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Iron in PDB 3rgs: Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand

Enzymatic activity of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand

All present enzymatic activity of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand:
1.11.1.6;

Protein crystallography data

The structure of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand, PDB code: 3rgs was solved by N.Purwar, M.Schmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.38 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.480, 140.720, 229.520, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.8

Iron Binding Sites:

The binding sites of Iron atom in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand (pdb code 3rgs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand, PDB code: 3rgs:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3rgs

Go back to Iron Binding Sites List in 3rgs
Iron binding site 1 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:10.5
occ:1.00
 FE A:HEM1 0.0 10.5 1.0
ND A:HEM1 2.0 9.7 1.0
NA A:HEM1 2.0 9.0 1.0
NB A:HEM1 2.0 10.1 1.0
NC A:HEM1 2.0 13.6 1.0
OH A:TYR357 2.0 9.3 1.0
N A:NH3502 2.1 11.6 0.8
C4D A:HEM1 3.0 8.9 1.0
C1A A:HEM1 3.0 10.2 1.0
C4A A:HEM1 3.0 9.5 1.0
C1D A:HEM1 3.0 10.8 1.0
C1B A:HEM1 3.0 9.5 1.0
C4B A:HEM1 3.0 10.5 1.0
C4C A:HEM1 3.0 13.2 1.0
C1C A:HEM1 3.1 13.9 1.0
CZ A:TYR357 3.1 12.0 1.0
CHA A:HEM1 3.4 7.6 1.0
CHD A:HEM1 3.4 10.7 1.0
CHB A:HEM1 3.4 10.0 1.0
CHC A:HEM1 3.4 12.5 1.0
CE2 A:TYR357 3.8 10.3 1.0
CE1 A:TYR357 4.0 9.9 1.0
C3D A:HEM1 4.2 8.7 1.0
NH2 A:ARG353 4.2 10.9 1.0
NE A:ARG353 4.2 13.3 1.0
C2D A:HEM1 4.3 9.4 1.0
C3A A:HEM1 4.3 10.9 1.0
C2A A:HEM1 4.3 10.6 1.0
C2B A:HEM1 4.3 8.3 1.0
C3B A:HEM1 4.3 10.6 1.0
C2C A:HEM1 4.3 15.2 1.0
C3C A:HEM1 4.3 15.4 1.0
O A:HOH566 4.4 34.4 1.0
CZ A:PHE160 4.4 11.5 1.0
O A:HOH705 4.5 52.7 0.0
NE2 A:HIS74 4.6 14.6 1.0
CG2 A:VAL73 4.6 14.7 1.0
CD2 A:HIS74 4.6 13.8 1.0
CZ A:ARG353 4.7 14.0 1.0
CE1 A:PHE160 5.0 12.8 1.0

Iron binding site 2 out of 4 in 3rgs

Go back to Iron Binding Sites List in 3rgs
Iron binding site 2 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1

b:11.0
occ:1.00
 FE B:HEM1 0.0 11.0 1.0
NB B:HEM1 2.0 11.0 1.0
ND B:HEM1 2.0 10.6 1.0
NC B:HEM1 2.0 15.3 1.0
NA B:HEM1 2.0 11.3 1.0
OH B:TYR357 2.0 9.0 1.0
N B:NH3502 2.1 13.2 1.0
C1D B:HEM1 3.0 10.2 1.0
C1B B:HEM1 3.0 10.9 1.0
C4B B:HEM1 3.0 11.8 1.0
C4D B:HEM1 3.0 10.2 1.0
C4A B:HEM1 3.0 11.1 1.0
C1C B:HEM1 3.0 15.8 1.0
C4C B:HEM1 3.0 14.3 1.0
C1A B:HEM1 3.1 9.7 1.0
CZ B:TYR357 3.1 10.8 1.0
CHD B:HEM1 3.4 11.6 1.0
CHC B:HEM1 3.4 13.9 1.0
CHB B:HEM1 3.4 10.9 1.0
CHA B:HEM1 3.4 10.2 1.0
CE2 B:TYR357 3.8 8.8 1.0
CE1 B:TYR357 4.0 9.4 1.0
NE B:ARG353 4.2 10.7 1.0
NH2 B:ARG353 4.2 8.8 1.0
C3D B:HEM1 4.3 9.2 1.0
C2D B:HEM1 4.3 10.2 1.0
C2B B:HEM1 4.3 11.9 1.0
C3B B:HEM1 4.3 12.1 1.0
C3A B:HEM1 4.3 11.3 1.0
C2C B:HEM1 4.3 17.3 1.0
C3C B:HEM1 4.3 15.8 1.0
C2A B:HEM1 4.3 11.0 1.0
CZ B:PHE160 4.4 6.2 1.0
O B:HOH1295 4.4 26.7 1.0
NE2 B:HIS74 4.6 16.1 1.0
CZ B:ARG353 4.6 12.2 1.0
CD2 B:HIS74 4.7 14.2 1.0
CG2 B:VAL73 4.7 13.2 1.0
CE1 B:PHE160 4.9 6.1 1.0

Iron binding site 3 out of 4 in 3rgs

Go back to Iron Binding Sites List in 3rgs
Iron binding site 3 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1

b:11.6
occ:1.00
 FE C:HEM1 0.0 11.6 1.0
OH C:TYR357 2.0 9.9 1.0
ND C:HEM1 2.0 11.8 1.0
NC C:HEM1 2.0 13.5 1.0
NA C:HEM1 2.0 10.3 1.0
NB C:HEM1 2.0 10.8 1.0
N C:NH3502 2.1 13.4 0.8
C4D C:HEM1 3.0 9.6 1.0
C1D C:HEM1 3.0 11.2 1.0
C4C C:HEM1 3.0 14.7 1.0
C4A C:HEM1 3.0 11.9 1.0
C1A C:HEM1 3.0 11.5 1.0
C1B C:HEM1 3.0 11.3 1.0
C1C C:HEM1 3.0 14.2 1.0
CZ C:TYR357 3.1 12.6 1.0
C4B C:HEM1 3.1 10.5 1.0
CHA C:HEM1 3.4 10.7 1.0
CHD C:HEM1 3.4 11.8 1.0
CHB C:HEM1 3.4 10.5 1.0
CHC C:HEM1 3.4 11.2 1.0
CE2 C:TYR357 3.8 10.7 1.0
CE1 C:TYR357 4.0 10.8 1.0
O C:HOH1440 4.1 25.4 1.0
NH2 C:ARG353 4.1 14.7 1.0
NE C:ARG353 4.1 11.7 1.0
C3D C:HEM1 4.2 10.4 1.0
C2D C:HEM1 4.3 10.9 1.0
C3C C:HEM1 4.3 14.7 1.0
C3A C:HEM1 4.3 11.4 1.0
C2A C:HEM1 4.3 11.7 1.0
C2C C:HEM1 4.3 15.3 1.0
C2B C:HEM1 4.3 10.9 1.0
C3B C:HEM1 4.3 10.9 1.0
CZ C:PHE160 4.4 11.0 1.0
O C:HOH597 4.5 51.4 0.0
CZ C:ARG353 4.6 13.6 1.0
NE2 C:HIS74 4.7 13.9 1.0
CD2 C:HIS74 4.7 12.9 1.0
CE1 C:PHE160 5.0 13.8 1.0

Iron binding site 4 out of 4 in 3rgs

Go back to Iron Binding Sites List in 3rgs
Iron binding site 4 out of 4 in the Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural and Kinetic Analysis of the Beef Liver Catalase with the Ammonia As A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1

b:12.0
occ:1.00
 FE D:HEM1 0.0 12.0 1.0
ND D:HEM1 2.0 13.2 1.0
NB D:HEM1 2.0 12.9 1.0
NA D:HEM1 2.0 12.8 1.0
NC D:HEM1 2.0 15.7 1.0
OH D:TYR357 2.0 9.8 1.0
N D:NH3502 2.1 13.4 1.0
C1D D:HEM1 3.0 14.0 1.0
C4D D:HEM1 3.0 11.9 1.0
C1A D:HEM1 3.0 11.9 1.0
C4A D:HEM1 3.0 12.6 1.0
C1B D:HEM1 3.0 13.9 1.0
C4B D:HEM1 3.0 14.4 1.0
C4C D:HEM1 3.1 14.7 1.0
C1C D:HEM1 3.1 15.1 1.0
CZ D:TYR357 3.1 11.1 1.0
CHA D:HEM1 3.4 12.0 1.0
CHB D:HEM1 3.4 13.6 1.0
CHD D:HEM1 3.4 14.0 1.0
CHC D:HEM1 3.4 13.1 1.0
CE2 D:TYR357 3.8 9.7 1.0
CE1 D:TYR357 4.0 9.8 1.0
O D:HOH778 4.1 31.8 1.0
NE D:ARG353 4.2 10.7 1.0
C3D D:HEM1 4.3 12.6 1.0
C2D D:HEM1 4.3 14.2 1.0
C3A D:HEM1 4.3 14.1 1.0
C2A D:HEM1 4.3 12.6 1.0
C2B D:HEM1 4.3 15.3 1.0
C3B D:HEM1 4.3 14.8 1.0
C2C D:HEM1 4.3 15.7 1.0
C3C D:HEM1 4.3 16.8 1.0
NH2 D:ARG353 4.3 10.4 1.0
CZ D:PHE160 4.4 12.2 1.0
CG2 D:VAL73 4.6 15.3 1.0
CZ D:ARG353 4.6 13.8 1.0
NE2 D:HIS74 4.6 14.6 1.0
CD2 D:HIS74 4.7 13.2 1.0
CE1 D:PHE160 5.0 13.8 1.0

Reference:

N.Purwar, J.M.Mcgarry, J.Kostera, A.A.Pacheco, M.Schmidt. Interaction of Nitric Oxide with Catalase: Structural and Kinetic Analysis. Biochemistry V. 50 4491 2011.
ISSN: ISSN 0006-2960
PubMed: 21524057
DOI: 10.1021/BI200130R
Page generated: Sun Aug 4 19:15:41 2024

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