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Magnesium in PDB 5h8v: Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 Crystal

Enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 Crystal

All present enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 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-1 Crystal, PDB code: 5h8v 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) 48.04 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.346, 103.346, 255.048, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.9

Other elements in 5h8v:

The structure of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 Crystal also contains other interesting chemical elements:

Iron (Fe) 10 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-1 Crystal (pdb code 5h8v). 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-1 Crystal, PDB code: 5h8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5h8v

Go back to Magnesium Binding Sites List in 5h8v
Magnesium binding site 1 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 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-1 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:8.2
occ:1.00
 ND2 A:ASN455 2.6 19.0 1.0
O A:ASN453 2.6 16.4 1.0
O A:HOH842 2.6 16.7 1.0
O A:VAL424 2.7 16.4 1.0
O A:HOH878 2.7 15.3 1.0
O A:HOH812 3.3 13.9 1.0
CG A:ASN455 3.3 19.5 1.0
OD1 A:ASN455 3.4 18.1 1.0
C A:VAL424 3.7 17.6 1.0
C A:ASN453 3.8 16.3 1.0
O A:GLN454 4.1 15.5 1.0
C A:GLN454 4.2 15.8 1.0
O A:ALA491 4.2 15.7 1.0
ND1 A:HIS423 4.3 18.6 1.0
O A:HOH813 4.3 17.9 1.0
N A:VAL424 4.3 19.6 1.0
CB A:GLN454 4.4 15.4 1.0
CE1 A:HIS423 4.4 19.5 1.0
N A:ASN455 4.5 16.2 1.0
OE1 A:GLN454 4.5 15.9 1.0
N A:ASN426 4.5 18.1 1.0
N A:ASP425 4.5 17.7 1.0
CB A:ASN455 4.6 18.6 1.0
CA A:GLN454 4.6 15.7 1.0
CA A:ASP425 4.6 18.0 1.0
CA A:VAL424 4.6 19.3 1.0
N A:GLN454 4.6 15.7 1.0
O A:LEU489 4.7 15.7 1.0
CB A:ASN453 4.7 17.0 1.0
CA A:ASN455 4.8 17.6 1.0
CA A:ASN453 4.9 17.0 1.0
N A:GLY427 4.9 19.9 1.0
O A:ASN488 4.9 18.2 1.0
C A:ASP425 5.0 18.4 1.0

Magnesium binding site 2 out of 4 in 5h8v

Go back to Magnesium Binding Sites List in 5h8v
Magnesium binding site 2 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 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-1 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:30.7
occ:1.00
 NH2 A:ARG193 3.1 22.1 1.0
O A:HOH903 3.1 17.7 1.0
O A:HOH908 3.1 28.0 1.0
N A:GLY189 3.1 21.8 1.0
CA A:GLY189 3.4 21.0 1.0
C A:GLY189 3.6 20.4 1.0
OH A:TYR106 3.6 30.5 1.0
O A:GLY189 3.6 19.8 1.0
CD A:LYS101 4.0 24.7 1.0
CZ A:ARG193 4.2 23.6 1.0
C A:CYS188 4.3 22.4 1.0
N A:ASP190 4.4 20.4 1.0
OD1 A:ASP190 4.4 19.8 1.0
CB A:LYS101 4.5 22.7 1.0
CB A:CYS188 4.5 24.4 1.0
CZ A:TYR106 4.7 27.0 1.0
NH1 A:ARG193 4.7 27.1 1.0
CA A:CYS188 4.7 22.8 1.0
CG A:LYS101 4.8 22.8 1.0
NH1 A:ARG275 4.9 25.0 1.0
CE A:LYS276 5.0 21.5 1.0

Magnesium binding site 3 out of 4 in 5h8v

Go back to Magnesium Binding Sites List in 5h8v
Magnesium binding site 3 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 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-1 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:8.8
occ:1.00
 ND2 B:ASN455 2.6 18.4 1.0
O B:ASN453 2.6 19.4 1.0
O B:HOH872 2.6 16.6 1.0
O B:VAL424 2.6 18.4 1.0
O B:HOH886 2.8 18.7 1.0
CG B:ASN455 3.3 18.3 1.0
O B:HOH833 3.3 13.3 1.0
OD1 B:ASN455 3.4 20.3 1.0
C B:VAL424 3.7 17.4 1.0
C B:ASN453 3.8 17.8 1.0
O B:GLN454 4.0 15.5 1.0
C B:GLN454 4.1 17.2 1.0
O B:ALA491 4.3 17.6 1.0
CB B:GLN454 4.3 17.8 1.0
ND1 B:HIS423 4.3 16.3 1.0
N B:VAL424 4.4 17.0 1.0
N B:ASN455 4.4 17.0 1.0
N B:ASN426 4.4 17.5 1.0
CE1 B:HIS423 4.5 16.5 1.0
OE1 B:GLN454 4.5 20.8 1.0
N B:ASP425 4.6 18.4 1.0
CA B:GLN454 4.6 17.8 1.0
CB B:ASN455 4.6 17.4 1.0
N B:GLN454 4.6 17.8 1.0
CA B:VAL424 4.6 16.8 1.0
CA B:ASP425 4.6 18.1 1.0
CA B:ASN455 4.7 16.8 1.0
CB B:ASN453 4.8 17.9 1.0
N B:GLY427 4.8 19.2 1.0
O B:LEU489 4.8 17.9 1.0
CA B:ASN453 4.9 17.7 1.0
C B:ASP425 4.9 18.2 1.0
O B:ASN488 5.0 18.3 1.0

Magnesium binding site 4 out of 4 in 5h8v

Go back to Magnesium Binding Sites List in 5h8v
Magnesium binding site 4 out of 4 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-1 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-1 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:27.1
occ:1.00
 O B:HOH932 2.7 19.3 1.0
NH2 B:ARG193 3.0 20.6 1.0
N B:GLY189 3.1 20.4 1.0
O B:HOH855 3.2 13.7 1.0
CA B:GLY189 3.4 20.6 1.0
OH B:TYR106 3.6 29.3 1.0
C B:GLY189 3.6 20.8 1.0
O B:GLY189 3.6 19.1 1.0
CD B:LYS101 4.0 25.1 1.0
CZ B:ARG193 4.2 21.6 1.0
C B:CYS188 4.3 21.4 1.0
OD1 B:ASP190 4.4 19.2 1.0
N B:ASP190 4.4 19.5 1.0
CB B:CYS188 4.5 21.8 1.0
CB B:LYS101 4.5 21.1 1.0
NH1 B:ARG193 4.6 20.4 1.0
CZ B:TYR106 4.6 26.4 1.0
CA B:CYS188 4.7 20.8 1.0
CG B:LYS101 4.8 23.3 1.0
CE B:LYS276 4.9 20.3 1.0
NH1 B:ARG275 5.0 26.6 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 15:42:52 2024

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