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Magnesium in PDB 1b4n: Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate

Protein crystallography data

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate, PDB code: 1b4n was solved by Y.L.Hu, S.Faham, R.Roy, M.W.W.Adams, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.400, 170.500, 180.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 24.4

Other elements in 1b4n:

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Iron (Fe) 16 atoms
Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate (pdb code 1b4n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate, PDB code: 1b4n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1b4n

Go back to Magnesium Binding Sites List in 1b4n
Magnesium binding site 1 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg623

b:16.5
occ:1.00
 MG1 A:PTE623 0.0 16.5 1.0
O5P A:PTE623 2.0 19.4 1.0
O1P A:PTE623 2.0 19.4 1.0
O A:ALA181 2.1 19.0 1.0
O A:ASN92 2.1 19.6 1.0
O A:HOH659 2.1 20.0 1.0
O A:HOH658 2.1 15.2 1.0
C A:ALA181 3.1 18.5 1.0
C A:ASN92 3.3 15.4 1.0
P1 A:PTE623 3.3 23.4 1.0
P2 A:PTE623 3.3 22.2 1.0
O7P A:PTE623 3.5 20.6 1.0
O3P A:PTE623 3.5 22.3 1.0
CA A:ALA182 3.9 17.9 1.0
N A:ALA182 3.9 18.7 1.0
CA A:LEU93 3.9 14.2 1.0
O A:HOH657 4.0 19.8 1.0
N A:LEU93 4.1 14.7 1.0
C1 A:PTE623 4.1 25.0 1.0
O A:HOH640 4.1 13.5 1.0
CB A:LEU93 4.2 14.5 1.0
CA A:ALA181 4.2 18.9 1.0
N A:ALA181 4.2 18.0 1.0
C21 A:PTE623 4.2 24.6 1.0
O4P A:PTE623 4.2 23.3 1.0
O8P A:PTE623 4.3 22.1 1.0
CB A:ALA182 4.3 18.2 1.0
N A:ASN92 4.4 12.8 1.0
CA A:ASN92 4.4 14.3 1.0
O6P A:PTE623 4.6 18.9 1.0
O2P A:PTE623 4.6 22.3 1.0
CB A:ALA181 4.7 20.4 1.0
O2 A:PTE623 4.8 25.2 1.0
N6 A:PTE623 4.9 24.6 1.0
CB A:ASN92 4.9 10.2 1.0
C2 A:PTE623 4.9 24.6 1.0

Magnesium binding site 2 out of 4 in 1b4n

Go back to Magnesium Binding Sites List in 1b4n
Magnesium binding site 2 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg623

b:14.7
occ:1.00
 MG1 B:PTE623 0.0 14.7 1.0
O1P B:PTE623 2.0 14.0 1.0
O5P B:PTE623 2.0 16.5 1.0
O B:ASN92 2.1 16.3 1.0
O B:ALA181 2.1 18.3 1.0
O B:HOH667 2.1 17.1 1.0
O B:HOH666 2.1 15.1 1.0
P2 B:PTE623 3.2 16.0 1.0
C B:ASN92 3.3 12.9 1.0
C B:ALA181 3.3 14.2 1.0
O7P B:PTE623 3.3 19.3 1.0
P1 B:PTE623 3.4 17.4 1.0
O3P B:PTE623 3.6 17.0 1.0
CA B:LEU93 3.8 14.8 1.0
C21 B:PTE623 4.0 22.9 1.0
N B:LEU93 4.0 13.7 1.0
CA B:ALA182 4.1 9.3 1.0
O8P B:PTE623 4.1 21.5 1.0
N B:ALA182 4.1 13.1 1.0
C1 B:PTE623 4.1 23.6 1.0
CB B:LEU93 4.1 15.2 1.0
O4P B:PTE623 4.3 21.2 1.0
N B:ASN92 4.3 12.0 1.0
CA B:ALA181 4.4 14.7 1.0
CA B:ASN92 4.4 11.2 1.0
N B:ALA181 4.4 14.3 1.0
CB B:ALA182 4.5 11.2 1.0
O B:HOH624 4.5 14.9 1.0
O6P B:PTE623 4.6 17.8 1.0
O2P B:PTE623 4.7 11.0 1.0
CB B:ASN92 4.8 10.8 1.0
O2 B:PTE623 4.9 21.9 1.0
C2 B:PTE623 4.9 21.4 1.0
CB B:ALA181 4.9 12.5 1.0
C3 B:PTE623 5.0 23.2 1.0

Magnesium binding site 3 out of 4 in 1b4n

Go back to Magnesium Binding Sites List in 1b4n
Magnesium binding site 3 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg623

b:19.4
occ:1.00
 MG1 C:PTE623 0.0 19.4 1.0
O1P C:PTE623 2.0 22.6 1.0
O5P C:PTE623 2.0 20.5 1.0
O C:ALA181 2.1 21.0 1.0
O C:ASN92 2.1 20.4 1.0
O C:HOH669 2.1 21.6 1.0
O C:HOH670 2.1 21.0 1.0
C C:ALA181 3.2 18.4 1.0
C C:ASN92 3.3 15.1 1.0
P1 C:PTE623 3.3 16.0 1.0
P2 C:PTE623 3.3 20.4 1.0
O3P C:PTE623 3.4 17.6 1.0
O7P C:PTE623 3.5 17.7 1.0
O C:HOH666 3.6 9.2 1.0
CA C:LEU93 3.9 14.3 1.0
N C:LEU93 4.0 15.5 1.0
CA C:ALA182 4.0 15.1 1.0
C1 C:PTE623 4.0 25.8 1.0
N C:ALA182 4.0 16.6 1.0
O4P C:PTE623 4.1 21.1 1.0
O8P C:PTE623 4.1 24.4 1.0
CB C:LEU93 4.1 14.9 1.0
C21 C:PTE623 4.1 23.5 1.0
CA C:ALA181 4.2 17.5 1.0
N C:ALA181 4.3 16.3 1.0
N C:ASN92 4.3 14.8 1.0
CA C:ASN92 4.4 14.6 1.0
CB C:ALA182 4.4 11.0 1.0
O2P C:PTE623 4.5 20.2 1.0
O6P C:PTE623 4.6 18.6 1.0
CB C:ALA181 4.7 12.9 1.0
C2 C:PTE623 4.8 25.1 1.0
CB C:ASN92 4.9 10.7 1.0
N6 C:PTE623 4.9 22.6 1.0

Magnesium binding site 4 out of 4 in 1b4n

Go back to Magnesium Binding Sites List in 1b4n
Magnesium binding site 4 out of 4 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, Complexed with Glutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg623

b:18.2
occ:1.00
 MG1 D:PTE623 0.0 18.2 1.0
O1P D:PTE623 2.0 18.2 1.0
O5P D:PTE623 2.0 19.2 1.0
O D:ASN92 2.1 19.2 1.0
O D:ALA181 2.1 18.7 1.0
O D:HOH671 2.1 20.3 1.0
O D:HOH672 2.1 17.8 1.0
C D:ALA181 3.2 14.0 1.0
C D:ASN92 3.3 17.0 1.0
P2 D:PTE623 3.3 18.0 1.0
P1 D:PTE623 3.3 13.8 1.0
O7P D:PTE623 3.4 17.2 1.0
O3P D:PTE623 3.5 15.8 1.0
CA D:ALA182 3.9 13.5 1.0
CA D:LEU93 3.9 16.9 1.0
N D:ALA182 4.0 13.4 1.0
N D:LEU93 4.0 17.4 1.0
C1 D:PTE623 4.0 23.1 1.0
C21 D:PTE623 4.1 22.4 1.0
O8P D:PTE623 4.1 21.6 1.0
O4P D:PTE623 4.1 22.4 1.0
CB D:LEU93 4.1 17.2 1.0
CA D:ALA181 4.3 16.6 1.0
O D:HOH642 4.3 32.6 1.0
CB D:ALA182 4.3 14.4 1.0
CA D:ASN92 4.3 15.3 1.0
N D:ALA181 4.3 18.9 1.0
N D:ASN92 4.4 16.6 1.0
O2P D:PTE623 4.6 17.7 1.0
O6P D:PTE623 4.7 11.6 1.0
C2 D:PTE623 4.8 23.5 1.0
CB D:ALA181 4.8 15.3 1.0
O2 D:PTE623 4.8 25.9 1.0
CB D:ASN92 4.9 12.3 1.0

Reference:

Y.Hu, S.Faham, R.Roy, M.W.Adams, D.C.Rees. Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus: the 1.85 A Resolution Crystal Structure and Its Mechanistic Implications. J.Mol.Biol. V. 286 899 1999.
ISSN: ISSN 0022-2836
PubMed: 10024458
DOI: 10.1006/JMBI.1998.2488
Page generated: Tue Aug 13 02:10:28 2024

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