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Molybdenum in PDB 3hrd: Crystal Structure of Nicotinate Dehydrogenase

Protein crystallography data

The structure of Crystal Structure of Nicotinate Dehydrogenase, PDB code: 3hrd was solved by N.Wagener, A.J.Pierik, R.Hille, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.43 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.069, 71.700, 214.485, 90.00, 90.23, 90.00
R / Rfree (%) 21.3 / 25.1

Other elements in 3hrd:

The structure of Crystal Structure of Nicotinate Dehydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 8 atoms
Calcium (Ca) 1 atom

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Nicotinate Dehydrogenase (pdb code 3hrd). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Crystal Structure of Nicotinate Dehydrogenase, PDB code: 3hrd:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 3hrd

Go back to Molybdenum Binding Sites List in 3hrd
Molybdenum binding site 1 out of 2 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo920

b:17.3
occ:1.00
MO B:MOS920 0.0 17.3 1.0
O1 B:MOS920 1.7 9.1 1.0
O2 B:MOS920 1.8 14.0 1.0
SE A:SE922 2.3 21.3 0.8
S7' B:MCN921 2.4 14.0 1.0
S8' B:MCN921 2.5 15.0 1.0
OE2 B:GLU289 3.1 15.7 1.0
C7' B:MCN921 3.4 15.6 1.0
C8' B:MCN921 3.5 15.7 1.0
CD B:GLU289 3.6 13.7 1.0
CA B:SER85 3.9 17.2 1.0
CB B:SER85 4.0 18.6 1.0
N B:ALA86 4.1 18.5 1.0
OE1 B:GLU289 4.1 13.0 1.0
CA A:GLY240 4.1 12.3 1.0
CG B:GLU289 4.2 12.4 1.0
N A:GLY240 4.2 14.0 1.0
C A:PHE239 4.4 14.5 1.0
O A:PHE239 4.4 14.8 1.0
CA A:ARG351 4.5 14.1 1.0
N A:ARG351 4.5 13.9 1.0
C B:SER85 4.6 17.2 1.0
C6' B:MCN921 4.8 14.2 1.0
NE2 A:GLN208 4.8 13.0 1.0
O B:THR84 4.8 14.6 1.0
CD1 A:LEU243 4.9 8.5 1.0
C9' B:MCN921 4.9 15.9 1.0

Molybdenum binding site 2 out of 2 in 3hrd

Go back to Molybdenum Binding Sites List in 3hrd
Molybdenum binding site 2 out of 2 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mo920

b:35.9
occ:1.00
MO F:MOS920 0.0 35.9 1.0
O1 F:MOS920 1.7 37.5 1.0
O2 F:MOS920 1.8 34.8 1.0
SE E:SE922 2.3 38.4 0.8
S7' F:MCN921 2.4 32.2 1.0
S8' F:MCN921 2.5 32.6 1.0
OE2 F:GLU289 2.9 34.5 1.0
CD F:GLU289 3.4 36.2 1.0
C7' F:MCN921 3.4 31.3 1.0
C8' F:MCN921 3.4 31.2 1.0
OE1 F:GLU289 3.9 35.6 1.0
CA F:SER85 4.0 33.7 1.0
CG F:GLU289 4.0 35.4 1.0
CB F:SER85 4.0 35.2 1.0
N F:ALA86 4.1 32.9 1.0
CA E:GLY240 4.2 28.1 1.0
N E:GLY240 4.4 28.6 1.0
CA E:ARG351 4.5 36.9 1.0
N E:ARG351 4.6 36.8 1.0
C E:PHE239 4.6 28.7 1.0
C F:SER85 4.6 32.1 1.0
O E:PHE239 4.6 30.2 1.0
O F:THR84 4.7 32.1 1.0
C6' F:MCN921 4.8 29.1 1.0
CD1 E:LEU243 4.8 35.9 1.0
C9' F:MCN921 4.9 30.9 1.0
NE2 E:GLN208 4.9 26.9 1.0

Reference:

N.Wagener, A.J.Pierik, A.Ibdah, R.Hille, H.Dobbek. The Mo-Se Active Site of Nicotinate Dehydrogenase Proc.Natl.Acad.Sci.Usa V. 106 11055 2009.
ISSN: ISSN 0027-8424
PubMed: 19549881
DOI: 10.1073/PNAS.0902210106
Page generated: Mon Jan 25 15:37:39 2021

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