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Iron 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:

Molybdenum (Mo) 2 atoms
Magnesium (Mg) 2 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Nicotinate Dehydrogenase (pdb code 3hrd). 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 Nicotinate Dehydrogenase, PDB code: 3hrd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3hrd

Go back to Iron Binding Sites List in 3hrd
Iron binding site 1 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe907

b:13.6
occ:1.00
FE1 D:FES907 0.0 13.6 1.0
S1 D:FES907 2.3 11.3 1.0
S2 D:FES907 2.3 10.2 1.0
SG D:CYS101 2.3 13.3 1.0
SG D:CYS138 2.4 14.3 1.0
FE2 D:FES907 2.7 13.2 1.0
CB D:CYS101 3.3 14.6 1.0
CB D:CYS138 3.3 7.7 1.0
N D:CYS101 3.5 14.0 1.0
O A:HOH510 3.7 15.3 1.0
CA D:CYS101 3.8 12.1 1.0
N D:GLY102 4.0 13.6 1.0
N D:CYS138 4.2 10.8 1.0
SG D:CYS136 4.2 10.7 1.0
C D:CYS101 4.3 12.1 1.0
CA D:CYS138 4.4 11.4 1.0
N D:TYR103 4.5 13.3 1.0
C D:GLN100 4.7 14.0 1.0
CB D:GLN100 4.7 15.9 1.0
SG D:CYS104 4.8 13.4 1.0
N D:ARG137 4.9 11.5 1.0
N D:CYS104 5.0 13.2 1.0
CA D:GLY102 5.0 12.6 1.0

Iron binding site 2 out of 8 in 3hrd

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Iron binding site 2 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe907

b:13.2
occ:1.00
FE2 D:FES907 0.0 13.2 1.0
S1 D:FES907 2.2 11.3 1.0
S2 D:FES907 2.3 10.2 1.0
SG D:CYS136 2.3 10.7 1.0
SG D:CYS104 2.4 13.4 1.0
FE1 D:FES907 2.7 13.6 1.0
CB D:CYS104 3.4 14.2 1.0
CB D:CYS136 3.4 9.7 1.0
CA D:CYS136 3.8 11.2 1.0
N D:CYS104 4.2 13.2 1.0
N D:ARG137 4.3 11.5 1.0
CA D:CYS104 4.4 12.4 1.0
CB D:CYS138 4.4 7.7 1.0
N D:CYS138 4.5 10.8 1.0
SG D:CYS138 4.5 14.3 1.0
C D:CYS136 4.5 11.5 1.0
SG D:CYS101 4.6 13.3 1.0
O D:HOH205 4.6 15.5 1.0
CG2 D:THR139 4.7 7.7 1.0
O D:LEU135 4.9 11.9 1.0
CD1 D:ILE144 4.9 14.5 1.0
N D:THR139 5.0 12.6 1.0

Iron binding site 3 out of 8 in 3hrd

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Iron binding site 3 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe908

b:15.3
occ:1.00
FE1 D:FES908 0.0 15.3 1.0
S1 D:FES908 2.2 11.7 1.0
S2 D:FES908 2.2 12.9 1.0
SG D:CYS42 2.4 12.4 1.0
SG D:CYS47 2.4 13.4 1.0
FE2 D:FES908 2.7 15.5 1.0
N D:CYS42 3.4 10.7 1.0
N D:CYS47 3.5 13.4 1.0
CB D:CYS42 3.5 8.8 1.0
CB D:CYS47 3.5 10.9 1.0
N D:GLY48 3.8 14.4 1.0
CA D:CYS47 3.9 13.5 1.0
N D:SER43 3.9 10.0 1.0
CA D:CYS42 3.9 11.4 1.0
N D:GLY41 4.2 11.6 1.0
C D:CYS47 4.2 13.7 1.0
C D:GLY41 4.3 11.9 1.0
N D:GLU46 4.3 16.1 1.0
C D:CYS42 4.3 11.5 1.0
N D:GLY45 4.4 17.2 1.0
SG D:CYS62 4.5 13.7 1.0
N D:ALA49 4.5 12.8 1.0
CA D:GLY41 4.5 10.2 1.0
C D:GLU46 4.5 14.9 1.0
N D:GLU44 4.6 17.0 1.0
C D:GLY45 4.6 16.2 1.0
SG D:CYS50 4.7 12.7 1.0
CA D:GLY45 4.7 16.2 1.0
CA D:GLY48 4.8 13.4 1.0
CA D:SER43 4.9 13.4 1.0
CA D:GLU46 4.9 16.1 1.0

Iron binding site 4 out of 8 in 3hrd

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Iron binding site 4 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe908

b:15.5
occ:1.00
FE2 D:FES908 0.0 15.5 1.0
S1 D:FES908 2.2 11.7 1.0
S2 D:FES908 2.3 12.9 1.0
SG D:CYS50 2.3 12.7 1.0
SG D:CYS62 2.4 13.7 1.0
FE1 D:FES908 2.7 15.3 1.0
CB D:CYS62 3.2 13.7 1.0
CB D:CYS50 3.4 11.3 1.0
N D:GLY45 4.1 17.2 1.0
N D:CYS62 4.2 13.7 1.0
N D:CYS50 4.3 12.9 1.0
CA D:CYS62 4.3 13.3 1.0
CA D:GLY45 4.4 16.2 1.0
CB D:THR60 4.4 13.1 1.0
SG D:CYS42 4.4 12.4 1.0
CG2 D:THR60 4.4 9.2 1.0
CA D:CYS50 4.5 11.6 1.0
N D:SER43 4.6 10.0 1.0
SG D:CYS47 4.7 13.4 1.0
N D:GLU44 4.9 17.0 1.0
N D:GLY48 4.9 14.4 1.0
CA D:SER43 4.9 13.4 1.0
CA D:THR60 5.0 13.3 1.0

Iron binding site 5 out of 8 in 3hrd

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Iron binding site 5 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe907

b:31.6
occ:1.00
FE1 H:FES907 0.0 31.6 1.0
S2 H:FES907 2.2 27.8 1.0
S1 H:FES907 2.2 29.4 1.0
SG H:CYS104 2.3 25.1 1.0
SG H:CYS136 2.6 36.0 1.0
FE2 H:FES907 2.7 30.2 1.0
CB H:CYS136 3.3 34.8 1.0
CB H:CYS104 3.3 29.3 1.0
CA H:CYS136 3.7 34.9 1.0
N H:CYS104 4.2 29.1 1.0
N H:ARG137 4.2 35.1 1.0
CB H:CYS138 4.4 31.3 1.0
CA H:CYS104 4.4 28.4 1.0
C H:CYS136 4.5 35.5 1.0
N H:CYS138 4.5 33.7 1.0
SG H:CYS138 4.5 28.4 1.0
SG H:CYS101 4.6 26.9 1.0
O H:LEU135 4.9 34.4 1.0
N H:CYS136 5.0 34.7 1.0
CA H:CYS138 5.0 34.4 1.0

Iron binding site 6 out of 8 in 3hrd

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Iron binding site 6 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe907

b:30.2
occ:1.00
FE2 H:FES907 0.0 30.2 1.0
S1 H:FES907 2.2 29.4 1.0
S2 H:FES907 2.2 27.8 1.0
SG H:CYS138 2.4 28.4 1.0
SG H:CYS101 2.5 26.9 1.0
FE1 H:FES907 2.7 31.6 1.0
CB H:CYS101 3.1 28.5 1.0
CB H:CYS138 3.2 31.3 1.0
N H:CYS101 3.6 29.9 1.0
CA H:CYS101 3.8 28.8 1.0
N H:GLY102 4.0 29.9 1.0
N H:CYS138 4.1 33.7 1.0
C H:CYS101 4.3 30.0 1.0
SG H:CYS136 4.3 36.0 1.0
CA H:CYS138 4.3 34.4 1.0
N H:TYR103 4.5 30.1 1.0
SG H:CYS104 4.7 25.1 1.0
N H:ARG137 4.7 35.1 1.0
CB H:GLN100 4.7 29.7 1.0
C H:GLN100 4.8 29.4 1.0

Iron binding site 7 out of 8 in 3hrd

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Iron binding site 7 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe908

b:36.2
occ:1.00
FE1 H:FES908 0.0 36.2 1.0
S1 H:FES908 2.1 37.6 1.0
S2 H:FES908 2.2 37.3 1.0
SG H:CYS47 2.4 34.3 1.0
SG H:CYS42 2.4 33.0 1.0
FE2 H:FES908 2.6 36.6 1.0
N H:CYS42 3.4 32.3 1.0
N H:CYS47 3.6 36.3 1.0
CB H:CYS42 3.7 34.2 1.0
CB H:CYS47 3.7 35.0 1.0
N H:SER43 3.9 37.3 1.0
N H:GLY48 3.9 32.3 1.0
CA H:CYS42 4.0 34.7 1.0
N H:GLY41 4.0 29.4 1.0
CA H:CYS47 4.1 34.1 1.0
N H:GLU46 4.2 39.6 1.0
C H:GLY41 4.2 30.8 1.0
N H:GLY45 4.3 41.2 1.0
C H:CYS42 4.4 36.1 1.0
CA H:GLY41 4.4 29.8 1.0
C H:CYS47 4.4 32.6 1.0
SG H:CYS62 4.4 41.7 1.0
N H:ALA49 4.6 31.3 1.0
CA H:GLY45 4.6 40.1 1.0
C H:GLU46 4.6 38.4 1.0
C H:GLY45 4.6 39.6 1.0
N H:GLU44 4.7 42.0 1.0
SG H:CYS50 4.7 33.5 1.0
CA H:GLU46 4.8 38.8 1.0
CA H:GLY48 4.9 31.6 1.0
CA H:SER43 4.9 39.8 1.0
N H:CYS50 4.9 30.1 1.0

Iron binding site 8 out of 8 in 3hrd

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Iron binding site 8 out of 8 in the Crystal Structure of Nicotinate Dehydrogenase


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 Nicotinate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe908

b:36.6
occ:1.00
FE2 H:FES908 0.0 36.6 1.0
S1 H:FES908 2.2 37.6 1.0
S2 H:FES908 2.2 37.3 1.0
SG H:CYS50 2.4 33.5 1.0
SG H:CYS62 2.5 41.7 1.0
FE1 H:FES908 2.6 36.2 1.0
CB H:CYS62 3.1 38.0 1.0
CB H:CYS50 3.4 29.8 1.0
N H:GLY45 4.0 41.2 1.0
CA H:GLY45 4.1 40.1 1.0
N H:CYS62 4.2 35.6 1.0
CA H:CYS62 4.3 36.7 1.0
N H:CYS50 4.3 30.1 1.0
SG H:CYS42 4.4 33.0 1.0
CA H:CYS50 4.4 30.7 1.0
CB H:THR60 4.5 38.9 1.0
SG H:CYS47 4.6 34.3 1.0
N H:SER43 4.7 37.3 1.0
CG2 H:THR60 4.7 36.9 1.0
C H:GLY45 4.8 39.6 1.0
N H:GLY48 4.9 32.3 1.0
N H:GLU44 5.0 42.0 1.0
CA H:SER43 5.0 39.8 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: Sun Aug 4 11:45:34 2024

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