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Magnesium in PDB 5h8y: Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal

Enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal

All present enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal:
1.8.7.1;

Protein crystallography data

The structure of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal, PDB code: 5h8y was solved by G.Kurisu, M.Nakayama, T.Hase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.07 / 2.20
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 176.219, 176.219, 195.315, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 24.7

Other elements in 5h8y:

The structure of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal also contains other interesting chemical elements:

Iron (Fe) 24 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal (pdb code 5h8y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal, PDB code: 5h8y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5h8y

Go back to Magnesium Binding Sites List in 5h8y
Magnesium binding site 1 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:8.3
occ:1.00
 OD1 A:ASN455 2.6 20.0 1.0
O A:ASN453 2.6 18.2 1.0
O A:HOH866 2.7 17.5 1.0
O A:VAL424 2.8 18.5 1.0
O A:HOH842 2.8 17.9 1.0
O A:HOH873 3.0 14.6 1.0
CG A:ASN455 3.3 18.9 1.0
ND2 A:ASN455 3.4 18.0 1.0
C A:VAL424 3.8 17.7 1.0
C A:ASN453 3.8 18.6 1.0
CD2 A:HIS423 4.1 17.5 1.0
O A:GLN454 4.1 15.5 1.0
C A:GLN454 4.1 16.7 1.0
O A:ALA491 4.2 20.1 1.0
NE2 A:HIS423 4.3 19.1 1.0
N A:VAL424 4.3 16.8 1.0
O A:HOH826 4.3 17.5 1.0
N A:ASN426 4.4 19.8 1.0
CB A:GLN454 4.4 17.8 1.0
N A:ASN455 4.4 17.1 1.0
CA A:GLN454 4.6 17.7 1.0
CB A:ASN455 4.6 18.0 1.0
N A:ASP425 4.6 18.4 1.0
NE2 A:GLN454 4.6 18.1 1.0
CA A:ASP425 4.6 19.1 1.0
N A:GLN454 4.7 18.0 1.0
CB A:ASN453 4.7 18.8 1.0
CA A:VAL424 4.7 18.0 1.0
O A:LEU489 4.8 19.3 1.0
CA A:ASN455 4.8 17.9 1.0
CA A:ASN453 4.8 18.9 1.0
N A:GLY427 4.8 19.9 1.0
O A:ASN488 4.9 19.4 1.0
C A:ASP425 4.9 19.6 1.0

Magnesium binding site 2 out of 4 in 5h8y

Go back to Magnesium Binding Sites List in 5h8y
Magnesium binding site 2 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:8.4
occ:1.00
 O B:ASN453 2.7 18.6 1.0
OD1 B:ASN455 2.7 20.0 1.0
O B:HOH834 2.7 19.1 1.0
O B:VAL424 2.7 17.2 1.0
O B:HOH827 3.0 16.9 1.0
O B:HOH872 3.2 14.8 1.0
CG B:ASN455 3.4 20.6 1.0
ND2 B:ASN455 3.5 21.2 1.0
C B:VAL424 3.7 19.1 1.0
C B:ASN453 3.9 19.6 1.0
O B:GLN454 4.0 21.1 1.0
O B:HOH877 4.1 25.7 1.0
CD2 B:HIS423 4.1 20.2 1.0
C B:GLN454 4.2 19.9 1.0
O B:ALA491 4.2 18.8 1.0
N B:ASN426 4.3 22.6 1.0
N B:VAL424 4.3 17.9 1.0
NE2 B:HIS423 4.3 22.9 1.0
CB B:GLN454 4.3 19.6 1.0
N B:ASN455 4.5 19.1 1.0
NE2 B:GLN454 4.6 18.9 1.0
CA B:ASP425 4.6 22.7 1.0
N B:ASP425 4.6 21.8 1.0
CA B:GLN454 4.6 19.6 1.0
CA B:VAL424 4.6 18.4 1.0
CB B:ASN455 4.7 19.4 1.0
N B:GLN454 4.7 19.6 1.0
CB B:ASN453 4.7 19.1 1.0
N B:GLY427 4.8 22.4 1.0
C B:ASP425 4.8 21.6 1.0
O B:LEU489 4.8 18.8 1.0
CA B:ASN455 4.9 19.4 1.0
O B:ASN488 4.9 20.7 1.0
CA B:ASN453 4.9 19.4 1.0

Magnesium binding site 3 out of 4 in 5h8y

Go back to Magnesium Binding Sites List in 5h8y
Magnesium binding site 3 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:12.0
occ:1.00
 OD1 C:ASN455 2.6 23.3 1.0
O C:ASN453 2.7 20.3 1.0
O C:HOH815 2.7 24.2 1.0
O C:VAL424 2.8 24.1 1.0
O C:HOH824 2.8 17.1 1.0
O C:HOH830 3.1 24.8 1.0
CG C:ASN455 3.3 22.1 1.0
ND2 C:ASN455 3.5 21.9 1.0
C C:VAL424 3.8 24.4 1.0
C C:ASN453 3.9 20.0 1.0
O C:GLN454 4.1 19.6 1.0
CD2 C:HIS423 4.1 25.2 1.0
C C:GLN454 4.2 20.6 1.0
O C:ALA491 4.2 22.5 1.0
NE2 C:HIS423 4.3 29.1 1.0
N C:VAL424 4.3 24.7 1.0
N C:ASN426 4.4 21.4 1.0
CB C:GLN454 4.4 20.4 1.0
N C:ASN455 4.5 22.5 1.0
NE2 C:GLN454 4.6 18.8 1.0
N C:ASP425 4.6 24.6 1.0
CA C:ASP425 4.6 23.9 1.0
CA C:GLN454 4.6 21.1 1.0
CB C:ASN455 4.6 22.0 1.0
CA C:VAL424 4.7 23.8 1.0
CB C:ASN453 4.7 18.8 1.0
N C:GLN454 4.7 19.7 1.0
O C:LEU489 4.8 22.1 1.0
N C:GLY427 4.8 26.8 1.0
CA C:ASN455 4.9 22.1 1.0
O C:ASN488 4.9 21.1 1.0
CA C:ASN453 4.9 19.2 1.0
C C:ASP425 4.9 25.0 1.0

Magnesium binding site 4 out of 4 in 5h8y

Go back to Magnesium Binding Sites List in 5h8y
Magnesium binding site 4 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-2 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:16.8
occ:1.00
 OD1 D:ASN455 2.6 28.7 1.0
O D:ASN453 2.6 28.6 1.0
O D:VAL424 2.7 29.9 1.0
O D:HOH802 2.7 27.0 1.0
O D:HOH805 3.0 22.4 1.0
CG D:ASN455 3.3 30.9 1.0
ND2 D:ASN455 3.4 33.7 1.0
C D:VAL424 3.7 31.6 1.0
C D:ASN453 3.8 28.9 1.0
O D:GLN454 4.0 33.1 1.0
C D:GLN454 4.1 29.4 1.0
ND1 D:HIS423 4.2 29.5 1.0
O D:ALA491 4.3 27.2 1.0
N D:VAL424 4.3 33.0 1.0
CB D:GLN454 4.3 27.7 1.0
N D:ASN426 4.4 31.4 1.0
CE1 D:HIS423 4.4 30.2 1.0
N D:ASN455 4.5 29.8 1.0
O D:HOH815 4.5 27.7 1.0
CA D:GLN454 4.5 28.6 1.0
N D:ASP425 4.6 32.4 1.0
CB D:ASN455 4.6 31.5 1.0
NE2 D:GLN454 4.6 26.7 1.0
CA D:VAL424 4.6 31.9 1.0
CA D:ASP425 4.6 31.3 1.0
N D:GLN454 4.7 28.2 1.0
CB D:ASN453 4.7 28.6 1.0
N D:GLY427 4.8 30.3 1.0
CA D:ASN455 4.8 30.4 1.0
O D:LEU489 4.8 22.6 1.0
C D:ASP425 4.9 31.5 1.0
CA D:ASN453 4.9 28.3 1.0
O D:ASN488 4.9 27.3 1.0

Reference:

J.Y.Kim, M.Nakayama, H.Toyota, G.Kurisu, T.Hase. Structural and Mutational Studies of An Electron Transfer Complex of Maize Sulfite Reductase and Ferredoxin. J.Biochem. V. 160 101 2016.
ISSN: ISSN 0021-924X
PubMed: 26920048
DOI: 10.1093/JB/MVW016
Page generated: Sun Sep 29 15:43:09 2024

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