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Zinc in PDB 4mec: Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX

Enzymatic activity of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX

All present enzymatic activity of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX:
1.14.99.3;

Protein crystallography data

The structure of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX, PDB code: 4mec was solved by M.Sugishima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.94 / 3.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.059, 73.167, 148.757, 86.41, 87.62, 86.25
R / Rfree (%) 24.9 / 29.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX (pdb code 4mec). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX, PDB code: 4mec:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4mec

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Zinc binding site 1 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:82.2
occ:1.00
 ZN A:ZNH300 0.0 82.2 1.0
NC A:ZNH300 2.0 77.2 1.0
NA A:ZNH300 2.1 81.5 1.0
NB A:ZNH300 2.1 81.7 1.0
ND A:ZNH300 2.1 77.9 1.0
NE2 A:HIS25 2.4 81.8 1.0
C1C A:ZNH300 3.1 77.9 1.0
C4C A:ZNH300 3.1 75.2 1.0
C1A A:ZNH300 3.1 81.5 1.0
C4B A:ZNH300 3.1 81.4 1.0
C4D A:ZNH300 3.1 78.4 1.0
C1D A:ZNH300 3.1 75.9 1.0
C4A A:ZNH300 3.1 82.4 1.0
C1B A:ZNH300 3.1 82.6 1.0
CE1 A:HIS25 3.2 84.0 1.0
CHC A:ZNH300 3.4 79.9 1.0
CHA A:ZNH300 3.4 80.1 1.0
CHD A:ZNH300 3.4 74.7 1.0
CD2 A:HIS25 3.5 81.8 1.0
CHB A:ZNH300 3.5 82.9 1.0
CA A:GLY143 4.1 82.3 1.0
N A:GLY143 4.2 81.2 1.0
C2C A:ZNH300 4.3 76.7 1.0
C3C A:ZNH300 4.3 75.1 1.0
C3B A:ZNH300 4.3 82.7 1.0
C2A A:ZNH300 4.3 83.2 1.0
C3A A:ZNH300 4.3 83.5 1.0
C2D A:ZNH300 4.3 75.9 1.0
C3D A:ZNH300 4.3 77.5 1.0
C2B A:ZNH300 4.3 83.2 1.0
ND1 A:HIS25 4.3 86.3 1.0
CG A:HIS25 4.5 84.7 1.0
CA A:GLY139 4.7 73.1 1.0
O A:GLY139 4.9 75.9 1.0
CB A:SER142 5.0 79.9 1.0

Zinc binding site 2 out of 7 in 4mec

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Zinc binding site 2 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:0.7
occ:1.00
 ZN B:ZNH300 0.0 0.7 1.0
NB B:ZNH300 2.1 0.6 1.0
NC B:ZNH300 2.1 0.2 1.0
NA B:ZNH300 2.1 0.8 1.0
ND B:ZNH300 2.1 0.7 1.0
NE2 B:HIS25 2.4 0.8 1.0
C1B B:ZNH300 3.1 0.6 1.0
C4B B:ZNH300 3.1 0.9 1.0
C4A B:ZNH300 3.1 0.7 1.0
C1C B:ZNH300 3.1 0.6 1.0
C4C B:ZNH300 3.1 0.7 1.0
C1A B:ZNH300 3.1 0.9 1.0
C1D B:ZNH300 3.1 0.4 1.0
C4D B:ZNH300 3.1 0.3 1.0
CE1 B:HIS25 3.3 0.4 1.0
CD2 B:HIS25 3.4 0.8 1.0
CHB B:ZNH300 3.4 0.6 1.0
CHC B:ZNH300 3.4 0.2 1.0
CHD B:ZNH300 3.5 0.9 1.0
CHA B:ZNH300 3.5 0.3 1.0
N B:GLY143 4.2 0.2 1.0
C3B B:ZNH300 4.3 0.1 1.0
C2B B:ZNH300 4.3 0.8 1.0
CA B:GLY143 4.3 0.8 1.0
C2C B:ZNH300 4.3 0.9 1.0
C3C B:ZNH300 4.3 0.6 1.0
C3A B:ZNH300 4.3 0.7 1.0
C2A B:ZNH300 4.3 0.8 1.0
C2D B:ZNH300 4.4 0.7 1.0
C3D B:ZNH300 4.4 1.0 1.0
CA B:GLY139 4.5 99.4 1.0
ND1 B:HIS25 4.5 0.1 1.0
O B:GLY139 4.5 0.5 1.0
CG B:HIS25 4.5 0.1 1.0
CB B:SER142 4.6 0.4 1.0
NZ C:LYS69 4.9 0.8 1.0
OE2 B:GLU29 5.0 0.7 1.0
C B:GLY139 5.0 99.9 1.0

Zinc binding site 3 out of 7 in 4mec

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Zinc binding site 3 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:1.0
occ:1.00
 ZN C:ZNH300 0.0 1.0 1.0
NC C:ZNH300 2.1 0.7 1.0
NB C:ZNH300 2.1 0.0 1.0
ND C:ZNH300 2.1 1.0 1.0
NA C:ZNH300 2.1 0.8 1.0
NE2 C:HIS25 2.5 0.7 1.0
C4C C:ZNH300 3.1 0.5 1.0
C1D C:ZNH300 3.1 1.0 1.0
C1C C:ZNH300 3.1 0.6 1.0
C4B C:ZNH300 3.1 0.8 1.0
C1B C:ZNH300 3.1 0.7 1.0
C4D C:ZNH300 3.1 0.5 1.0
C4A C:ZNH300 3.1 0.8 1.0
C1A C:ZNH300 3.1 0.7 1.0
CE1 C:HIS25 3.3 0.5 1.0
CHD C:ZNH300 3.4 0.8 1.0
CHC C:ZNH300 3.5 0.9 1.0
CHB C:ZNH300 3.5 0.8 1.0
CHA C:ZNH300 3.5 0.0 1.0
CD2 C:HIS25 3.6 0.2 1.0
C3B C:ZNH300 4.3 0.9 1.0
C2B C:ZNH300 4.3 1.0 1.0
C3C C:ZNH300 4.3 0.9 1.0
C2D C:ZNH300 4.3 0.4 1.0
C2C C:ZNH300 4.3 0.8 1.0
C3D C:ZNH300 4.3 0.3 1.0
C3A C:ZNH300 4.4 0.2 1.0
C2A C:ZNH300 4.4 0.7 1.0
ND1 C:HIS25 4.5 0.6 1.0
CG C:HIS25 4.7 0.1 1.0
CA C:GLY143 4.8 0.6 1.0
O C:GLY139 5.0 1.0 1.0

Zinc binding site 4 out of 7 in 4mec

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Zinc binding site 4 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:0.1
occ:1.00
 ZN D:ZNH300 0.0 0.1 1.0
NB D:ZNH300 2.1 0.0 1.0
NC D:ZNH300 2.1 0.4 1.0
NA D:ZNH300 2.1 0.9 1.0
ND D:ZNH300 2.1 0.9 1.0
NE2 D:HIS25 2.7 0.2 1.0
CE1 D:HIS25 2.9 0.1 1.0
C4B D:ZNH300 3.1 0.2 1.0
C1C D:ZNH300 3.1 0.5 1.0
C1A D:ZNH300 3.1 0.7 1.0
C1B D:ZNH300 3.1 0.6 1.0
C4C D:ZNH300 3.1 0.1 1.0
C4D D:ZNH300 3.1 0.0 1.0
C4A D:ZNH300 3.1 0.7 1.0
C1D D:ZNH300 3.2 0.0 1.0
CHC D:ZNH300 3.4 0.7 1.0
CHA D:ZNH300 3.4 0.5 1.0
CHB D:ZNH300 3.5 0.0 1.0
CHD D:ZNH300 3.5 0.6 1.0
CD2 D:HIS25 3.8 0.4 1.0
ND1 D:HIS25 4.0 0.1 1.0
C3B D:ZNH300 4.3 0.4 1.0
C2C D:ZNH300 4.3 0.3 1.0
C2B D:ZNH300 4.3 0.8 1.0
C3C D:ZNH300 4.3 0.1 1.0
C2A D:ZNH300 4.3 0.7 1.0
C3A D:ZNH300 4.3 0.2 1.0
C3D D:ZNH300 4.4 0.6 1.0
C2D D:ZNH300 4.4 0.4 1.0
CB D:SER142 4.4 0.2 1.0
CG D:HIS25 4.5 0.0 1.0
CA D:GLY139 4.7 0.0 1.0

Zinc binding site 5 out of 7 in 4mec

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Zinc binding site 5 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:0.0
occ:1.00
 ZN E:ZNH300 0.0 0.0 1.0
NC E:ZNH300 2.1 0.5 1.0
NA E:ZNH300 2.1 0.8 1.0
ND E:ZNH300 2.1 0.6 1.0
NB E:ZNH300 2.1 0.5 1.0
NE2 E:HIS25 2.5 0.1 1.0
C4C E:ZNH300 3.1 0.5 1.0
C1C E:ZNH300 3.1 0.1 1.0
C4B E:ZNH300 3.1 0.8 1.0
C1D E:ZNH300 3.1 0.5 1.0
C1B E:ZNH300 3.1 0.3 1.0
C4D E:ZNH300 3.1 0.7 1.0
C4A E:ZNH300 3.1 0.6 1.0
C1A E:ZNH300 3.1 0.6 1.0
CHD E:ZNH300 3.4 0.1 1.0
CE1 E:HIS25 3.4 0.3 1.0
CHC E:ZNH300 3.4 0.8 1.0
CHA E:ZNH300 3.5 0.6 1.0
CHB E:ZNH300 3.5 1.0 1.0
CD2 E:HIS25 3.5 0.3 1.0
C3C E:ZNH300 4.3 0.9 1.0
C2C E:ZNH300 4.3 0.9 1.0
C3B E:ZNH300 4.3 0.1 1.0
C2B E:ZNH300 4.3 0.8 1.0
C2D E:ZNH300 4.3 0.1 1.0
C3A E:ZNH300 4.3 0.9 1.0
C2A E:ZNH300 4.3 0.4 1.0
C3D E:ZNH300 4.3 0.5 1.0
CA E:GLY139 4.4 0.9 1.0
ND1 E:HIS25 4.6 0.5 1.0
CG E:HIS25 4.6 0.4 1.0
OG E:SER142 4.7 0.7 1.0
CA E:GLY143 4.8 0.7 1.0
N E:GLY143 5.0 0.1 1.0
O E:GLY139 5.0 0.9 1.0

Zinc binding site 6 out of 7 in 4mec

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Zinc binding site 6 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:0.6
occ:1.00
 NE2 F:HIS25 2.2 0.1 1.0
O F:SER142 3.1 0.9 1.0
CE1 F:HIS25 3.1 0.1 1.0
CD2 F:HIS25 3.3 0.0 1.0
CA F:GLY143 3.6 0.0 1.0
CA F:GLY139 3.7 0.4 1.0
C F:SER142 3.8 0.7 1.0
O F:LEU138 3.8 0.9 1.0
O F:GLY139 4.0 0.4 1.0
N F:GLY143 4.1 0.1 1.0
O F:GLY143 4.1 0.4 1.0
C F:GLY143 4.1 0.8 1.0
ND1 F:HIS25 4.3 1.0 1.0
C F:GLY139 4.3 0.5 1.0
CG F:HIS25 4.4 0.7 1.0
N F:GLY139 4.6 0.6 1.0
C F:LEU138 4.6 0.3 1.0

Zinc binding site 7 out of 7 in 4mec

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Zinc binding site 7 out of 7 in the Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rat Heme Oxygenase-1 in Complex with Zn(II)- Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn300

b:0.8
occ:1.00
 NE2 G:HIS25 2.2 0.1 1.0
CE1 G:HIS25 2.8 0.7 1.0
CD2 G:HIS25 3.3 0.6 1.0
CB G:GLU29 3.7 0.7 1.0
ND1 G:HIS25 3.9 0.4 1.0
CG G:HIS25 4.2 0.9 1.0
CD1 G:LEU138 4.6 0.9 1.0
CA G:GLY139 4.7 0.1 1.0
CA G:GLU29 4.9 0.9 1.0
OE1 G:GLN38 4.9 0.5 1.0

Reference:

E.Harada, M.Sugishima, J.Harada, M.Noguchi, K.Fukuyama, K.Sugase. Mechanism of the Distal Regulation of Substrate Binding Through Intrinsic Fluctuation in An Enzyme To Be Published.
Page generated: Sun Oct 27 02:23:23 2024

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