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Iron in PDB 3d19: Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus

Protein crystallography data

The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19 was solved by J.B.Bonanno, Y.Patskovsky, J.Freeman, K.T.Bain, S.Chang, S.Ozyurt, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.825, 136.378, 87.060, 90.00, 102.84, 90.00
R / Rfree (%) 20.6 / 26.8

Other elements in 3d19:

The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus (pdb code 3d19). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3d19

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Iron binding site 1 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:41.7
occ:1.00
OE2 A:GLU259 2.1 38.5 1.0
OE1 A:GLU128 2.1 47.1 1.0
NE2 A:HIS37 2.3 39.0 1.0
NE2 A:HIS255 2.3 35.2 1.0
O A:HOH327 2.4 42.1 1.0
CD A:GLU128 3.0 45.8 1.0
MG A:MG301 3.0 31.0 1.0
CD A:GLU259 3.1 37.5 1.0
CE1 A:HIS37 3.2 40.8 1.0
CD2 A:HIS255 3.2 37.4 1.0
OE2 A:GLU128 3.2 49.5 1.0
CD2 A:HIS37 3.3 37.4 1.0
CE1 A:HIS255 3.3 41.1 1.0
OE1 A:GLU259 3.5 40.0 1.0
CG2 A:ILE33 3.6 27.8 1.0
ND1 A:HIS37 4.3 40.4 1.0
CG A:HIS255 4.4 35.6 1.0
CG A:HIS37 4.4 37.6 1.0
CG A:GLU128 4.4 38.5 1.0
CG A:GLU259 4.4 36.1 1.0
ND1 A:HIS255 4.4 37.7 1.0
CD1 A:ILE33 4.6 26.1 1.0
NE2 A:HIS124 4.7 27.7 1.0
CD2 A:HIS124 4.9 28.7 1.0
CB A:ILE33 4.9 31.1 1.0
CB A:GLU128 4.9 36.8 1.0
NE2 A:HIS165 4.9 37.2 1.0

Iron binding site 2 out of 6 in 3d19

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Iron binding site 2 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:42.1
occ:1.00
OE2 B:GLU259 2.1 31.6 1.0
OE1 B:GLU128 2.1 36.0 1.0
NE2 B:HIS37 2.2 30.4 1.0
NE2 B:HIS255 2.3 38.8 1.0
O B:HOH341 2.6 43.8 1.0
MG B:MG301 3.0 37.2 1.0
CD B:GLU128 3.0 34.1 1.0
CD B:GLU259 3.0 30.4 1.0
CE1 B:HIS37 3.1 33.1 1.0
OE2 B:GLU128 3.2 35.6 1.0
CE1 B:HIS255 3.2 37.0 1.0
OE1 B:GLU259 3.3 26.8 1.0
CD2 B:HIS37 3.3 33.4 1.0
CD2 B:HIS255 3.3 38.6 1.0
CG2 B:ILE33 3.4 32.7 1.0
ND1 B:HIS37 4.3 32.6 1.0
ND1 B:HIS255 4.4 38.2 1.0
CG B:GLU259 4.4 32.0 1.0
CG B:HIS37 4.4 34.5 1.0
CG B:HIS255 4.4 39.1 1.0
CG B:GLU128 4.4 32.9 1.0
NE2 B:HIS124 4.5 33.6 1.0
CD2 B:HIS124 4.6 32.2 1.0
CB B:ILE33 4.8 30.5 1.0
NE2 B:HIS165 4.9 28.5 1.0
CB B:GLU128 4.9 34.4 1.0
CD1 B:ILE33 4.9 25.1 1.0

Iron binding site 3 out of 6 in 3d19

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Iron binding site 3 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:38.7
occ:1.00
OE1 C:GLU128 2.1 33.2 1.0
NE2 C:HIS37 2.1 37.2 1.0
OE2 C:GLU259 2.2 33.4 1.0
O C:HOH312 2.3 40.5 1.0
NE2 C:HIS255 2.3 28.5 1.0
CD C:GLU128 3.0 32.6 1.0
MG C:MG301 3.0 35.3 1.0
CE1 C:HIS37 3.1 34.8 1.0
CE1 C:HIS255 3.2 30.1 1.0
OE2 C:GLU128 3.2 33.5 1.0
CD2 C:HIS37 3.2 34.6 1.0
CD C:GLU259 3.2 30.4 1.0
CD2 C:HIS255 3.4 30.8 1.0
CG2 C:ILE33 3.5 30.4 1.0
OE1 C:GLU259 3.6 30.6 1.0
ND1 C:HIS37 4.2 33.0 1.0
CG C:HIS37 4.3 33.7 1.0
ND1 C:HIS255 4.3 27.4 1.0
CG C:GLU128 4.4 31.2 1.0
NE2 C:HIS124 4.4 37.0 1.0
CG C:HIS255 4.5 30.9 1.0
CD1 C:ILE33 4.5 28.7 1.0
CG C:GLU259 4.6 33.7 1.0
CD2 C:HIS124 4.6 35.4 1.0
CB C:GLU128 4.8 33.5 1.0
CB C:ILE33 4.8 33.0 1.0

Iron binding site 4 out of 6 in 3d19

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Iron binding site 4 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:47.0
occ:1.00
OE1 D:GLU128 2.1 53.3 1.0
O D:HOH310 2.2 39.7 1.0
OE2 D:GLU259 2.2 38.3 1.0
NE2 D:HIS255 2.2 41.7 1.0
NE2 D:HIS37 2.3 42.0 1.0
CD D:GLU259 3.0 39.5 1.0
MG D:MG301 3.0 35.9 1.0
CE1 D:HIS37 3.1 43.6 1.0
CD D:GLU128 3.1 48.7 1.0
OE1 D:GLU259 3.1 38.7 1.0
CD2 D:HIS255 3.1 43.1 1.0
OE2 D:GLU128 3.3 49.5 1.0
CE1 D:HIS255 3.3 39.8 1.0
CD2 D:HIS37 3.4 42.5 1.0
CG2 D:ILE33 3.6 38.8 1.0
ND1 D:HIS37 4.3 43.6 1.0
CG D:HIS255 4.3 39.5 1.0
ND1 D:HIS255 4.4 40.6 1.0
CG D:GLU128 4.5 45.5 1.0
CG D:HIS37 4.5 44.4 1.0
CG D:GLU259 4.5 37.9 1.0
NE2 D:HIS124 4.5 45.3 1.0
CD2 D:HIS124 4.7 45.3 1.0
CD1 D:ILE33 4.8 39.0 1.0
CB D:GLU128 4.8 43.5 1.0
CB D:ILE33 4.8 40.9 1.0
CG2 D:THR125 5.0 40.2 1.0

Iron binding site 5 out of 6 in 3d19

Go back to Iron Binding Sites List in 3d19
Iron binding site 5 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:53.8
occ:1.00
OE1 E:GLU128 2.0 45.0 1.0
OE2 E:GLU259 2.1 55.5 1.0
NE2 E:HIS255 2.2 50.1 1.0
NE2 E:HIS37 2.3 43.9 1.0
O E:HOH308 2.6 43.6 1.0
CD E:GLU128 2.8 44.5 1.0
MG E:MG301 2.9 40.2 1.0
OE2 E:GLU128 3.0 44.6 1.0
CD E:GLU259 3.1 55.1 1.0
CE1 E:HIS37 3.1 42.4 1.0
CE1 E:HIS255 3.1 50.9 1.0
CD2 E:HIS255 3.2 51.4 1.0
OE1 E:GLU259 3.3 58.0 1.0
CD2 E:HIS37 3.4 44.4 1.0
CG2 E:ILE33 3.5 46.9 1.0
CG E:GLU128 4.3 45.3 1.0
ND1 E:HIS255 4.3 51.4 1.0
ND1 E:HIS37 4.3 43.6 1.0
CG E:HIS255 4.4 50.9 1.0
CG E:GLU259 4.5 52.5 1.0
CG E:HIS37 4.5 45.3 1.0
NE2 E:HIS124 4.6 39.8 1.0
CD2 E:HIS124 4.7 41.0 1.0
CB E:GLU128 4.7 45.5 1.0
CB E:ILE33 4.9 47.9 1.0
CD1 E:ILE33 5.0 42.5 1.0
NE2 E:HIS165 5.0 42.6 1.0

Iron binding site 6 out of 6 in 3d19

Go back to Iron Binding Sites List in 3d19
Iron binding site 6 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe302

b:45.1
occ:1.00
NE2 F:HIS37 2.1 38.7 1.0
OE2 F:GLU259 2.2 36.8 1.0
OE1 F:GLU128 2.2 44.3 1.0
O F:HOH316 2.3 52.0 1.0
NE2 F:HIS255 2.4 43.1 1.0
CE1 F:HIS37 2.8 38.8 1.0
CD F:GLU128 3.0 42.8 1.0
MG F:MG301 3.1 36.4 1.0
CD F:GLU259 3.2 39.0 1.0
OE2 F:GLU128 3.2 43.2 1.0
CD2 F:HIS37 3.2 37.4 1.0
CD2 F:HIS255 3.4 42.6 1.0
OE1 F:GLU259 3.4 43.7 1.0
CE1 F:HIS255 3.4 43.3 1.0
CG2 F:ILE33 3.6 41.9 1.0
ND1 F:HIS37 4.0 40.0 1.0
CG F:HIS37 4.3 39.8 1.0
CG F:GLU128 4.5 42.0 1.0
NE2 F:HIS124 4.5 38.1 1.0
ND1 F:HIS255 4.5 39.3 1.0
CG F:HIS255 4.5 40.4 1.0
CG F:GLU259 4.6 41.3 1.0
CD2 F:HIS124 4.6 38.1 1.0
CD1 F:ILE33 4.7 42.6 1.0
CB F:ILE33 4.8 43.3 1.0
CB F:GLU128 4.9 42.5 1.0
CG2 F:THR125 5.0 38.9 1.0

Reference:

J.B.Bonanno, Y.Patskovsky, J.Freeman, K.T.Bain, S.Chang, S.Ozyurt, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus. To Be Published.
Page generated: Sun Aug 4 08:41:10 2024

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