Sun Dec 13 15:16:03 2020

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