Atomistry » Magnesium » PDB 5h2f-5hi8 » 5h8v
Atomistry »
  Magnesium »
    PDB 5h2f-5hi8 »
      5h8v »

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: Mon Dec 14 20:26:15 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy