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Magnesium in PDB 3cus: Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution

Enzymatic activity of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution

All present enzymatic activity of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution:
1.12.2.1;

Protein crystallography data

The structure of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.400, 99.960, 182.690, 90.00, 92.23, 90.00
R / Rfree (%) 18.5 / 22.2

Other elements in 3cus:

The structure of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution also contains other interesting chemical elements:

Nickel (Ni) 3 atoms
Iron (Fe) 36 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution (pdb code 3cus). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3cus

Go back to Magnesium Binding Sites List in 3cus
Magnesium binding site 1 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg553

b:13.6
occ:1.00
 O Q:HOH564 2.0 13.3 1.0
O Q:HOH565 2.0 13.2 1.0
O Q:HOH563 2.0 13.2 1.0
O Q:LEU495 2.2 13.9 1.0
OE2 Q:GLU53 2.2 14.6 1.0
NE2 Q:HIS549 2.2 13.9 1.0
CD Q:GLU53 3.1 14.3 1.0
CE1 Q:HIS549 3.2 13.9 1.0
CD2 Q:HIS549 3.2 13.9 1.0
C Q:LEU495 3.4 14.3 1.0
OE1 Q:GLU53 3.4 13.7 1.0
N Q:LEU495 3.9 13.8 1.0
OE2 Q:GLU334 4.0 13.8 1.0
OE1 Q:GLN494 4.1 12.8 1.0
CA Q:LEU495 4.1 14.6 1.0
OE1 Q:GLU334 4.2 11.5 1.0
NZ Q:LYS372 4.2 14.3 1.0
ND1 Q:HIS549 4.3 13.8 1.0
CB Q:LEU495 4.3 14.3 1.0
O Q:HOH570 4.3 4.1 1.0
O Q:HOH594 4.3 10.0 1.0
CG Q:HIS549 4.3 13.7 1.0
N Q:VAL496 4.4 14.7 1.0
CG Q:GLU53 4.5 14.2 1.0
CD Q:LYS372 4.5 14.8 1.0
CD Q:GLU334 4.5 12.7 1.0
CE Q:LYS372 4.6 15.3 1.0
CA Q:VAL496 4.7 14.5 1.0
C Q:GLN494 4.9 14.3 1.0
CG2 Q:VAL496 5.0 14.1 1.0

Magnesium binding site 2 out of 3 in 3cus

Go back to Magnesium Binding Sites List in 3cus
Magnesium binding site 2 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg553

b:13.4
occ:1.00
 O R:HOH565 2.0 14.2 1.0
O R:HOH566 2.0 13.5 1.0
O R:HOH564 2.1 13.7 1.0
OE2 R:GLU53 2.1 13.9 1.0
O R:LEU495 2.2 14.3 1.0
NE2 R:HIS549 2.2 14.2 1.0
CD R:GLU53 3.0 14.4 1.0
CD2 R:HIS549 3.2 14.0 1.0
CE1 R:HIS549 3.2 14.0 1.0
OE1 R:GLU53 3.2 14.1 1.0
C R:LEU495 3.3 14.6 1.0
N R:LEU495 3.7 14.3 1.0
CA R:LEU495 4.0 14.7 1.0
OE1 R:GLN494 4.0 13.4 1.0
OE2 R:GLU334 4.1 13.0 1.0
O R:HOH607 4.1 15.6 1.0
CB R:LEU495 4.3 14.2 1.0
OE1 R:GLU334 4.3 14.0 1.0
CG R:GLU53 4.3 14.7 1.0
ND1 R:HIS549 4.3 13.4 1.0
CG R:HIS549 4.3 13.7 1.0
NZ R:LYS372 4.3 14.3 1.0
N R:VAL496 4.4 14.7 1.0
O R:HOH570 4.4 6.5 1.0
CD R:LYS372 4.6 14.2 1.0
CE R:LYS372 4.6 14.3 1.0
CD R:GLU334 4.6 13.9 1.0
C R:GLN494 4.7 14.3 1.0
CA R:VAL496 4.8 14.5 1.0
CA R:GLN494 5.0 14.3 1.0

Magnesium binding site 3 out of 3 in 3cus

Go back to Magnesium Binding Sites List in 3cus
Magnesium binding site 3 out of 3 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg553

b:13.7
occ:1.00
 O S:HOH563 2.0 14.1 1.0
O S:HOH564 2.0 13.6 1.0
O S:HOH562 2.0 13.6 1.0
O S:LEU495 2.1 14.6 1.0
OE2 S:GLU53 2.1 14.3 1.0
NE2 S:HIS549 2.2 13.8 1.0
CE1 S:HIS549 3.1 13.9 1.0
CD S:GLU53 3.1 14.5 1.0
CD2 S:HIS549 3.2 13.7 1.0
C S:LEU495 3.3 14.5 1.0
OE1 S:GLU53 3.5 14.6 1.0
N S:LEU495 3.8 14.3 1.0
CA S:LEU495 4.0 14.6 1.0
OE1 S:GLN494 4.1 14.5 1.0
O S:HOH584 4.2 8.9 1.0
NZ S:LYS372 4.2 14.4 1.0
OE2 S:GLU334 4.2 12.9 1.0
OE1 S:GLU334 4.2 13.6 1.0
ND1 S:HIS549 4.2 13.9 1.0
CB S:LEU495 4.2 14.3 1.0
O S:HOH566 4.3 10.7 1.0
CG S:HIS549 4.3 13.8 1.0
N S:VAL496 4.4 14.7 1.0
CG S:GLU53 4.4 14.2 1.0
CD S:GLU334 4.6 14.5 1.0
CE S:LYS372 4.6 14.0 1.0
CD S:LYS372 4.7 13.8 1.0
CA S:VAL496 4.7 14.4 1.0
C S:GLN494 4.8 14.3 1.0

Reference:

F.Leroux, S.Dementin, B.Burlat, L.Cournac, A.Volbeda, S.Champ, L.Martin, B.Guigliarelli, P.Bertrand, J.Fontecilla-Camps, M.Rousset. Experimental Approaches to Kinetics of Gas Diffusion in Hydrogenase Proc.Natl.Acad.Sci.Usa V. 105 11188 2008.
ISSN: ISSN 0027-8424
PubMed: 18685111
DOI: 10.1073/PNAS.0803689105
Page generated: Wed Aug 14 11:55:29 2024

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