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Iron in PDB 3fpv: Crystal Structure of Hbps

Protein crystallography data

The structure of Crystal Structure of Hbps, PDB code: 3fpv was solved by D.Ortiz De Orue Lucana, G.Bogel, P.Zou, M.R.Groves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 2.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 152.522, 152.522, 152.522, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 26.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Hbps (pdb code 3fpv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Hbps, PDB code: 3fpv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3fpv

Go back to Iron Binding Sites List in 3fpv
Iron binding site 1 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe157

b:72.6
occ:1.00
 OE1 A:GLN75 3.1 64.8 1.0
OG A:SER79 3.3 64.5 1.0
O A:HOH385 3.4 45.9 1.0
O G:HOH850 3.4 47.1 1.0
CG A:GLN75 3.5 64.1 1.0
CB A:SER79 3.6 64.4 1.0
CB A:ALA135 3.6 67.2 1.0
CD A:GLN75 3.7 64.3 1.0
CD1 G:ILE110 3.8 64.3 1.0
CA A:SER76 3.9 63.9 1.0
CZ2 G:TRP90 4.2 64.5 1.0
N A:GLY136 4.2 67.6 1.0
CB A:SER76 4.3 63.9 1.0
O A:GLN75 4.4 64.1 1.0
N A:SER76 4.4 64.0 1.0
CG1 G:ILE110 4.5 64.7 1.0
CA A:ALA135 4.5 67.2 1.0
C A:GLN75 4.5 64.1 1.0
CA A:GLY136 4.5 67.8 1.0
CG2 G:ILE110 4.5 64.8 1.0
C A:ALA135 4.5 67.4 1.0
O A:HOH439 4.6 53.9 1.0
CB A:GLN75 4.9 64.1 1.0
CE2 G:TRP90 4.9 64.5 1.0
NE1 G:TRP90 4.9 64.4 1.0

Iron binding site 2 out of 8 in 3fpv

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Iron binding site 2 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe157

b:55.6
occ:1.00
 O B:HOH383 3.0 36.7 1.0
O F:HOH613 3.2 38.7 1.0
OE1 B:GLN75 3.2 64.0 1.0
OG B:SER79 3.3 64.4 1.0
CB B:ALA135 3.5 67.9 1.0
CG B:GLN75 3.5 64.0 1.0
CB B:SER79 3.6 64.3 1.0
CD B:GLN75 3.8 63.9 1.0
CD1 F:ILE110 3.8 63.8 1.0
CA B:SER76 4.0 64.2 1.0
CZ2 F:TRP90 4.1 64.2 1.0
N B:GLY136 4.3 68.4 1.0
CB B:SER76 4.3 64.2 1.0
CA B:ALA135 4.4 67.9 1.0
CA B:GLY136 4.5 68.6 1.0
C B:ALA135 4.5 68.1 1.0
CG1 F:ILE110 4.5 64.4 1.0
N B:SER76 4.5 64.1 1.0
O B:HOH557 4.6 38.4 1.0
CG2 F:ILE110 4.6 64.6 1.0
O B:GLN75 4.7 64.2 1.0
C B:GLN75 4.7 64.2 1.0
CE2 F:TRP90 4.9 64.2 1.0
CH2 F:TRP90 4.9 64.3 1.0
CB B:GLN75 4.9 64.2 1.0
NE1 F:TRP90 4.9 64.3 1.0

Iron binding site 3 out of 8 in 3fpv

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Iron binding site 3 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe157

b:77.6
occ:1.00
 OG C:SER79 3.2 65.3 1.0
OE1 C:GLN75 3.3 64.4 1.0
CG C:GLN75 3.4 64.1 1.0
CB C:SER79 3.5 65.0 1.0
CD1 D:ILE110 3.6 64.9 1.0
CD C:GLN75 3.8 64.2 1.0
CB C:ALA135 3.8 67.7 1.0
CA C:SER76 4.0 64.1 1.0
CZ2 D:TRP90 4.1 63.8 1.0
CG2 D:ILE110 4.3 64.8 1.0
CB C:SER76 4.3 64.0 1.0
CG1 D:ILE110 4.4 64.7 1.0
O C:HOH440 4.4 54.9 1.0
N C:GLY136 4.5 68.0 1.0
O C:GLN75 4.5 64.1 1.0
N C:SER76 4.5 64.1 1.0
C C:GLN75 4.5 64.1 1.0
CA C:GLY136 4.6 68.3 1.0
CA C:ALA135 4.6 67.7 1.0
CB C:GLN75 4.7 64.1 1.0
C C:ALA135 4.7 67.8 1.0
CE2 D:TRP90 4.8 63.9 1.0
NE1 D:TRP90 4.9 63.8 1.0
CH2 D:TRP90 4.9 63.8 1.0

Iron binding site 4 out of 8 in 3fpv

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Iron binding site 4 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe157

b:72.2
occ:1.00
 O D:HOH386 3.1 48.0 1.0
OG D:SER79 3.3 66.0 1.0
OE1 D:GLN75 3.3 64.5 1.0
CB D:SER79 3.5 65.6 1.0
CB D:ALA135 3.6 67.5 1.0
CG D:GLN75 3.6 64.2 1.0
CD1 B:ILE110 3.8 63.6 1.0
CD D:GLN75 3.9 64.3 1.0
CA D:SER76 4.0 64.8 1.0
CZ2 B:TRP90 4.3 64.7 1.0
CG1 B:ILE110 4.4 63.7 1.0
N D:GLY136 4.4 68.0 1.0
CA D:ALA135 4.4 67.5 1.0
CB D:SER76 4.5 64.8 1.0
CG2 B:ILE110 4.5 63.8 1.0
CA D:GLY136 4.5 68.2 1.0
O D:GLN75 4.6 64.6 1.0
C D:ALA135 4.6 67.7 1.0
N D:SER76 4.6 64.7 1.0
C D:GLN75 4.6 64.6 1.0
O D:HOH624 4.7 60.0 1.0
CB D:GLN75 5.0 64.4 1.0
NZ D:LYS83 5.0 65.2 1.0

Iron binding site 5 out of 8 in 3fpv

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Iron binding site 5 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe157

b:0.6
occ:1.00
 OE1 E:GLN75 3.2 69.1 1.0
OG E:SER79 3.4 70.1 1.0
CB E:ALA135 3.4 70.7 1.0
CG E:GLN75 3.7 69.7 1.0
CB E:SER79 3.7 69.8 1.0
CD E:GLN75 3.8 69.9 1.0
CA E:SER76 3.9 69.7 1.0
CD1 H:ILE110 4.0 62.2 1.0
CA E:GLY136 4.1 71.6 1.0
CB E:SER76 4.1 69.7 1.0
N E:GLY136 4.2 71.3 1.0
CA E:ALA135 4.2 70.7 1.0
C E:ALA135 4.3 71.0 1.0
N E:SER76 4.5 69.7 1.0
CZ2 H:TRP90 4.7 61.9 1.0
CG1 H:ILE110 4.7 62.3 1.0
C E:GLN75 4.7 69.6 1.0
O E:GLN75 4.7 69.6 1.0
CG2 H:ILE110 4.8 62.2 1.0
NZ E:LYS83 4.9 68.9 1.0
O E:ALA135 5.0 71.0 1.0
C E:SER76 5.0 69.7 1.0

Iron binding site 6 out of 8 in 3fpv

Go back to Iron Binding Sites List in 3fpv
Iron binding site 6 out of 8 in the Crystal Structure of Hbps


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 Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe158

b:99.5
occ:1.00
 OG G:SER79 3.2 64.9 1.0
CD1 E:ILE110 3.4 69.5 1.0
CG G:GLN75 3.6 64.7 1.0
CB G:SER79 3.6 64.9 1.0
CB G:ALA135 3.6 67.4 1.0
OE1 G:GLN75 3.6 64.5 1.0
CZ2 E:TRP90 3.8 66.5 1.0
O G:HOH1190 3.9 58.2 1.0
CD G:GLN75 4.1 64.6 1.0
CA G:SER76 4.3 64.9 1.0
N G:GLY136 4.4 67.8 1.0
CG1 E:ILE110 4.5 69.6 1.0
CH2 E:TRP90 4.5 66.5 1.0
CA G:ALA135 4.5 67.5 1.0
CG2 E:ILE110 4.5 69.8 1.0
CA G:GLY136 4.6 68.0 1.0
C G:ALA135 4.7 67.6 1.0
CB G:SER76 4.7 64.8 1.0
CE2 E:TRP90 4.7 66.6 1.0
NZ G:LYS83 4.7 64.3 1.0
O G:GLN75 4.7 64.8 1.0
C G:GLN75 4.8 64.8 1.0
N G:SER76 4.8 64.8 1.0
CB G:GLN75 4.9 64.8 1.0
NE1 E:TRP90 5.0 66.6 1.0

Iron binding site 7 out of 8 in 3fpv

Go back to Iron Binding Sites List in 3fpv
Iron binding site 7 out of 8 in the Crystal Structure of Hbps


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe157

b:69.7
occ:1.00
 O F:HOH705 3.0 48.1 1.0
OG F:SER79 3.1 64.2 1.0
OE1 F:GLN75 3.3 64.6 1.0
CB F:SER79 3.4 64.3 1.0
CG F:GLN75 3.5 64.4 1.0
CB F:ALA135 3.6 67.6 1.0
CD F:GLN75 3.8 64.5 1.0
CD1 C:ILE110 3.9 64.5 1.0
CA F:SER76 3.9 64.2 1.0
N F:GLY136 4.3 67.8 1.0
CA F:GLY136 4.3 67.8 1.0
CB F:SER76 4.3 64.2 1.0
O F:GLN75 4.4 64.3 1.0
CG1 C:ILE110 4.4 64.4 1.0
CA F:ALA135 4.4 67.7 1.0
N F:SER76 4.5 64.2 1.0
CZ2 C:TRP90 4.5 65.4 1.0
C F:ALA135 4.5 67.7 1.0
CG2 C:ILE110 4.5 64.5 1.0
C F:GLN75 4.5 64.3 1.0
CB F:GLN75 4.8 64.4 1.0
CA F:SER79 5.0 64.3 1.0
C F:SER76 5.0 64.2 1.0

Iron binding site 8 out of 8 in 3fpv

Go back to Iron Binding Sites List in 3fpv
Iron binding site 8 out of 8 in the Crystal Structure of Hbps


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Hbps within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe157

b:80.9
occ:1.00
 OG H:SER79 3.1 63.7 1.0
OE1 H:GLN75 3.1 64.5 1.0
CB H:SER79 3.4 63.6 1.0
CG H:GLN75 3.5 64.4 1.0
CB H:ALA135 3.6 66.9 1.0
CD1 A:ILE110 3.7 64.7 1.0
CD H:GLN75 3.7 64.4 1.0
CA H:SER76 4.0 64.2 1.0
CZ2 A:TRP90 4.2 64.2 1.0
CG1 A:ILE110 4.3 64.8 1.0
CB H:SER76 4.4 64.2 1.0
O H:GLN75 4.4 64.4 1.0
CG2 A:ILE110 4.5 64.8 1.0
N H:SER76 4.5 64.3 1.0
N H:GLY136 4.5 67.2 1.0
CA H:ALA135 4.5 66.9 1.0
C H:GLN75 4.6 64.4 1.0
C H:ALA135 4.7 67.0 1.0
CA H:GLY136 4.8 67.3 1.0
CB H:GLN75 4.9 64.5 1.0
CH2 A:TRP90 4.9 64.2 1.0
O H:HOH1029 4.9 61.7 1.0
CA H:SER79 5.0 63.7 1.0
CE2 A:TRP90 5.0 64.3 1.0
NZ H:LYS83 5.0 62.7 1.0

Reference:

D.Ortiz De Orue Lucana, G.Bogel, P.Zou, M.R.Groves. The Oligomeric Assembly of the Novel Haem-Degrading Protein Hbps Is Essential For Interaction with Its Cognate Two-Component Sensor Kinase J.Mol.Biol. V. 386 1108 2009.
ISSN: ISSN 0022-2836
PubMed: 19244623
DOI: 10.1016/J.JMB.2009.01.017
Page generated: Sun Aug 4 10:18:43 2024

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