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Molybdenum in PDB 1ogy: Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides

Enzymatic activity of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides

All present enzymatic activity of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides:
1.7.99.4;

Protein crystallography data

The structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides, PDB code: 1ogy was solved by P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.-M.Adriano, D.Pignol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 123.000, 225.200, 154.600, 90.00, 92.10, 90.00
R / Rfree (%) 25 / 26.9

Other elements in 1ogy:

The structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron (Fe) 48 atoms

Molybdenum Binding Sites:

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

Molybdenum binding site 1 out of 8 in 1ogy

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Molybdenum binding site 1 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1802

b:24.2
occ:1.00
SG A:CYS152 2.1 19.4 1.0
S12 A:MGD1804 2.4 10.0 1.0
S13 A:MGD1804 2.4 18.0 1.0
S12 A:MGD1803 2.5 16.0 1.0
S13 A:MGD1803 2.7 12.5 1.0
CB A:CYS152 3.0 15.9 1.0
C12 A:MGD1804 3.4 12.1 1.0
C13 A:MGD1804 3.4 12.9 1.0
C12 A:MGD1803 3.6 11.6 1.0
C13 A:MGD1803 3.6 12.1 1.0
CA A:GLY383 3.9 11.6 1.0
N A:GLN384 4.0 11.5 1.0
NE2 A:GLN384 4.1 18.5 1.0
CA A:CYS152 4.2 15.5 1.0
C A:GLY383 4.2 12.0 1.0
CG A:GLN384 4.3 16.4 1.0
N A:GLY383 4.5 11.6 1.0
SD A:MET346 4.7 10.0 1.0
NH2 A:ARG694 4.7 12.7 1.0
CD A:GLN384 4.7 17.1 1.0
NH1 A:ARG694 4.8 13.5 1.0
CE1 A:HIS700 4.8 10.0 1.0
CE A:MET346 4.9 10.2 1.0
NE2 A:HIS700 4.9 11.0 1.0
C11 A:MGD1804 4.9 12.0 1.0
C14 A:MGD1804 4.9 10.5 1.0
CA A:GLN384 5.0 12.2 1.0

Molybdenum binding site 2 out of 8 in 1ogy

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Molybdenum binding site 2 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo1802

b:38.7
occ:1.00
SG C:CYS152 2.3 39.3 1.0
S12 C:MGD1803 2.4 25.5 1.0
S13 C:MGD1804 2.5 27.4 1.0
S12 C:MGD1804 2.5 23.3 1.0
S13 C:MGD1803 2.7 19.5 1.0
CB C:CYS152 2.9 37.0 1.0
C12 C:MGD1803 3.5 23.2 1.0
C13 C:MGD1804 3.5 25.1 1.0
C12 C:MGD1804 3.5 25.1 1.0
C13 C:MGD1803 3.5 20.6 1.0
NE2 C:GLN384 3.9 32.5 1.0
CA C:GLY383 3.9 24.6 1.0
N C:GLN384 4.0 24.3 1.0
CG C:GLN384 4.2 30.7 1.0
CA C:CYS152 4.2 36.5 1.0
C C:GLY383 4.3 24.5 1.0
CD C:GLN384 4.6 32.3 1.0
SD C:MET346 4.6 33.2 1.0
N C:GLY383 4.6 24.5 1.0
CE1 C:HIS700 4.8 24.3 1.0
NH1 C:ARG694 4.8 30.1 1.0
NH2 C:ARG694 4.8 32.6 1.0
NE2 C:HIS700 4.8 24.2 1.0
CA C:GLN384 4.9 24.9 1.0
CB C:GLN384 4.9 27.5 1.0
CE C:MET346 5.0 30.1 1.0
C14 C:MGD1804 5.0 25.8 1.0
C11 C:MGD1803 5.0 24.3 1.0

Molybdenum binding site 3 out of 8 in 1ogy

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Molybdenum binding site 3 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mo1802

b:28.5
occ:1.00
SG E:CYS152 2.1 26.2 1.0
S12 E:MGD1804 2.4 10.0 1.0
S12 E:MGD1803 2.4 14.4 1.0
S13 E:MGD1803 2.5 16.1 1.0
S13 E:MGD1804 2.6 16.0 1.0
CB E:CYS152 2.9 23.6 1.0
C12 E:MGD1804 3.4 11.3 1.0
C13 E:MGD1803 3.5 11.9 1.0
C12 E:MGD1803 3.5 12.5 1.0
C13 E:MGD1804 3.5 11.7 1.0
CA E:GLY383 4.0 15.0 1.0
CA E:CYS152 4.1 23.0 1.0
NE2 E:GLN384 4.1 23.5 1.0
N E:GLN384 4.1 19.6 1.0
C E:GLY383 4.4 17.6 1.0
CG E:GLN384 4.4 22.6 1.0
SD E:MET346 4.5 20.5 1.0
N E:GLY383 4.6 12.7 1.0
NH2 E:ARG694 4.7 24.4 1.0
NH1 E:ARG694 4.7 22.9 1.0
CD E:GLN384 4.8 22.3 1.0
CE1 E:HIS700 4.8 13.0 1.0
CE E:MET346 4.8 16.7 1.0
NE2 E:HIS700 4.9 13.0 1.0
C14 E:MGD1803 4.9 10.0 1.0
C11 E:MGD1804 4.9 11.2 1.0
C E:CYS152 5.0 22.1 1.0
C11 E:MGD1803 5.0 13.6 1.0
N E:CYS152 5.0 23.2 1.0

Molybdenum binding site 4 out of 8 in 1ogy

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Molybdenum binding site 4 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mo1802

b:35.6
occ:1.00
SG G:CYS152 2.2 40.2 1.0
S12 G:MGD1804 2.3 31.0 1.0
S13 G:MGD1803 2.5 26.1 1.0
S12 G:MGD1803 2.5 28.2 1.0
S13 G:MGD1804 2.6 42.5 1.0
CB G:CYS152 2.8 40.5 1.0
C12 G:MGD1804 3.4 35.2 1.0
C13 G:MGD1804 3.5 34.6 1.0
C13 G:MGD1803 3.5 26.1 1.0
C12 G:MGD1803 3.5 26.5 1.0
CA G:GLY383 3.9 26.2 1.0
NE2 G:GLN384 4.0 34.7 1.0
CA G:CYS152 4.1 39.3 1.0
N G:GLN384 4.1 27.6 1.0
C G:GLY383 4.4 26.9 1.0
CG G:GLN384 4.4 31.5 1.0
SD G:MET346 4.4 46.0 1.0
N G:GLY383 4.6 25.6 1.0
NH2 G:ARG694 4.7 35.3 1.0
CE G:MET346 4.7 46.2 1.0
CD G:GLN384 4.8 34.0 1.0
NH1 G:ARG694 4.8 34.5 1.0
C G:CYS152 4.9 37.8 1.0
CE1 G:HIS700 4.9 26.1 1.0
C11 G:MGD1804 4.9 35.7 1.0
N G:CYS152 5.0 40.8 1.0
NE2 G:HIS700 5.0 26.3 1.0

Molybdenum binding site 5 out of 8 in 1ogy

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Molybdenum binding site 5 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mo1802

b:66.7
occ:1.00
SG I:CYS152 2.3 57.7 1.0
S12 I:MGD1803 2.4 40.7 1.0
S12 I:MGD1804 2.6 60.5 1.0
S13 I:MGD1804 2.7 64.5 1.0
S13 I:MGD1803 2.8 41.8 1.0
CB I:CYS152 2.8 55.2 1.0
C12 I:MGD1803 3.5 41.7 1.0
C13 I:MGD1803 3.6 39.5 1.0
C13 I:MGD1804 3.7 59.9 1.0
C12 I:MGD1804 3.7 60.8 1.0
NE2 I:GLN384 3.8 46.6 1.0
CA I:GLY383 3.8 49.4 1.0
N I:GLN384 3.8 46.7 1.0
CG I:GLN384 4.1 45.7 1.0
CA I:CYS152 4.1 54.5 1.0
C I:GLY383 4.2 48.1 1.0
CD I:GLN384 4.5 46.6 1.0
N I:GLY383 4.5 51.4 1.0
SD I:MET346 4.6 50.6 1.0
CB I:GLN384 4.8 46.3 1.0
CA I:GLN384 4.9 45.8 1.0
NE2 I:HIS700 4.9 50.0 1.0
CE1 I:HIS700 4.9 48.8 1.0
C I:CYS152 4.9 53.2 1.0
NH2 I:ARG694 5.0 58.9 1.0
N I:CYS152 5.0 56.3 1.0
C11 I:MGD1803 5.0 44.5 1.0
NH1 I:ARG694 5.0 57.2 1.0

Molybdenum binding site 6 out of 8 in 1ogy

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Molybdenum binding site 6 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mo1802

b:40.1
occ:1.00
SG K:CYS152 2.3 40.1 1.0
S12 K:MGD1803 2.4 40.0 1.0
S13 K:MGD1803 2.5 31.6 1.0
S12 K:MGD1804 2.5 34.6 1.0
S13 K:MGD1804 2.5 39.0 1.0
CB K:CYS152 2.8 38.4 1.0
C12 K:MGD1804 3.5 34.5 1.0
C13 K:MGD1804 3.5 33.8 1.0
C13 K:MGD1803 3.5 34.1 1.0
C12 K:MGD1803 3.5 35.2 1.0
CA K:GLY383 4.0 27.9 1.0
NE2 K:GLN384 4.0 31.0 1.0
N K:GLN384 4.0 27.9 1.0
CA K:CYS152 4.1 37.6 1.0
CG K:GLN384 4.3 29.9 1.0
C K:GLY383 4.3 27.6 1.0
N K:GLY383 4.6 28.3 1.0
NH2 K:ARG694 4.7 53.9 1.0
SD K:MET346 4.7 36.1 1.0
CD K:GLN384 4.7 30.8 1.0
NH1 K:ARG694 4.8 53.7 1.0
CE1 K:HIS700 4.8 26.8 1.0
CE K:MET346 4.9 33.9 1.0
NE2 K:HIS700 4.9 27.0 1.0
C11 K:MGD1804 5.0 35.0 1.0
C K:CYS152 5.0 36.2 1.0
C14 K:MGD1804 5.0 31.6 1.0
C11 K:MGD1803 5.0 35.5 1.0

Molybdenum binding site 7 out of 8 in 1ogy

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Molybdenum binding site 7 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mo1802

b:39.8
occ:1.00
SG M:CYS152 2.3 41.7 1.0
S12 M:MGD1803 2.5 27.0 1.0
S12 M:MGD1804 2.5 28.5 1.0
S13 M:MGD1804 2.5 34.1 1.0
S13 M:MGD1803 2.6 25.6 1.0
CB M:CYS152 2.9 38.5 1.0
C13 M:MGD1804 3.4 29.4 1.0
C12 M:MGD1804 3.4 28.6 1.0
C12 M:MGD1803 3.5 24.1 1.0
C13 M:MGD1803 3.5 23.7 1.0
CA M:GLY383 3.9 29.8 1.0
N M:GLN384 4.0 29.1 1.0
NE2 M:GLN384 4.1 28.5 1.0
CA M:CYS152 4.2 38.3 1.0
C M:GLY383 4.3 29.1 1.0
CG M:GLN384 4.3 27.9 1.0
N M:GLY383 4.6 30.7 1.0
SD M:MET346 4.7 37.1 1.0
CD M:GLN384 4.7 27.9 1.0
NH2 M:ARG694 4.7 33.8 1.0
NH1 M:ARG694 4.7 33.5 1.0
CE1 M:HIS700 4.8 28.1 1.0
NE2 M:HIS700 4.8 29.0 1.0
C14 M:MGD1804 4.9 27.9 1.0
CE M:MET346 4.9 32.8 1.0
C11 M:MGD1804 4.9 28.2 1.0
C11 M:MGD1803 5.0 24.6 1.0
CA M:GLN384 5.0 29.4 1.0

Molybdenum binding site 8 out of 8 in 1ogy

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Molybdenum binding site 8 out of 8 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mo1802

b:62.4
occ:1.00
S12 O:MGD1804 2.4 51.2 1.0
SG O:CYS152 2.4 51.9 1.0
S12 O:MGD1803 2.5 42.0 1.0
S13 O:MGD1804 2.6 49.9 1.0
S13 O:MGD1803 2.6 38.0 1.0
CB O:CYS152 3.0 50.3 1.0
C12 O:MGD1804 3.4 50.2 1.0
C13 O:MGD1804 3.4 49.5 1.0
C12 O:MGD1803 3.6 41.7 1.0
C13 O:MGD1803 3.6 39.4 1.0
CA O:GLY383 3.7 43.9 1.0
N O:GLN384 3.9 43.4 1.0
NE2 O:GLN384 4.0 47.5 1.0
C O:GLY383 4.1 43.5 1.0
CG O:GLN384 4.2 46.4 1.0
CA O:CYS152 4.3 49.0 1.0
N O:GLY383 4.5 45.1 1.0
SD O:MET346 4.6 45.2 1.0
CD O:GLN384 4.7 47.9 1.0
NH2 O:ARG694 4.7 61.9 1.0
CE1 O:HIS700 4.8 53.3 1.0
NH1 O:ARG694 4.8 61.3 1.0
NE2 O:HIS700 4.8 53.2 1.0
C14 O:MGD1804 4.9 49.6 1.0
CA O:GLN384 4.9 43.0 1.0
C11 O:MGD1804 4.9 50.2 1.0
CE O:MET346 4.9 41.8 1.0
CB O:GLN384 4.9 44.5 1.0

Reference:

P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.-M.Adriano, D.Pignol. Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase Nat.Struct.Biol. V. 10 928 2003.
ISSN: ISSN 1072-8368
PubMed: 14528294
DOI: 10.1038/NSB994
Page generated: Tue Dec 15 05:16:23 2020

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