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Iron in PDB 2nya: Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli

Enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli

All present enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli:
1.7.99.4;

Protein crystallography data

The structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli, PDB code: 2nya was solved by B.J.N.Jepson, D.J.Richardson, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.449, 94.596, 131.211, 90.00, 96.34, 90.00
R / Rfree (%) 18.1 / 24.3

Other elements in 2nya:

The structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli (pdb code 2nya). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli, PDB code: 2nya:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2nya

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Iron binding site 1 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


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 the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:24.1
occ:1.00
 FE1 A:SF42001 0.0 24.1 1.0
S3 A:SF42001 2.3 27.0 1.0
S4 A:SF42001 2.3 28.0 1.0
S2 A:SF42001 2.3 28.1 1.0
SG A:CYS45 2.4 29.1 1.0
FE3 A:SF42001 2.7 27.9 1.0
FE2 A:SF42001 2.7 25.5 1.0
FE4 A:SF42001 2.7 24.9 1.0
CB A:CYS45 3.3 30.7 1.0
N A:CYS45 3.8 31.4 1.0
S1 A:SF42001 3.8 26.3 1.0
CA A:CYS45 4.1 30.4 1.0
N A:GLY48 4.4 29.0 1.0
CD1 A:ILE186 4.4 23.2 1.0
O A:HOH4250 4.7 48.6 1.0
NZ A:LYS47 4.7 30.9 1.0
CG A:PRO185 4.8 25.6 1.0
CD A:PRO185 4.8 24.7 1.0
C A:CYS45 4.8 29.8 1.0
SG A:CYS13 4.8 22.0 1.0
CA A:GLY48 4.8 29.0 1.0
C A:ASN44 4.9 33.3 1.0
O A:CYS45 4.9 29.1 1.0
SG A:CYS17 4.9 23.5 1.0
SG A:CYS10 4.9 18.4 1.0

Iron binding site 2 out of 8 in 2nya

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Iron binding site 2 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


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 the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:25.5
occ:1.00
 FE2 A:SF42001 0.0 25.5 1.0
S4 A:SF42001 2.3 28.0 1.0
S3 A:SF42001 2.3 27.0 1.0
S1 A:SF42001 2.3 26.3 1.0
SG A:CYS17 2.3 23.5 1.0
FE1 A:SF42001 2.7 24.1 1.0
FE3 A:SF42001 2.8 27.9 1.0
FE4 A:SF42001 2.8 24.9 1.0
CB A:CYS17 3.1 22.1 1.0
S2 A:SF42001 4.0 28.1 1.0
CD1 A:ILE186 4.0 23.2 1.0
N A:CYS17 4.1 21.3 1.0
CA A:CYS17 4.2 22.4 1.0
CG1 A:ILE186 4.3 23.4 1.0
CB A:ILE186 4.3 23.6 1.0
CB A:THR15 4.5 19.8 1.0
CG2 A:THR15 4.5 18.4 1.0
CB A:CYS10 4.8 17.3 1.0
SG A:CYS10 4.8 18.4 1.0
SG A:CYS13 4.9 22.0 1.0
N A:CYS45 5.0 31.4 1.0

Iron binding site 3 out of 8 in 2nya

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Iron binding site 3 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


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 the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:27.9
occ:1.00
 FE3 A:SF42001 0.0 27.9 1.0
S2 A:SF42001 2.3 28.1 1.0
S4 A:SF42001 2.3 28.0 1.0
S1 A:SF42001 2.3 26.3 1.0
SG A:CYS13 2.5 22.0 1.0
FE1 A:SF42001 2.7 24.1 1.0
FE4 A:SF42001 2.7 24.9 1.0
FE2 A:SF42001 2.8 25.5 1.0
CB A:CYS13 3.4 19.9 1.0
N A:CYS13 3.8 20.6 1.0
S3 A:SF42001 3.9 27.0 1.0
CA A:CYS13 4.0 20.2 1.0
CB A:THR15 4.0 19.8 1.0
OG1 A:THR15 4.0 19.3 1.0
O A:CYS13 4.1 19.3 1.0
O A:HOH4250 4.1 48.6 1.0
C A:CYS13 4.2 19.9 1.0
SG A:CYS10 4.8 18.4 1.0
SG A:CYS45 4.8 29.1 1.0
N A:THR15 4.8 19.0 1.0
CD A:PRO185 4.8 24.7 1.0
SG A:CYS17 4.8 23.5 1.0
C A:PHE12 4.8 21.0 1.0
CG2 A:THR15 4.9 18.4 1.0
CA A:THR15 5.0 19.4 1.0

Iron binding site 4 out of 8 in 2nya

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Iron binding site 4 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


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 the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:24.9
occ:1.00
 FE4 A:SF42001 0.0 24.9 1.0
S2 A:SF42001 2.3 28.1 1.0
S3 A:SF42001 2.3 27.0 1.0
SG A:CYS10 2.3 18.4 1.0
S1 A:SF42001 2.3 26.3 1.0
FE3 A:SF42001 2.7 27.9 1.0
FE1 A:SF42001 2.7 24.1 1.0
FE2 A:SF42001 2.8 25.5 1.0
CB A:CYS10 3.3 17.3 1.0
S4 A:SF42001 4.0 28.0 1.0
CB A:PHE12 4.2 21.8 1.0
CA A:GLY48 4.3 29.0 1.0
N A:GLY48 4.4 29.0 1.0
N A:CYS13 4.4 20.6 1.0
SG A:CYS45 4.6 29.1 1.0
N A:PHE12 4.6 20.3 1.0
CA A:CYS10 4.7 18.2 1.0
CA A:PHE12 4.7 21.2 1.0
CB A:CYS17 4.7 22.1 1.0
SG A:CYS17 4.8 23.5 1.0
C A:PHE12 4.8 21.0 1.0
CD1 A:PHE12 4.9 22.7 1.0
SG A:CYS13 5.0 22.0 1.0

Iron binding site 5 out of 8 in 2nya

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Iron binding site 5 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe5001

b:30.2
occ:1.00
 FE1 F:SF45001 0.0 30.2 1.0
S3 F:SF45001 2.3 29.6 1.0
S4 F:SF45001 2.3 25.4 1.0
S2 F:SF45001 2.3 29.8 1.0
SG F:CYS45 2.5 31.5 1.0
FE3 F:SF45001 2.7 26.9 1.0
FE2 F:SF45001 2.7 26.1 1.0
FE4 F:SF45001 2.8 27.1 1.0
CB F:CYS45 3.1 34.0 1.0
S1 F:SF45001 3.9 27.0 1.0
N F:CYS45 4.1 35.0 1.0
CA F:CYS45 4.2 33.7 1.0
CG F:PRO185 4.4 27.8 1.0
O F:HOH7259 4.4 40.1 1.0
N F:GLY48 4.5 31.1 1.0
CD F:PRO185 4.5 26.6 1.0
NZ F:LYS47 4.6 29.0 1.0
CD1 F:ILE186 4.8 25.8 1.0
SG F:CYS13 4.8 25.8 1.0
C F:CYS45 4.8 33.1 1.0
CB F:PRO185 4.9 26.6 1.0
SG F:CYS17 4.9 24.7 1.0
CE F:LYS47 4.9 29.7 1.0
CA F:GLY48 5.0 31.2 1.0

Iron binding site 6 out of 8 in 2nya

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Iron binding site 6 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe5001

b:26.1
occ:1.00
 FE2 F:SF45001 0.0 26.1 1.0
SG F:CYS17 2.2 24.7 1.0
S3 F:SF45001 2.3 29.6 1.0
S4 F:SF45001 2.3 25.4 1.0
S1 F:SF45001 2.3 27.0 1.0
FE1 F:SF45001 2.7 30.2 1.0
FE4 F:SF45001 2.7 27.1 1.0
FE3 F:SF45001 2.8 26.9 1.0
CB F:CYS17 3.1 27.5 1.0
S2 F:SF45001 4.0 29.8 1.0
CG1 F:ILE186 4.2 26.4 1.0
CA F:CYS17 4.3 27.5 1.0
N F:CYS17 4.3 27.3 1.0
CD1 F:ILE186 4.3 25.8 1.0
CB F:ILE186 4.3 26.8 1.0
CB F:THR15 4.7 25.6 1.0
SG F:CYS10 4.8 22.1 1.0
CB F:CYS10 4.8 23.5 1.0
CG2 F:THR15 4.8 25.4 1.0

Iron binding site 7 out of 8 in 2nya

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Iron binding site 7 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe5001

b:26.9
occ:1.00
 FE3 F:SF45001 0.0 26.9 1.0
S2 F:SF45001 2.3 29.8 1.0
S1 F:SF45001 2.3 27.0 1.0
S4 F:SF45001 2.3 25.4 1.0
SG F:CYS13 2.5 25.8 1.0
FE4 F:SF45001 2.6 27.1 1.0
FE1 F:SF45001 2.7 30.2 1.0
FE2 F:SF45001 2.8 26.1 1.0
CB F:CYS13 3.5 22.9 1.0
N F:CYS13 3.7 23.5 1.0
S3 F:SF45001 3.9 29.6 1.0
CA F:CYS13 4.0 23.5 1.0
OG1 F:THR15 4.0 23.8 1.0
CB F:THR15 4.1 25.6 1.0
O F:HOH7259 4.1 40.1 1.0
O F:CYS13 4.3 21.6 1.0
C F:CYS13 4.3 23.2 1.0
CD F:PRO185 4.6 26.6 1.0
SG F:CYS17 4.7 24.7 1.0
SG F:CYS10 4.8 22.1 1.0
C F:PHE12 4.8 23.9 1.0
N F:THR15 4.8 23.9 1.0
CB F:PHE12 4.9 24.4 1.0
SG F:CYS45 4.9 31.5 1.0

Iron binding site 8 out of 8 in 2nya

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Iron binding site 8 out of 8 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe5001

b:27.1
occ:1.00
 FE4 F:SF45001 0.0 27.1 1.0
S2 F:SF45001 2.3 29.8 1.0
S3 F:SF45001 2.3 29.6 1.0
S1 F:SF45001 2.3 27.0 1.0
SG F:CYS10 2.4 22.1 1.0
FE3 F:SF45001 2.6 26.9 1.0
FE2 F:SF45001 2.7 26.1 1.0
FE1 F:SF45001 2.8 30.2 1.0
CB F:CYS10 3.3 23.5 1.0
S4 F:SF45001 3.9 25.4 1.0
CB F:PHE12 4.1 24.4 1.0
N F:CYS13 4.3 23.5 1.0
CA F:GLY48 4.5 31.2 1.0
N F:GLY48 4.6 31.1 1.0
CB F:CYS17 4.6 27.5 1.0
SG F:CYS45 4.7 31.5 1.0
SG F:CYS17 4.7 24.7 1.0
N F:PHE12 4.7 23.6 1.0
CA F:PHE12 4.7 24.0 1.0
CA F:CYS10 4.8 23.2 1.0
C F:PHE12 4.9 23.9 1.0
CD1 F:PHE12 4.9 25.7 1.0
SG F:CYS13 5.0 25.8 1.0

Reference:

B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, D.J.Richardson. Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase From Escherichia Coli J.Biol.Chem. V. 282 6425 2007.
ISSN: ISSN 0021-9258
PubMed: 17130127
DOI: 10.1074/JBC.M607353200
Page generated: Sun Aug 4 00:52:48 2024

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