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Iron in PDB 2hk6: Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site

Enzymatic activity of Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site

All present enzymatic activity of Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site:
4.99.1.1;

Protein crystallography data

The structure of Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site, PDB code: 2hk6 was solved by S.Al-Karadaghi, T.Karlberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.650, 49.980, 118.850, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22

Other elements in 2hk6:

The structure of Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site (pdb code 2hk6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site, PDB code: 2hk6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2hk6

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Iron binding site 1 out of 4 in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site


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 B. Subtilis Ferrochelatase with Iron Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:16.5
occ:0.87
 O A:HOH926 1.8 28.5 1.0
O A:HOH674 2.1 22.1 1.0
NE2 A:HIS183 2.2 13.1 1.0
OE2 A:GLU264 2.2 23.2 1.0
O A:HOH675 2.3 17.1 1.0
CE1 A:HIS183 3.1 13.6 1.0
CD2 A:HIS183 3.2 14.0 1.0
CD A:GLU264 3.2 21.2 1.0
OE1 A:GLU264 3.5 23.2 1.0
OH A:TYR13 3.9 20.3 1.0
O A:SER222 4.0 14.9 1.0
CZ A:TYR13 4.2 19.1 1.0
ND1 A:HIS183 4.2 13.2 1.0
O A:HOH794 4.3 26.4 1.0
CG A:HIS183 4.3 11.9 1.0
CG A:GLU264 4.5 17.8 1.0
CE1 A:TYR13 4.7 18.7 1.0
CB A:SER222 4.7 12.8 1.0
CE2 A:TYR13 4.8 19.3 1.0

Iron binding site 2 out of 4 in 2hk6

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Iron binding site 2 out of 4 in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site


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 B. Subtilis Ferrochelatase with Iron Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:15.0
occ:0.63
 O A:HOH745 1.5 24.7 1.0
O A:HOH750 1.9 25.8 1.0
O A:HOH748 2.1 30.7 1.0
NE2 A:HIS201 2.1 14.4 1.0
O A:HOH747 2.3 23.6 1.0
O A:HOH746 2.3 31.4 1.0
CD2 A:HIS201 3.0 14.5 1.0
CE1 A:HIS201 3.2 15.5 1.0
O A:HOH837 4.1 29.6 1.0
O A:HOH749 4.1 27.2 1.0
CG A:HIS201 4.2 12.9 1.0
ND1 A:HIS201 4.3 14.4 1.0
O A:HOH773 4.3 25.2 1.0
O A:HOH880 4.4 34.3 1.0
O A:HOH654 4.4 18.5 1.0
CB A:VAL218 4.5 10.6 1.0
O A:HOH796 4.6 22.5 1.0
CG1 A:VAL218 4.9 11.5 1.0

Iron binding site 3 out of 4 in 2hk6

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Iron binding site 3 out of 4 in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site


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 B. Subtilis Ferrochelatase with Iron Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:15.7
occ:0.55
 OE1 A:GLU73 2.1 20.2 1.0
O A:HOH865 2.2 30.0 1.0
O A:HOH743 2.2 24.7 1.0
ND1 A:HIS70 2.3 12.4 1.0
O A:HOH866 2.3 25.0 1.0
O A:HOH742 2.4 30.5 1.0
CE1 A:HIS70 3.1 12.1 1.0
CD A:GLU73 3.1 17.7 1.0
CG A:HIS70 3.4 10.3 1.0
OE2 A:GLU73 3.4 22.5 1.0
CB A:HIS70 3.8 9.4 1.0
CA A:HIS70 4.1 9.2 1.0
O A:HOH688 4.2 20.9 1.0
NE2 A:HIS70 4.3 10.0 1.0
O A:HOH658 4.3 13.8 1.0
O A:HOH709 4.3 19.8 1.0
O A:HOH949 4.4 46.0 1.0
CD2 A:HIS70 4.4 11.2 1.0
CG A:GLU73 4.5 16.5 1.0
CB A:GLU73 4.8 13.9 1.0
N A:HIS70 5.0 8.7 1.0

Iron binding site 4 out of 4 in 2hk6

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Iron binding site 4 out of 4 in the Crystal Structure of B. Subtilis Ferrochelatase with Iron Bound at the Active Site


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 B. Subtilis Ferrochelatase with Iron Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:16.3
occ:0.37
 OE1 A:GLN69 2.0 11.5 1.0
O A:HOH744 2.1 20.8 1.0
O A:HOH733 2.2 18.5 1.0
O A:HOH752 2.3 46.9 1.0
O A:HOH751 2.6 36.4 1.0
NE2 A:HIS65 2.6 24.0 1.0
CD A:GLN69 3.1 13.9 1.0
CE1 A:HIS65 3.4 23.8 1.0
CD2 A:HIS65 3.6 21.4 1.0
NE2 A:GLN69 3.7 14.4 1.0
O A:HOH824 4.0 15.0 1.0
CG A:GLN69 4.3 9.8 1.0
CB A:GLN69 4.4 8.6 1.0
OD1 A:ASN66 4.5 11.3 1.0
ND1 A:HIS65 4.6 25.2 1.0
CG A:HIS65 4.7 17.2 1.0
O A:HOH658 4.9 13.8 1.0

Reference:

M.D.Hansson, T.Karlberg, M.A.Rahardja, S.Al-Karadaghi, M.Hansson. Amino Acid Residues HIS183 and GLU264 in Bacillus Subtilis Ferrochelatase Direct and Facilitate the Insertion of Metal Ion Into Protoporphyrin IX Biochemistry V. 46 87 2007.
ISSN: ISSN 0006-2960
PubMed: 17198378
DOI: 10.1021/BI061760A
Page generated: Sat Aug 3 22:59:35 2024

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