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Iron in PDB 3g4y: Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity

Protein crystallography data

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity, PDB code: 3g4y was solved by J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.23 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.190, 43.810, 83.290, 90.00, 121.77, 90.00
R / Rfree (%) 18.2 / 21.1

Other elements in 3g4y:

The structure of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity (pdb code 3g4y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity, PDB code: 3g4y:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3g4y

Go back to Iron Binding Sites List in 3g4y
Iron binding site 1 out of 2 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe147

b:14.5
occ:1.00
FE A:HEM147 0.0 14.5 1.0
C A:CMO148 1.9 12.3 1.0
NB A:HEM147 2.0 12.9 1.0
NC A:HEM147 2.0 10.9 1.0
ND A:HEM147 2.0 13.5 1.0
NA A:HEM147 2.0 12.8 1.0
NE2 A:HIS101 2.1 12.4 1.0
C1A A:HEM147 3.1 13.4 1.0
C4D A:HEM147 3.1 12.6 1.0
C4B A:HEM147 3.1 14.2 1.0
C1C A:HEM147 3.1 10.6 1.0
C4C A:HEM147 3.1 13.4 1.0
C1D A:HEM147 3.1 15.1 1.0
C1B A:HEM147 3.1 15.8 1.0
CE1 A:HIS101 3.1 12.7 1.0
C4A A:HEM147 3.1 15.6 1.0
CD2 A:HIS101 3.1 14.9 1.0
O A:CMO148 3.1 16.8 1.0
CHA A:HEM147 3.4 14.7 1.0
CHC A:HEM147 3.4 14.3 1.0
CHD A:HEM147 3.4 13.5 1.0
CHB A:HEM147 3.5 15.0 1.0
ND1 A:HIS101 4.2 15.1 1.0
CG A:HIS101 4.2 13.7 1.0
C3D A:HEM147 4.3 15.4 1.0
C2A A:HEM147 4.3 14.5 1.0
C2D A:HEM147 4.3 14.7 1.0
C2B A:HEM147 4.3 15.5 1.0
C2C A:HEM147 4.3 13.2 1.0
C3C A:HEM147 4.3 12.6 1.0
C3A A:HEM147 4.3 14.8 1.0
C3B A:HEM147 4.3 15.0 1.0
CE1 A:HIS69 4.8 18.9 1.0
CE1 A:PHE111 5.0 17.5 1.0

Iron binding site 2 out of 2 in 3g4y

Go back to Iron Binding Sites List in 3g4y
Iron binding site 2 out of 2 in the Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ligand Migration and Cavities Within Scapharca Dimeric Hemoglobin: Wild Type with Co Bound to Heme and Chloromethyl Benzene Bound to the XE4 Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe147

b:14.0
occ:1.00
FE B:HEM147 0.0 14.0 1.0
C B:CMO148 1.9 13.2 1.0
NB B:HEM147 2.0 13.4 1.0
NC B:HEM147 2.0 12.5 1.0
ND B:HEM147 2.0 13.1 1.0
NA B:HEM147 2.0 14.8 1.0
NE2 B:HIS101 2.1 15.0 1.0
C4B B:HEM147 3.0 14.2 1.0
C1B B:HEM147 3.1 16.0 1.0
C1C B:HEM147 3.1 12.5 1.0
C4D B:HEM147 3.1 13.9 1.0
CD2 B:HIS101 3.1 12.8 1.0
C4C B:HEM147 3.1 11.2 1.0
C1A B:HEM147 3.1 14.3 1.0
C4A B:HEM147 3.1 13.8 1.0
C1D B:HEM147 3.1 14.1 1.0
CE1 B:HIS101 3.1 14.0 1.0
O B:CMO148 3.1 17.0 1.0
CHC B:HEM147 3.4 13.9 1.0
CHA B:HEM147 3.4 13.4 1.0
CHB B:HEM147 3.4 16.2 1.0
CHD B:HEM147 3.5 12.4 1.0
ND1 B:HIS101 4.2 14.2 1.0
CG B:HIS101 4.2 13.2 1.0
C2C B:HEM147 4.3 12.5 1.0
C2B B:HEM147 4.3 16.8 1.0
C2A B:HEM147 4.3 15.3 1.0
C3B B:HEM147 4.3 15.5 1.0
C3D B:HEM147 4.3 14.1 1.0
C3A B:HEM147 4.3 15.8 1.0
C3C B:HEM147 4.3 12.6 1.0
C2D B:HEM147 4.3 14.9 1.0
CE1 B:HIS69 4.8 14.9 1.0
CD1 B:LEU73 4.9 20.9 1.0

Reference:

J.E.Knapp, R.Pahl, J.Cohen, J.C.Nichols, K.Schulten, Q.H.Gibson, V.Srajer, W.E.Royer. Ligand Migration and Cavities Within Scapharca Dimeric Hbi: Studies By Time-Resolved Crystallo-Graphy, Xe Binding, and Computational Analysis. Structure V. 17 1494 2009.
ISSN: ISSN 0969-2126
PubMed: 19913484
DOI: 10.1016/J.STR.2009.09.004
Page generated: Sun Dec 13 15:06:12 2020

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