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Magnesium in PDB 4ucx: Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucx was solved by A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.Delacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.600, 99.270, 182.080, 90.00, 92.32, 90.00
R / Rfree (%) 19.676 / 23.068

Other elements in 4ucx:

The structure of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase 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 the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ucx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ucx

Go back to Magnesium Binding Sites List in 4ucx
Magnesium binding site 1 out of 4 in the Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1553

b:26.1
occ:1.00
 O Q:HOH2018 2.0 23.2 1.0
O Q:HOH2088 2.0 22.0 1.0
O Q:HOH2017 2.0 28.3 1.0
O Q:LEU495 2.1 26.6 1.0
OE2 Q:GLU53 2.1 27.4 1.0
NE2 Q:HIS549 2.2 23.3 1.0
CD Q:GLU53 3.1 26.9 1.0
CE1 Q:HIS549 3.2 27.8 1.0
CD2 Q:HIS549 3.3 20.6 1.0
C Q:LEU495 3.3 26.8 1.0
OE1 Q:GLU53 3.5 30.1 1.0
N Q:LEU495 3.7 24.6 1.0
OE2 Q:GLU334 3.9 24.6 1.0
CA Q:LEU495 4.0 25.6 1.0
OE1 Q:GLN494 4.0 27.6 1.0
OE1 Q:GLU334 4.1 30.9 1.0
O Q:HOH2094 4.3 16.9 1.0
CB Q:LEU495 4.3 23.6 1.0
NZ Q:LYS372 4.3 29.6 1.0
ND1 Q:HIS549 4.3 20.9 1.0
O Q:HOH2107 4.3 16.9 1.0
N Q:VAL496 4.3 26.7 1.0
CG Q:HIS549 4.4 24.1 1.0
CG Q:GLU53 4.5 29.4 1.0
CD Q:GLU334 4.5 31.6 1.0
CD Q:LYS372 4.6 27.1 1.0
CA Q:VAL496 4.7 23.2 1.0
C Q:GLN494 4.7 27.2 1.0
CE Q:LYS372 4.8 26.3 1.0

Magnesium binding site 2 out of 4 in 4ucx

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Magnesium binding site 2 out of 4 in the Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1559

b:47.2
occ:1.00
 O C:HOH2067 2.0 18.6 1.0
O Q:HOH2056 2.2 16.2 1.0
OD1 Q:ASN181 2.3 26.9 1.0
CG Q:ASN181 3.5 27.9 1.0
N Q:ASN181 3.8 25.9 1.0
CA Q:ASN181 3.9 25.1 1.0
CB Q:ASN181 4.3 26.6 1.0
OE1 C:GLU215 4.4 35.4 1.0
O C:SER196 4.4 33.9 1.0
CD1 Q:LEU185 4.4 26.0 1.0
ND2 Q:ASN181 4.5 24.4 1.0
O2 Q:GOL1562 4.5 40.3 1.0
CD2 C:PHE198 4.7 33.0 1.0
CG2 Q:THR180 4.7 26.2 1.0
OE1 A:GLN62 4.8 36.9 1.0
NE2 A:GLN62 4.9 32.1 1.0
C Q:THR180 4.9 24.4 1.0
O C:PHE198 4.9 32.4 1.0

Magnesium binding site 3 out of 4 in 4ucx

Go back to Magnesium Binding Sites List in 4ucx
Magnesium binding site 3 out of 4 in the Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1553

b:28.4
occ:1.00
 O R:HOH2017 2.0 30.6 1.0
O R:HOH2076 2.0 27.5 1.0
O R:HOH2016 2.0 27.9 1.0
NE2 R:HIS549 2.2 28.2 1.0
O R:LEU495 2.2 26.0 1.0
OE2 R:GLU53 2.3 35.7 1.0
CE1 R:HIS549 3.1 26.9 1.0
CD R:GLU53 3.1 33.5 1.0
CD2 R:HIS549 3.3 24.7 1.0
OE1 R:GLU53 3.4 33.7 1.0
C R:LEU495 3.4 30.9 1.0
N R:LEU495 3.8 33.0 1.0
OE2 R:GLU334 3.9 28.1 1.0
OE1 R:GLN494 4.0 35.6 1.0
CA R:LEU495 4.0 32.3 1.0
OE1 R:GLU334 4.2 29.1 1.0
O R:HOH2082 4.2 19.1 1.0
ND1 R:HIS549 4.2 27.3 1.0
CB R:LEU495 4.3 34.1 1.0
O R:HOH2093 4.3 17.3 1.0
CG R:HIS549 4.4 28.5 1.0
NZ R:LYS372 4.4 26.1 1.0
CD R:GLU334 4.5 23.7 1.0
N R:VAL496 4.5 24.7 1.0
CG R:GLU53 4.5 36.5 1.0
CD R:LYS372 4.5 37.1 1.0
CE R:LYS372 4.7 27.6 1.0
CA R:VAL496 4.7 25.5 1.0
C R:GLN494 4.8 32.6 1.0
CG2 R:VAL496 5.0 29.6 1.0

Magnesium binding site 4 out of 4 in 4ucx

Go back to Magnesium Binding Sites List in 4ucx
Magnesium binding site 4 out of 4 in the Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the T18G Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1553

b:24.5
occ:1.00
 O S:HOH2018 2.0 25.9 1.0
O S:HOH2077 2.0 28.7 1.0
O S:HOH2017 2.0 31.2 1.0
O S:LEU495 2.1 30.3 1.0
NE2 S:HIS549 2.1 20.8 1.0
OE2 S:GLU53 2.1 27.2 1.0
CE1 S:HIS549 3.0 26.7 1.0
CD S:GLU53 3.1 34.6 1.0
CD2 S:HIS549 3.2 32.4 1.0
C S:LEU495 3.2 29.6 1.0
OE1 S:GLU53 3.4 31.8 1.0
N S:LEU495 3.7 30.7 1.0
CA S:LEU495 3.9 28.7 1.0
OE2 S:GLU334 4.0 33.5 1.0
CB S:LEU495 4.2 23.6 1.0
ND1 S:HIS549 4.2 19.0 1.0
O S:HOH2083 4.2 12.1 1.0
O S:HOH2094 4.2 10.9 1.0
OE1 S:GLN494 4.3 35.0 1.0
OE1 S:GLU334 4.3 29.0 1.0
CG S:HIS549 4.3 18.8 1.0
N S:VAL496 4.3 30.4 1.0
NZ S:LYS372 4.3 44.4 1.0
CG S:GLU53 4.4 32.4 1.0
CE S:LYS372 4.5 41.2 1.0
CD S:GLU334 4.6 38.0 1.0
CA S:VAL496 4.7 31.6 1.0
C S:GLN494 4.7 32.0 1.0
CD S:LYS372 4.7 39.8 1.0

Reference:

A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.De Lacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin. A Threonine Stabilizes the Nic and Nir Catalytic Intermediates of [Nife]-Hydrogenase During Catalysis in Nife-Hydrogenase J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.630491
Page generated: Tue Aug 20 04:37:03 2024

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