Atomistry » Magnesium » PDB 5h2f-5hi8 » 5h8y
Atomistry »
  Magnesium »
    PDB 5h2f-5hi8 »
      5h8y »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy