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Magnesium in PDB 9e15: Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1

Enzymatic activity of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1

All present enzymatic activity of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1:
1.12.1.3;

Protein crystallography data

The structure of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1, PDB code: 9e15 was solved by W.N.Lanzilotta, P.M.Mcternan, M.W.W.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.84 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 94.235, 111.148, 141.091, 90.06, 90.02, 90
R / Rfree (%) 26.7 / 30.6

Other elements in 9e15:

The structure of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 also contains other interesting chemical elements:

Iron (Fe) 104 atoms
Nickel (Ni) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 (pdb code 9e15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1, PDB code: 9e15:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 9e15

Go back to Magnesium Binding Sites List in 9e15
Magnesium binding site 1 out of 2 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg504

b:18.4
occ:1.00
 OE1 H:GLU46 2.6 44.6 1.0
NE2 H:HIS424 2.7 33.4 1.0
O H:ILE374 3.2 39.3 1.0
OE2 H:GLU46 3.2 39.6 1.0
CD H:GLU46 3.2 37.9 1.0
CE1 H:HIS424 3.5 39.9 1.0
CD2 H:HIS424 3.7 35.6 1.0
O H:HOH626 4.0 27.5 1.0
NZ H:LYS259 4.4 44.5 1.0
OD1 H:ASP373 4.4 34.8 1.0
C H:ILE374 4.4 34.0 1.0
CE H:LYS259 4.5 49.8 1.0
ND1 H:HIS424 4.6 35.6 1.0
CG H:GLU46 4.6 40.5 1.0
CG H:HIS424 4.7 34.6 1.0
CG1 G:VAL106 4.8 38.9 1.0
N H:ILE374 4.8 23.5 1.0

Magnesium binding site 2 out of 2 in 9e15

Go back to Magnesium Binding Sites List in 9e15
Magnesium binding site 2 out of 2 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg506

b:26.3
occ:1.00
 O P:ILE374 2.5 37.9 1.0
NE2 P:HIS424 2.6 60.2 1.0
OE2 P:GLU46 3.2 46.2 1.0
CE1 P:HIS424 3.3 47.4 1.0
OE1 P:GLU46 3.7 47.7 1.0
C P:ILE374 3.7 44.3 1.0
CD P:GLU46 3.7 54.7 1.0
CD2 P:HIS424 3.8 54.0 1.0
OD1 P:ASP373 4.2 51.9 1.0
N P:ILE374 4.3 40.4 1.0
ND1 P:HIS424 4.5 48.6 1.0
CA P:ILE374 4.6 45.0 1.0
N P:ILE375 4.6 41.6 1.0
CG1 P:ILE375 4.8 47.7 1.0
CA P:ILE375 4.8 47.0 1.0
CG P:HIS424 4.8 49.9 1.0
CG1 O:VAL106 4.9 48.2 1.0
OE1 P:GLU250 5.0 42.3 1.0

Reference:

X.Xiao, G.J.Schut, X.Feng, P.M.Mcternan, D.K.Haja, W.N.Lanzilotta, M.W.W.Adams, H.Li. Structural Insights Into the Biotechnologically Relevant Reversible Nadph-Oxidizing Nife-Hydrogenase From P.Furiosus. Structure 2025.
ISSN: ISSN 0969-2126
PubMed: 40570843
DOI: 10.1016/J.STR.2025.05.017
Page generated: Sat Aug 16 00:52:12 2025

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