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Iron in PDB 3fvb: Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis

Protein crystallography data

The structure of Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis, PDB code: 3fvb was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.81
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 174.810, 174.810, 174.810, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.5

Other elements in 3fvb:

The structure of Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis (pdb code 3fvb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis, PDB code: 3fvb:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3fvb

Go back to Iron Binding Sites List in 3fvb
Iron binding site 1 out of 3 in the Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe163

b:32.5
occ:1.00
NC A:HEM162 2.1 36.6 1.0
NB A:HEM162 2.2 36.9 1.0
NA A:HEM162 2.2 40.5 1.0
ND A:HEM162 2.2 40.3 1.0
SD A:MET52 2.3 25.2 1.0
SD B:MET52 2.3 25.5 1.0
C1C A:HEM162 3.1 37.1 1.0
C4B A:HEM162 3.1 37.5 1.0
C4C A:HEM162 3.1 38.3 1.0
C1A A:HEM162 3.1 41.6 1.0
C4D A:HEM162 3.1 41.5 1.0
C1D A:HEM162 3.2 39.9 1.0
C4A A:HEM162 3.2 40.7 1.0
C1B A:HEM162 3.2 38.8 1.0
CE A:MET52 3.2 25.3 1.0
CE B:MET52 3.2 25.1 1.0
CHC A:HEM162 3.4 37.5 1.0
CHA A:HEM162 3.5 41.2 1.0
CHD A:HEM162 3.5 38.9 1.0
CHB A:HEM162 3.6 39.8 1.0
CG B:MET52 3.6 21.8 1.0
CG A:MET52 3.7 22.2 1.0
C2C A:HEM162 4.3 38.0 1.0
C3C A:HEM162 4.3 37.5 1.0
C3D A:HEM162 4.3 41.9 1.0
C2A A:HEM162 4.3 42.4 1.0
C3B A:HEM162 4.4 38.7 1.0
C2D A:HEM162 4.4 41.0 1.0
CB B:MET52 4.4 19.2 1.0
C3A A:HEM162 4.4 41.5 1.0
CB A:MET52 4.4 19.4 1.0
C2B A:HEM162 4.4 37.9 1.0

Iron binding site 2 out of 3 in 3fvb

Go back to Iron Binding Sites List in 3fvb
Iron binding site 2 out of 3 in the Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe164

b:41.5
occ:1.00
OE2 A:GLU127 2.0 27.8 1.0
OE1 A:GLU51 2.1 31.1 1.0
OE2 A:GLU18 2.2 24.7 1.0
ND1 A:HIS54 2.2 24.1 1.0
OE1 A:GLU18 2.4 23.1 1.0
N3 A:IMD171 2.5 33.0 1.0
CD A:GLU18 2.6 24.0 1.0
CE1 A:HIS54 3.0 26.2 1.0
CD A:GLU127 3.0 27.6 1.0
CD A:GLU51 3.3 31.2 1.0
C2 A:IMD171 3.3 35.0 1.0
CG A:HIS54 3.3 22.9 1.0
OE1 A:GLU127 3.4 29.3 1.0
C4 A:IMD171 3.6 35.5 1.0
CB A:HIS54 3.8 20.6 1.0
OE2 A:GLU51 3.9 38.6 1.0
CG A:GLU18 4.1 22.2 1.0
NE2 A:HIS54 4.2 25.3 1.0
O A:HOH351 4.3 40.7 1.0
CG A:GLU127 4.3 22.5 1.0
CG A:GLU51 4.4 24.1 1.0
CD2 A:HIS54 4.4 22.9 1.0
CB A:GLU51 4.4 21.2 1.0
OH A:TYR101 4.5 28.7 1.0
N1 A:IMD171 4.5 35.1 1.0
CA A:GLU51 4.6 20.5 1.0
CE2 A:TYR101 4.6 22.7 1.0
C5 A:IMD171 4.7 36.4 1.0

Iron binding site 3 out of 3 in 3fvb

Go back to Iron Binding Sites List in 3fvb
Iron binding site 3 out of 3 in the Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ferritin (Bacterioferritin) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe162

b:42.4
occ:1.00
OE2 B:GLU127 2.0 28.7 1.0
OE1 B:GLU51 2.1 30.9 1.0
ND1 B:HIS54 2.2 24.2 1.0
OE2 B:GLU18 2.2 25.4 1.0
OE1 B:GLU18 2.4 23.3 1.0
N3 B:IMD167 2.6 35.9 1.0
CD B:GLU18 2.6 23.8 1.0
CE1 B:HIS54 2.9 26.3 1.0
CD B:GLU127 3.0 27.8 1.0
CD B:GLU51 3.2 31.1 1.0
CG B:HIS54 3.3 23.1 1.0
OE1 B:GLU127 3.4 29.1 1.0
C2 B:IMD167 3.4 37.0 1.0
C4 B:IMD167 3.6 36.6 1.0
CB B:HIS54 3.8 20.9 1.0
OE2 B:GLU51 3.9 38.4 1.0
CG B:GLU18 4.1 21.8 1.0
NE2 B:HIS54 4.1 25.6 1.0
CG B:GLU51 4.3 23.1 1.0
CD2 B:HIS54 4.3 23.0 1.0
CG B:GLU127 4.4 23.1 1.0
O B:HOH350 4.4 37.2 1.0
CB B:GLU51 4.4 20.6 1.0
OH B:TYR101 4.4 29.8 1.0
CA B:GLU51 4.5 20.1 1.0
N1 B:IMD167 4.7 38.2 1.0
CE2 B:TYR101 4.7 24.5 1.0
C5 B:IMD167 4.8 38.1 1.0
CB B:GLU18 5.0 19.6 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), Seattle Structural Genomics Center For Infectious Disease (Ssgcid). N/A N/A.
Page generated: Sun Dec 13 15:05:59 2020

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