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Lead in PDB 2qd5: Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound

Enzymatic activity of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound

All present enzymatic activity of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound:
4.99.1.1;

Protein crystallography data

The structure of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound, PDB code: 2qd5 was solved by A.E.Meldock, T.A.Dailey, T.A.Ross, H.A.Dailey, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.26 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.218, 92.811, 109.808, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28

Other elements in 2qd5:

The structure of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Lead Binding Sites:

The binding sites of Lead atom in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound (pdb code 2qd5). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 4 binding sites of Lead where determined in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound, PDB code: 2qd5:
Jump to Lead binding site number: 1; 2; 3; 4;

Lead binding site 1 out of 4 in 2qd5

Go back to Lead Binding Sites List in 2qd5
Lead binding site 1 out of 4 in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pb1101

b:51.1
occ:0.25
 PB A:PB1101 0.0 51.1 0.2
OXT A:ACY803 1.3 65.2 0.8
PB A:PB1101 2.0 49.0 0.2
ND A:PP9901 2.3 49.0 1.0
NA A:PP9901 2.4 49.8 1.0
NB A:PP9901 2.4 49.4 1.0
NC A:PP9901 2.4 48.7 1.0
C A:ACY803 2.7 64.5 0.8
C1D A:PP9901 3.1 49.0 1.0
C4D A:PP9901 3.2 49.3 1.0
C4A A:PP9901 3.2 50.3 1.0
C1B A:PP9901 3.3 49.9 1.0
C1A A:PP9901 3.3 50.0 1.0
C4C A:PP9901 3.3 47.5 1.0
C1C A:PP9901 3.3 48.1 1.0
C4B A:PP9901 3.4 49.4 1.0
O A:ACY803 3.4 64.9 0.8
CHB A:PP9901 3.4 50.0 1.0
CHA A:PP9901 3.4 49.3 1.0
CHD A:PP9901 3.5 47.6 1.0
CHC A:PP9901 3.6 48.9 1.0
CH3 A:ACY803 3.7 64.9 0.8
O A:ACY801 3.8 55.4 0.8
C3D A:PP9901 4.4 48.8 1.0
CD2 A:HIS263 4.5 38.1 1.0
C2D A:PP9901 4.5 48.7 1.0
C3A A:PP9901 4.5 50.5 1.0
C2A A:PP9901 4.5 50.7 1.0
C2B A:PP9901 4.6 49.7 1.0
C3B A:PP9901 4.6 49.2 1.0
C3C A:PP9901 4.8 46.6 1.0
C2C A:PP9901 4.8 46.9 1.0
CG A:HIS263 5.0 37.4 1.0
CB A:HIS263 5.0 35.8 1.0
C A:ACY801 5.0 55.1 0.8

Lead binding site 2 out of 4 in 2qd5

Go back to Lead Binding Sites List in 2qd5
Lead binding site 2 out of 4 in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pb1101

b:49.0
occ:0.25
 PB A:PB1101 0.0 49.0 0.2
O A:ACY801 1.9 55.4 0.8
PB A:PB1101 2.0 51.1 0.2
ND A:PP9901 2.3 49.0 1.0
NB A:PP9901 2.3 49.4 1.0
NC A:PP9901 2.3 48.7 1.0
NA A:PP9901 2.4 49.8 1.0
C1D A:PP9901 3.0 49.0 1.0
C A:ACY801 3.1 55.1 0.8
C4D A:PP9901 3.1 49.3 1.0
C4C A:PP9901 3.2 47.5 1.0
C4A A:PP9901 3.2 50.3 1.0
C1C A:PP9901 3.2 48.1 1.0
C1B A:PP9901 3.2 49.9 1.0
C4B A:PP9901 3.2 49.4 1.0
C1A A:PP9901 3.3 50.0 1.0
OXT A:ACY803 3.3 65.2 0.8
CHD A:PP9901 3.4 47.6 1.0
CHA A:PP9901 3.4 49.3 1.0
CHB A:PP9901 3.4 50.0 1.0
CHC A:PP9901 3.5 48.9 1.0
OXT A:ACY801 3.9 55.2 0.8
CH3 A:ACY801 4.1 55.0 0.8
C3D A:PP9901 4.3 48.8 1.0
C2D A:PP9901 4.4 48.7 1.0
C2B A:PP9901 4.5 49.7 1.0
C3B A:PP9901 4.5 49.2 1.0
C3A A:PP9901 4.5 50.5 1.0
C2A A:PP9901 4.6 50.7 1.0
C A:ACY803 4.6 64.5 0.8
C3C A:PP9901 4.7 46.6 1.0
C2C A:PP9901 4.7 46.9 1.0
CE A:MET76 4.9 49.6 1.0

Lead binding site 3 out of 4 in 2qd5

Go back to Lead Binding Sites List in 2qd5
Lead binding site 3 out of 4 in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pb1102

b:43.1
occ:0.25
 PB B:PB1102 0.0 43.1 0.2
PB B:PB1102 1.8 43.9 0.2
O B:ACY1106 1.8 42.0 0.8
NB B:PP91105 2.3 43.0 1.0
NA B:PP91105 2.4 43.4 1.0
ND B:PP91105 2.4 42.5 1.0
NC B:PP91105 2.4 42.5 1.0
C B:ACY1106 3.0 42.8 0.8
C4D B:PP91105 3.1 43.0 1.0
C4A B:PP91105 3.2 44.0 1.0
C1D B:PP91105 3.2 42.5 1.0
C1B B:PP91105 3.2 43.5 1.0
C1A B:PP91105 3.2 43.9 1.0
C1C B:PP91105 3.3 42.3 1.0
C4C B:PP91105 3.3 41.3 1.0
C4B B:PP91105 3.3 43.2 1.0
CHB B:PP91105 3.4 43.6 1.0
CHA B:PP91105 3.4 42.6 1.0
CHD B:PP91105 3.5 41.2 1.0
CHC B:PP91105 3.6 42.9 1.0
OXT B:ACY1106 3.9 44.5 0.8
CH3 B:ACY1106 3.9 43.2 0.8
C3D B:PP91105 4.4 42.9 1.0
CD2 B:HIS763 4.5 35.1 1.0
C2D B:PP91105 4.5 42.3 1.0
C3A B:PP91105 4.5 44.5 1.0
C2A B:PP91105 4.5 45.0 1.0
C2B B:PP91105 4.5 43.1 1.0
C3B B:PP91105 4.6 42.7 1.0
O1 B:OXY1001 4.6 62.1 1.0
C2C B:PP91105 4.7 41.1 1.0
C3C B:PP91105 4.8 40.9 1.0
CG B:HIS763 5.0 35.4 1.0

Lead binding site 4 out of 4 in 2qd5

Go back to Lead Binding Sites List in 2qd5
Lead binding site 4 out of 4 in the Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Structure of Wild Type Human Ferrochelatase in Complex with A Lead- Porphyrin Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pb1102

b:43.9
occ:0.25
 PB B:PB1102 0.0 43.9 0.2
PB B:PB1102 1.8 43.1 0.2
ND B:PP91105 2.3 42.5 1.0
NC B:PP91105 2.3 42.5 1.0
NB B:PP91105 2.4 43.0 1.0
NA B:PP91105 2.4 43.4 1.0
O1 B:OXY1001 2.9 62.1 1.0
C4D B:PP91105 3.1 43.0 1.0
C1D B:PP91105 3.1 42.5 1.0
C1A B:PP91105 3.2 43.9 1.0
C1C B:PP91105 3.2 42.3 1.0
C4A B:PP91105 3.2 44.0 1.0
C1B B:PP91105 3.2 43.5 1.0
C4B B:PP91105 3.3 43.2 1.0
C4C B:PP91105 3.3 41.3 1.0
CHA B:PP91105 3.3 42.6 1.0
CHB B:PP91105 3.4 43.6 1.0
CHD B:PP91105 3.5 41.2 1.0
CHC B:PP91105 3.5 42.9 1.0
O2 B:OXY1001 3.6 63.5 1.0
O B:ACY1106 3.6 42.0 0.8
C3D B:PP91105 4.3 42.9 1.0
C2D B:PP91105 4.4 42.3 1.0
C2A B:PP91105 4.5 45.0 1.0
C3A B:PP91105 4.5 44.5 1.0
C3B B:PP91105 4.5 42.7 1.0
C2B B:PP91105 4.6 43.1 1.0
C2C B:PP91105 4.7 41.1 1.0
C3C B:PP91105 4.8 40.9 1.0
CE B:MET576 4.8 42.9 1.0
C B:ACY1106 4.8 42.8 0.8
SD B:MET576 4.9 44.0 1.0

Reference:

A.E.Medlock, T.A.Dailey, T.A.Ross, H.A.Dailey, W.N.Lanzilotta. A Pi-Helix Switch Selective For Porphyrin Deprotonation and Product Release in Human Ferrochelatase. J.Mol.Biol. V. 373 1006 2007.
ISSN: ISSN 0022-2836
PubMed: 17884090
DOI: 10.1016/J.JMB.2007.08.040
Page generated: Thu Oct 10 10:05:21 2024

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