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Iron in PDB 3mvc: High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans

Protein crystallography data

The structure of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans, PDB code: 3mvc was solved by J.Yoon, M.A.Herzik Jr, M.B.Winter, R.Tran, C.Olea Jr, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.70 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.582, 76.347, 62.696, 90.00, 91.76, 90.00
R / Rfree (%) 16.1 / 20.5

Other elements in 3mvc:

The structure of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans also contains other interesting chemical elements:

Praseodymium (Pr) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans (pdb code 3mvc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans, PDB code: 3mvc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3mvc

Go back to Iron Binding Sites List in 3mvc
Iron binding site 1 out of 2 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:16.2
occ:1.00
FE A:HEM500 0.0 16.2 1.0
NE2 A:HIS286 2.0 15.7 1.0
NC A:HEM500 2.0 17.0 1.0
NE2 A:HIS254 2.0 16.5 1.0
ND A:HEM500 2.0 18.5 1.0
NB A:HEM500 2.1 14.1 1.0
NA A:HEM500 2.1 15.6 1.0
CE1 A:HIS286 2.9 15.2 1.0
CE1 A:HIS254 3.0 18.0 1.0
C4C A:HEM500 3.0 20.8 1.0
C1D A:HEM500 3.0 17.4 1.0
CD2 A:HIS254 3.0 17.0 1.0
CD2 A:HIS286 3.0 14.8 1.0
C1C A:HEM500 3.1 15.5 1.0
C1B A:HEM500 3.1 16.3 1.0
C4D A:HEM500 3.1 19.6 1.0
C4A A:HEM500 3.1 17.0 1.0
C4B A:HEM500 3.1 15.7 1.0
C1A A:HEM500 3.1 20.4 1.0
CHD A:HEM500 3.4 20.0 1.0
CHB A:HEM500 3.4 15.2 1.0
CHC A:HEM500 3.5 14.8 1.0
CHA A:HEM500 3.5 21.3 1.0
ND1 A:HIS286 4.0 15.8 1.0
ND1 A:HIS254 4.1 18.7 1.0
CG A:HIS286 4.1 15.0 1.0
CG A:HIS254 4.2 16.1 1.0
C3C A:HEM500 4.2 15.6 1.0
C2C A:HEM500 4.3 14.2 1.0
C2D A:HEM500 4.3 25.1 1.0
C2B A:HEM500 4.3 20.8 1.0
C3D A:HEM500 4.3 25.4 1.0
C3B A:HEM500 4.3 17.0 1.0
C3A A:HEM500 4.3 20.3 1.0
C2A A:HEM500 4.3 20.8 1.0

Iron binding site 2 out of 2 in 3mvc

Go back to Iron Binding Sites List in 3mvc
Iron binding site 2 out of 2 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:16.4
occ:1.00
FE B:HEM500 0.0 16.4 1.0
NC B:HEM500 2.0 15.4 1.0
NE2 B:HIS286 2.0 17.4 1.0
ND B:HEM500 2.0 17.9 1.0
NA B:HEM500 2.1 18.8 1.0
NB B:HEM500 2.1 14.5 1.0
NE2 B:HIS254 2.1 17.5 1.0
CD2 B:HIS286 2.9 17.8 1.0
CD2 B:HIS254 3.0 13.9 1.0
C4D B:HEM500 3.0 19.5 1.0
C1C B:HEM500 3.1 17.3 1.0
C4C B:HEM500 3.1 18.4 1.0
C1D B:HEM500 3.1 18.9 1.0
C4B B:HEM500 3.1 15.8 1.0
C1A B:HEM500 3.1 21.6 1.0
CE1 B:HIS286 3.1 18.4 1.0
C1B B:HEM500 3.1 16.2 1.0
CE1 B:HIS254 3.1 21.4 1.0
C4A B:HEM500 3.1 18.4 1.0
CHA B:HEM500 3.4 21.4 1.0
CHC B:HEM500 3.4 15.6 1.0
CHD B:HEM500 3.4 19.1 1.0
CHB B:HEM500 3.5 18.1 1.0
CG B:HIS286 4.1 14.4 1.0
ND1 B:HIS286 4.1 15.8 1.0
CG B:HIS254 4.2 13.8 1.0
ND1 B:HIS254 4.2 18.3 1.0
C2C B:HEM500 4.3 19.4 1.0
C3C B:HEM500 4.3 18.1 1.0
C3D B:HEM500 4.3 24.3 1.0
C2D B:HEM500 4.3 23.7 1.0
C3B B:HEM500 4.3 15.8 1.0
C2A B:HEM500 4.3 22.5 1.0
C2B B:HEM500 4.3 19.6 1.0
C3A B:HEM500 4.3 22.8 1.0

Reference:

J.Yoon, M.A.Herzik, M.B.Winter, R.Tran, C.Olea, M.A.Marletta. Structure and Properties of A Bis-Histidyl Ligated Globin From Caenorhabditis Elegans. Biochemistry V. 49 5662 2010.
ISSN: ISSN 0006-2960
PubMed: 20518498
DOI: 10.1021/BI100710A
Page generated: Sun Dec 13 15:12:55 2020

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