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Iron in PDB 4xgs: Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin

Enzymatic activity of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin

All present enzymatic activity of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin, PDB code: 4xgs was solved by S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.62 / 2.25
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 129.025, 129.025, 172.750, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 18.3

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin (pdb code 4xgs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin, PDB code: 4xgs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4xgs

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Iron binding site 1 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:42.8
occ:1.00
 FE1 A:OFO201 0.0 42.8 1.0
O A:OFO201 2.0 30.6 1.0
OE2 A:GLU50 2.0 38.8 1.0
OE1 A:GLU130 2.2 41.9 1.0
OE1 A:GLU94 2.2 31.3 1.0
OE2 A:GLU94 2.6 28.8 1.0
CD A:GLU94 2.7 31.4 1.0
CD A:GLU50 2.9 35.2 1.0
CD A:GLU130 3.2 38.0 1.0
OE1 A:GLU50 3.2 30.3 1.0
FE2 A:OFO201 3.4 27.0 1.0
CG A:GLU130 3.5 33.8 1.0
NE2 A:HIS46 3.8 36.6 1.0
OE1 A:GLN127 4.0 28.7 1.0
CG A:GLU94 4.2 30.4 1.0
CE1 A:HIS53 4.2 32.5 1.0
CB A:GLU130 4.2 32.9 1.0
CG A:GLU50 4.3 31.5 1.0
OE2 A:GLU130 4.3 43.9 1.0
OH A:TYR24 4.3 39.2 1.0
CD1 A:ILE97 4.4 26.1 1.0
ND1 A:HIS53 4.4 34.8 1.0
CD2 A:HIS46 4.5 35.9 1.0
CE2 A:TYR24 4.5 35.4 1.0
NE2 A:GLN127 4.8 30.3 1.0
CD A:GLN127 4.8 31.3 1.0
OH A:OFO201 4.9 24.4 1.0
CZ A:TYR24 4.9 41.8 1.0
CE1 A:HIS46 4.9 38.3 1.0

Iron binding site 2 out of 12 in 4xgs

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Iron binding site 2 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:27.0
occ:1.00
 FE2 A:OFO201 0.0 27.0 1.0
O A:OFO201 2.0 30.6 1.0
OE1 A:GLU50 2.1 30.3 1.0
OE2 A:GLU17 2.1 31.0 1.0
ND1 A:HIS53 2.1 34.8 1.0
OH A:OFO201 2.3 24.4 1.0
CD A:GLU17 2.9 27.9 1.0
CE1 A:HIS53 3.0 32.5 1.0
CD A:GLU50 3.1 35.2 1.0
CG A:HIS53 3.2 30.0 1.0
OE1 A:GLU17 3.2 31.2 1.0
FE1 A:OFO201 3.4 42.8 1.0
OE2 A:GLU50 3.5 38.8 1.0
CB A:HIS53 3.6 29.5 1.0
OE1 A:GLN127 3.8 28.7 1.0
NE2 A:HIS53 4.2 34.4 1.0
CG A:GLU17 4.3 27.0 1.0
CD2 A:HIS53 4.3 32.2 1.0
CG A:GLU50 4.4 31.5 1.0
CD1 A:ILE97 4.5 26.1 1.0
CA A:GLU50 4.5 27.2 1.0
CG2 A:ILE97 4.5 24.9 1.0
CB A:GLU50 4.7 29.0 1.0
CB A:GLU17 4.7 26.8 1.0
O A:GLU50 4.9 25.9 1.0
CD A:GLN127 4.9 31.3 1.0

Iron binding site 3 out of 12 in 4xgs

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Iron binding site 3 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:37.6
occ:1.00
 FE1 B:OFO201 0.0 37.6 1.0
O B:OFO201 1.9 31.8 1.0
OE2 B:GLU50 2.0 32.3 1.0
OE1 B:GLU130 2.1 39.8 1.0
OE1 B:GLU94 2.1 32.5 1.0
OE2 B:GLU94 2.6 27.2 1.0
CD B:GLU94 2.7 30.2 1.0
CD B:GLU50 2.9 35.3 1.0
CD B:GLU130 3.1 37.3 1.0
OE1 B:GLU50 3.2 30.7 1.0
FE2 B:OFO201 3.4 25.0 1.0
CG B:GLU130 3.6 35.4 1.0
NE2 B:HIS46 3.8 36.0 1.0
OE1 B:GLN127 3.9 26.4 1.0
CG B:GLU94 4.1 28.4 1.0
OE2 B:GLU130 4.2 49.6 1.0
CG B:GLU50 4.2 31.0 1.0
CB B:GLU130 4.2 34.2 1.0
CE1 B:HIS53 4.3 28.6 1.0
CD1 B:ILE97 4.3 27.5 1.0
CD2 B:HIS46 4.3 37.8 1.0
ND1 B:HIS53 4.4 30.4 1.0
OH B:TYR24 4.4 42.0 1.0
CE2 B:TYR24 4.5 36.2 1.0
NE2 B:GLN127 4.7 28.1 1.0
CD B:GLN127 4.7 29.4 1.0
OH B:OFO201 4.8 24.9 1.0
CE1 B:HIS46 4.9 39.2 1.0
OE2 B:GLU17 5.0 27.5 1.0
CZ B:TYR24 5.0 43.5 1.0

Iron binding site 4 out of 12 in 4xgs

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Iron binding site 4 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:25.0
occ:1.00
 FE2 B:OFO201 0.0 25.0 1.0
OE2 B:GLU17 2.0 27.5 1.0
O B:OFO201 2.0 31.8 1.0
OE1 B:GLU50 2.1 30.7 1.0
ND1 B:HIS53 2.2 30.4 1.0
OH B:OFO201 2.3 24.9 1.0
CD B:GLU17 2.9 29.6 1.0
CE1 B:HIS53 3.1 28.6 1.0
CG B:HIS53 3.2 26.9 1.0
CD B:GLU50 3.2 35.3 1.0
OE1 B:GLU17 3.3 28.6 1.0
FE1 B:OFO201 3.4 37.6 1.0
CB B:HIS53 3.5 29.3 1.0
OE2 B:GLU50 3.6 32.3 1.0
OE1 B:GLN127 3.7 26.4 1.0
NE2 B:HIS53 4.2 29.7 1.0
CD2 B:HIS53 4.3 28.2 1.0
CG B:GLU17 4.3 28.0 1.0
CD1 B:ILE97 4.5 27.5 1.0
CG B:GLU50 4.5 31.0 1.0
CA B:GLU50 4.6 28.4 1.0
CG2 B:ILE97 4.6 25.3 1.0
OE1 B:GLU130 4.6 39.8 1.0
CB B:GLU17 4.7 27.8 1.0
CB B:GLU50 4.8 29.4 1.0
CD B:GLN127 4.8 29.4 1.0
O B:GLU50 5.0 27.8 1.0
CA B:HIS53 5.0 29.8 1.0

Iron binding site 5 out of 12 in 4xgs

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Iron binding site 5 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:39.7
occ:1.00
 FE1 C:OFO201 0.0 39.7 1.0
O C:OFO201 1.8 31.7 1.0
OE2 C:GLU50 1.9 37.7 1.0
OE1 C:GLU130 2.0 37.5 1.0
OE1 C:GLU94 2.2 30.3 1.0
OE2 C:GLU94 2.7 29.1 1.0
CD C:GLU94 2.7 27.7 1.0
CD C:GLU50 2.8 34.8 1.0
OE1 C:GLU50 3.1 28.7 1.0
CD C:GLU130 3.2 37.3 1.0
FE2 C:OFO201 3.4 26.1 1.0
CG C:GLU130 3.7 37.3 1.0
NE2 C:HIS46 3.9 34.0 1.0
OE1 C:GLN127 4.1 28.2 1.0
CG C:GLU50 4.1 33.3 1.0
CE1 C:HIS53 4.2 32.6 1.0
OE2 C:GLU130 4.2 41.4 1.0
CG C:GLU94 4.2 28.0 1.0
CD1 C:ILE97 4.2 32.2 1.0
CB C:GLU130 4.3 34.8 1.0
ND1 C:HIS53 4.3 30.6 1.0
CD2 C:HIS46 4.4 32.0 1.0
CE2 C:TYR24 4.4 39.8 1.0
OH C:TYR24 4.4 45.4 1.0
NE2 C:GLN127 4.7 32.2 1.0
OH C:OFO201 4.8 23.8 1.0
CD C:GLN127 4.8 27.7 1.0
CZ C:TYR24 4.9 47.8 1.0
CE2 C:PHE134 5.0 29.7 1.0

Iron binding site 6 out of 12 in 4xgs

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Iron binding site 6 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:26.1
occ:1.00
 FE2 C:OFO201 0.0 26.1 1.0
OE2 C:GLU17 2.0 28.0 1.0
O C:OFO201 2.0 31.7 1.0
OE1 C:GLU50 2.1 28.7 1.0
ND1 C:HIS53 2.1 30.6 1.0
OH C:OFO201 2.2 23.8 1.0
CD C:GLU17 3.0 29.1 1.0
CE1 C:HIS53 3.0 32.6 1.0
CG C:HIS53 3.1 28.4 1.0
CD C:GLU50 3.2 34.8 1.0
OE1 C:GLU17 3.3 26.4 1.0
FE1 C:OFO201 3.4 39.7 1.0
CB C:HIS53 3.5 28.3 1.0
OE2 C:GLU50 3.6 37.7 1.0
OE1 C:GLN127 3.8 28.2 1.0
NE2 C:HIS53 4.1 29.4 1.0
CD2 C:HIS53 4.2 28.0 1.0
CG C:GLU17 4.3 28.6 1.0
CG2 C:ILE97 4.4 27.4 1.0
CD1 C:ILE97 4.5 32.2 1.0
CG C:GLU50 4.5 33.3 1.0
CA C:GLU50 4.5 28.2 1.0
OE1 C:GLU130 4.6 37.5 1.0
CB C:GLU50 4.7 32.5 1.0
CB C:GLU17 4.7 29.0 1.0
CD C:GLN127 4.9 27.7 1.0
O C:GLU50 4.9 26.7 1.0
CA C:HIS53 5.0 27.5 1.0

Iron binding site 7 out of 12 in 4xgs

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Iron binding site 7 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:41.3
occ:1.00
 FE1 D:OFO201 0.0 41.3 1.0
O D:OFO201 1.8 33.1 1.0
OE2 D:GLU130 1.9 44.2 1.0
OE2 D:GLU50 1.9 32.9 1.0
OE1 D:GLU94 2.2 29.9 1.0
OE2 D:GLU94 2.6 32.8 1.0
CD D:GLU94 2.7 29.3 1.0
CD D:GLU50 2.8 33.6 1.0
CD D:GLU130 3.0 40.2 1.0
OE1 D:GLU50 3.2 31.2 1.0
FE2 D:OFO201 3.4 27.9 1.0
CG D:GLU130 3.5 35.6 1.0
NE2 D:HIS46 3.9 34.4 1.0
OE1 D:GLN127 4.0 28.3 1.0
OE1 D:GLU130 4.0 47.9 1.0
CE1 D:HIS53 4.1 33.3 1.0
CG D:GLU50 4.1 32.6 1.0
CG D:GLU94 4.2 26.5 1.0
CB D:GLU130 4.2 32.9 1.0
ND1 D:HIS53 4.3 30.7 1.0
OH D:TYR24 4.3 40.5 1.0
CD1 D:ILE97 4.3 29.4 1.0
CD2 D:HIS46 4.3 34.0 1.0
CE2 D:TYR24 4.5 41.0 1.0
NE2 D:GLN127 4.7 29.9 1.0
OH D:OFO201 4.8 28.5 1.0
CD D:GLN127 4.8 29.7 1.0
CZ D:TYR24 4.9 44.8 1.0

Iron binding site 8 out of 12 in 4xgs

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Iron binding site 8 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:27.9
occ:1.00
 FE2 D:OFO201 0.0 27.9 1.0
ND1 D:HIS53 2.0 30.7 1.0
OE1 D:GLU50 2.0 31.2 1.0
OE2 D:GLU17 2.1 30.8 1.0
O D:OFO201 2.1 33.1 1.0
OH D:OFO201 2.2 28.5 1.0
CE1 D:HIS53 2.9 33.3 1.0
CD D:GLU17 3.0 29.5 1.0
CD D:GLU50 3.0 33.6 1.0
CG D:HIS53 3.1 28.7 1.0
OE1 D:GLU17 3.3 30.1 1.0
FE1 D:OFO201 3.4 41.3 1.0
CB D:HIS53 3.4 28.6 1.0
OE2 D:GLU50 3.5 32.9 1.0
OE1 D:GLN127 3.8 28.3 1.0
NE2 D:HIS53 4.1 29.3 1.0
CD2 D:HIS53 4.1 28.6 1.0
CG D:GLU17 4.3 28.8 1.0
CG D:GLU50 4.4 32.6 1.0
CG2 D:ILE97 4.5 27.8 1.0
CD1 D:ILE97 4.5 29.4 1.0
OE2 D:GLU130 4.6 44.2 1.0
CA D:GLU50 4.6 28.8 1.0
CB D:GLU50 4.6 30.2 1.0
CB D:GLU17 4.8 27.5 1.0
CD D:GLN127 4.9 29.7 1.0
O D:GLU50 4.9 29.6 1.0
CA D:HIS53 5.0 27.8 1.0

Iron binding site 9 out of 12 in 4xgs

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Iron binding site 9 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:37.9
occ:1.00
 FE1 E:OFO201 0.0 37.9 1.0
OE2 E:GLU50 1.9 28.7 1.0
O E:OFO201 2.0 31.8 1.0
OE1 E:GLU130 2.0 40.6 1.0
OE1 E:GLU94 2.1 31.0 1.0
OE2 E:GLU94 2.6 29.4 1.0
CD E:GLU94 2.7 27.7 1.0
CD E:GLU50 2.9 30.1 1.0
CD E:GLU130 3.1 41.3 1.0
OE1 E:GLU50 3.1 28.0 1.0
FE2 E:OFO201 3.4 26.8 1.0
CG E:GLU130 3.5 33.6 1.0
NE2 E:HIS46 3.8 33.4 1.0
OE1 E:GLN127 4.0 27.4 1.0
CG E:GLU94 4.2 25.7 1.0
OE2 E:GLU130 4.2 48.5 1.0
CB E:GLU130 4.2 29.8 1.0
CG E:GLU50 4.2 30.5 1.0
CE1 E:HIS53 4.2 29.8 1.0
CD1 E:ILE97 4.3 26.9 1.0
OH E:TYR24 4.3 41.2 1.0
ND1 E:HIS53 4.4 29.1 1.0
CD2 E:HIS46 4.4 37.7 1.0
CE2 E:TYR24 4.4 37.5 1.0
NE2 E:GLN127 4.8 25.6 1.0
CD E:GLN127 4.8 23.5 1.0
CZ E:TYR24 4.8 41.6 1.0
OH E:OFO201 4.9 23.3 1.0
CE1 E:HIS46 4.9 34.1 1.0
CE2 E:PHE134 5.0 28.3 1.0

Iron binding site 10 out of 12 in 4xgs

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Iron binding site 10 out of 12 in the Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure Analysis of Novel Iron Uptake Mechanism of Gram- Negative Bacterial Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:26.8
occ:1.00
 FE2 E:OFO201 0.0 26.8 1.0
O E:OFO201 1.9 31.8 1.0
OE1 E:GLU17 2.1 24.8 1.0
OE1 E:GLU50 2.1 28.0 1.0
ND1 E:HIS53 2.1 29.1 1.0
OH E:OFO201 2.3 23.3 1.0
CD E:GLU17 2.9 27.6 1.0
CE1 E:HIS53 3.1 29.8 1.0
CG E:HIS53 3.1 29.3 1.0
CD E:GLU50 3.2 30.1 1.0
OE2 E:GLU17 3.3 27.1 1.0
CB E:HIS53 3.4 25.9 1.0
FE1 E:OFO201 3.4 37.9 1.0
OE2 E:GLU50 3.6 28.7 1.0
OE1 E:GLN127 3.8 27.4 1.0
NE2 E:HIS53 4.2 29.2 1.0
CD2 E:HIS53 4.3 26.0 1.0
CG E:GLU17 4.3 24.8 1.0
CG2 E:ILE97 4.4 27.6 1.0
CD1 E:ILE97 4.5 26.9 1.0
CG E:GLU50 4.5 30.5 1.0
CA E:GLU50 4.6 28.6 1.0
OE1 E:GLU130 4.6 40.6 1.0
CB E:GLU17 4.7 22.9 1.0
CB E:GLU50 4.7 29.1 1.0
CA E:HIS53 4.9 26.9 1.0
O E:GLU50 4.9 25.7 1.0
CD E:GLN127 4.9 23.5 1.0

Reference:

S.Kim, J.H.Lee, J.H.Seok, Y.H.Park, S.W.Jung, A.E.Cho, C.Lee, M.S.Chung, K.H.Kim. Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins From Gram-Negative Bacteria J. Mol. Biol. V. 428 5007 2016.
ISSN: ESSN 1089-8638
PubMed: 27777002
DOI: 10.1016/J.JMB.2016.10.022
Page generated: Mon Aug 5 15:32:38 2024

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