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Iron in PDB 3b0m: M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf

Enzymatic activity of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf

All present enzymatic activity of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf:
1.7.7.1;

Protein crystallography data

The structure of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf, PDB code: 3b0m was solved by S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.59 / 1.90
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.152, 133.152, 77.586, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.7

Other elements in 3b0m:

The structure of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf (pdb code 3b0m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf, PDB code: 3b0m:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3b0m

Go back to Iron Binding Sites List in 3b0m
Iron binding site 1 out of 5 in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:13.5
occ:1.00
 FE A:SRM601 0.0 13.5 1.0
NB A:SRM601 2.0 11.4 1.0
NC A:SRM601 2.1 10.0 1.0
ND A:SRM601 2.1 12.4 1.0
NA A:SRM601 2.1 12.8 1.0
O A:HOH1001 2.3 15.6 1.0
SG A:CYS485 2.4 12.4 1.0
C1B A:SRM601 3.0 9.8 1.0
C4A A:SRM601 3.0 12.9 1.0
C4C A:SRM601 3.0 10.3 1.0
C1D A:SRM601 3.0 12.7 1.0
C4B A:SRM601 3.1 8.8 1.0
C4D A:SRM601 3.1 11.8 1.0
C1C A:SRM601 3.1 11.0 1.0
C1A A:SRM601 3.1 11.5 1.0
CHB A:SRM601 3.3 9.3 1.0
CHD A:SRM601 3.3 11.5 1.0
CB A:CYS485 3.4 10.7 1.0
CHC A:SRM601 3.4 10.3 1.0
CHA A:SRM601 3.5 11.6 1.0
O A:HOH1002 4.1 38.7 1.0
FE2 A:SF4602 4.2 11.7 1.0
CA A:CYS485 4.3 11.2 1.0
C2B A:SRM601 4.3 8.7 1.0
O A:HOH1054 4.3 12.3 1.0
C3C A:SRM601 4.3 10.5 1.0
C3B A:SRM601 4.3 8.3 1.0
C3D A:SRM601 4.3 11.2 1.0
C2D A:SRM601 4.3 10.9 1.0
C3A A:SRM601 4.3 10.7 1.0
C2C A:SRM601 4.4 11.3 1.0
C2A A:SRM601 4.4 13.4 1.0
NZ A:LYS224 4.5 11.3 1.0
NH2 A:ARG109 4.8 13.0 1.0
CDB A:SRM601 4.8 8.4 1.0
CAB A:SRM601 5.0 8.7 1.0

Iron binding site 2 out of 5 in 3b0m

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Iron binding site 2 out of 5 in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.6
occ:1.00
 FE1 A:SF4602 0.0 12.6 1.0
S3 A:SF4602 2.3 12.4 1.0
S2 A:SF4602 2.3 12.6 1.0
S4 A:SF4602 2.3 13.1 1.0
SG A:CYS481 2.3 12.6 1.0
FE3 A:SF4602 2.7 12.4 1.0
FE2 A:SF4602 2.7 11.7 1.0
FE4 A:SF4602 2.8 11.3 1.0
CB A:CYS481 3.4 11.2 1.0
N A:CYS481 3.5 11.2 1.0
CA A:CYS481 3.9 11.5 1.0
S1 A:SF4602 3.9 12.4 1.0
CB A:ASN483 4.1 12.2 1.0
C A:GLY480 4.2 11.7 1.0
O A:CYS481 4.2 12.2 1.0
C A:CYS481 4.3 11.3 1.0
ND2 A:ASN483 4.3 13.8 1.0
CB A:GLN448 4.4 14.6 1.0
SG A:CYS446 4.5 12.4 1.0
N A:GLY480 4.6 10.7 1.0
CA A:GLY480 4.6 10.8 1.0
N A:ASN483 4.7 11.4 1.0
SG A:CYS485 4.7 12.4 1.0
CG A:ASN483 4.7 14.4 1.0
CA A:ALA449 4.7 12.8 1.0
N A:ALA449 4.7 13.1 1.0
C A:GLN448 4.8 13.7 1.0
SG A:CYS440 4.9 9.8 1.0
O A:GLY480 4.9 11.3 1.0
CA A:ASN483 4.9 12.5 1.0
O A:GLN448 4.9 12.4 1.0

Iron binding site 3 out of 5 in 3b0m

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Iron binding site 3 out of 5 in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:11.7
occ:1.00
 FE2 A:SF4602 0.0 11.7 1.0
SG A:CYS485 2.2 12.4 1.0
S4 A:SF4602 2.3 13.1 1.0
S1 A:SF4602 2.3 12.4 1.0
S3 A:SF4602 2.3 12.4 1.0
FE4 A:SF4602 2.7 11.3 1.0
FE1 A:SF4602 2.7 12.6 1.0
FE3 A:SF4602 2.8 12.4 1.0
CB A:CYS485 3.2 10.7 1.0
NA A:SRM601 3.7 12.8 1.0
S2 A:SF4602 3.8 12.6 1.0
C4A A:SRM601 3.9 12.9 1.0
CHB A:SRM601 4.0 9.3 1.0
N A:CYS485 4.2 10.3 1.0
FE A:SRM601 4.2 13.5 1.0
CB A:ASN483 4.3 12.2 1.0
CA A:CYS485 4.3 11.2 1.0
C3A A:SRM601 4.4 10.7 1.0
C1A A:SRM601 4.4 11.5 1.0
C1B A:SRM601 4.6 9.8 1.0
SG A:CYS440 4.6 9.8 1.0
ND A:SRM601 4.6 12.4 1.0
CB A:CYS440 4.7 9.3 1.0
NB A:SRM601 4.7 11.4 1.0
C4D A:SRM601 4.8 11.8 1.0
SG A:CYS481 4.8 12.6 1.0
CHA A:SRM601 4.8 11.6 1.0
SG A:CYS446 4.8 12.4 1.0
ND2 A:ASN483 4.9 13.8 1.0
C2A A:SRM601 5.0 13.4 1.0

Iron binding site 4 out of 5 in 3b0m

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Iron binding site 4 out of 5 in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.4
occ:1.00
 FE3 A:SF4602 0.0 12.4 1.0
SG A:CYS446 2.3 12.4 1.0
S1 A:SF4602 2.3 12.4 1.0
S2 A:SF4602 2.3 12.6 1.0
S4 A:SF4602 2.3 13.1 1.0
FE1 A:SF4602 2.7 12.6 1.0
FE4 A:SF4602 2.8 11.3 1.0
FE2 A:SF4602 2.8 11.7 1.0
CB A:CYS446 3.2 12.6 1.0
S3 A:SF4602 3.9 12.4 1.0
C3A A:SRM601 4.3 10.7 1.0
CBA A:SRM601 4.4 11.2 1.0
N A:ALA449 4.4 13.1 1.0
CB A:GLN448 4.5 14.6 1.0
CB A:ALA449 4.7 13.0 1.0
CA A:CYS446 4.7 12.5 1.0
C4A A:SRM601 4.7 12.9 1.0
SG A:CYS481 4.7 12.6 1.0
CA A:ALA449 4.8 12.8 1.0
CDA A:SRM601 4.8 15.7 1.0
SG A:CYS440 4.8 9.8 1.0
N A:GLY442 4.8 10.6 1.0
SG A:CYS485 4.9 12.4 1.0
C A:GLN448 5.0 13.7 1.0

Iron binding site 5 out of 5 in 3b0m

Go back to Iron Binding Sites List in 3b0m
Iron binding site 5 out of 5 in the M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of M175K Mutant of Assimilatory Nitrite Reductase (NII3) From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:11.3
occ:1.00
 FE4 A:SF4602 0.0 11.3 1.0
S2 A:SF4602 2.2 12.6 1.0
SG A:CYS440 2.3 9.8 1.0
S1 A:SF4602 2.3 12.4 1.0
S3 A:SF4602 2.3 12.4 1.0
FE2 A:SF4602 2.7 11.7 1.0
FE3 A:SF4602 2.8 12.4 1.0
FE1 A:SF4602 2.8 12.6 1.0
CB A:CYS440 3.2 9.3 1.0
N A:GLY480 3.6 10.7 1.0
S4 A:SF4602 3.9 13.1 1.0
CA A:GLY480 4.1 10.8 1.0
N A:GLY442 4.1 10.6 1.0
OG1 A:THR479 4.2 9.2 1.0
N A:CYS481 4.4 11.2 1.0
SG A:CYS485 4.5 12.4 1.0
CB A:CYS485 4.5 10.7 1.0
CA A:CYS440 4.6 9.2 1.0
N A:THR441 4.6 9.6 1.0
CA A:GLY442 4.6 10.4 1.0
C A:GLY480 4.6 11.7 1.0
C A:CYS440 4.7 9.6 1.0
C A:THR479 4.7 11.4 1.0
SG A:CYS446 4.9 12.4 1.0
CA A:THR479 4.9 10.0 1.0

Reference:

S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi. Structure-Function Relationship of Assimilatory Nitrite Reductases From the Leaf and Root of Tobacco Based on High Resolution Structures Protein Sci. V. 21 383 2012.
ISSN: ISSN 0961-8368
PubMed: 22238192
DOI: 10.1002/PRO.2025
Page generated: Sun Aug 4 07:30:10 2024

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