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Magnesium in PDB 4urh: High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase, PDB code: 4urh was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.530, 99.820, 182.420, 90.00, 92.46, 90.00
R / Rfree (%) 14.164 / 18.526

Other elements in 4urh:

The structure of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Iron (Fe) 48 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase (pdb code 4urh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase, PDB code: 4urh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4urh

Go back to Magnesium Binding Sites List in 4urh
Magnesium binding site 1 out of 5 in the High-Resolution Structure of Partially Oxidized 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 High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1552

b:7.3
occ:1.00
 O Q:HOH2048 2.0 8.8 1.0
O Q:HOH2279 2.1 8.0 1.0
O Q:HOH2047 2.1 8.0 1.0
OE2 Q:GLU53 2.2 8.3 1.0
O Q:LEU495 2.2 8.0 1.0
NE2 Q:HIS549 2.2 6.8 1.0
CE1 Q:HIS549 3.1 6.6 1.0
CD Q:GLU53 3.1 8.1 1.0
CD2 Q:HIS549 3.2 7.6 1.0
C Q:LEU495 3.4 8.6 1.0
OE1 Q:GLU53 3.4 8.3 1.0
N Q:LEU495 3.8 8.0 1.0
CA Q:LEU495 4.1 7.3 1.0
OE1 Q:GLN494 4.1 9.4 1.0
OE2 Q:GLU334 4.1 9.5 1.0
OE1 Q:GLU334 4.2 9.4 1.0
O Q:HOH2317 4.2 8.2 1.0
NZ Q:LYS372 4.2 9.6 1.0
O Q:HOH2288 4.3 9.4 1.0
ND1 Q:HIS549 4.3 8.8 1.0
CB Q:LEU495 4.3 7.3 1.0
CG Q:HIS549 4.4 7.6 1.0
N Q:VAL496 4.4 8.1 1.0
CG Q:GLU53 4.5 8.5 1.0
CD Q:GLU334 4.6 9.2 1.0
CD Q:LYS372 4.6 8.2 1.0
CE Q:LYS372 4.7 8.0 1.0
CA Q:VAL496 4.7 7.3 1.0
C Q:GLN494 4.8 7.1 1.0

Magnesium binding site 2 out of 5 in 4urh

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Magnesium binding site 2 out of 5 in the High-Resolution Structure of Partially Oxidized 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 High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1554

b:19.1
occ:0.50
 O C:HOH2186 2.0 12.9 0.7
O C:HOH2168 2.2 15.5 0.5
O Q:HOH2171 2.3 15.1 1.0
OD1 Q:ASN181 2.4 14.8 1.0
O A:HOH2083 2.5 22.9 1.0
O A:HOH2082 2.5 14.5 0.5
O C:HOH2172 2.8 20.7 0.5
CG Q:ASN181 3.6 11.1 1.0
O C:HOH2064 3.9 27.2 1.0
N Q:ASN181 4.0 11.2 1.0
CA Q:ASN181 4.2 10.8 1.0
O A:HOH2027 4.2 26.1 1.0
O C:SER196 4.2 15.2 1.0
OE1 C:GLU215 4.3 20.2 1.0
CB Q:ASN181 4.5 11.1 1.0
CD2 C:PHE198 4.5 14.2 1.0
ND2 Q:ASN181 4.6 12.6 1.0
O C:PHE198 4.6 17.3 1.0
CD1 Q:LEU185 4.7 12.0 1.0
NE2 A:GLN62 4.8 24.9 1.0
CB C:PHE198 4.8 12.2 1.0
O Q:HOH2173 4.9 24.6 1.0
OE1 A:GLN62 4.9 21.7 1.0
N C:PHE198 4.9 13.7 1.0
CG2 Q:THR180 4.9 13.8 1.0

Magnesium binding site 3 out of 5 in 4urh

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Magnesium binding site 3 out of 5 in the High-Resolution Structure of Partially Oxidized 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 High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1552

b:8.9
occ:0.50
 MG R:MG1552 0.0 8.9 0.5
MG R:MG1552 0.8 7.7 0.5
O R:HOH2040 2.0 10.8 0.5
O R:HOH3039 2.0 7.7 0.5
O R:HOH2039 2.0 10.1 0.5
O R:HOH2203 2.1 7.9 0.5
OE2 R:GLU53 2.1 9.5 0.5
O R:LEU495 2.1 9.3 0.5
OE2 R:GLU53 2.2 10.1 0.5
NE2 R:HIS549 2.2 9.2 0.5
O R:HOH3203 2.4 6.8 0.5
O R:LEU495 2.5 7.9 0.5
O R:HOH3040 2.8 8.8 0.5
CD R:GLU53 2.9 10.5 0.5
CE1 R:HIS549 3.1 10.2 0.5
CD R:GLU53 3.2 12.1 0.5
OE1 R:GLU53 3.2 9.7 0.5
CD2 R:HIS549 3.3 11.3 0.5
C R:LEU495 3.3 9.7 0.5
OE1 R:GLU53 3.5 11.4 0.5
C R:LEU495 3.6 9.3 0.5
N R:LEU495 3.8 9.7 0.5
O R:HOH3228 3.8 8.7 0.5
N R:LEU495 3.9 8.4 0.5
CA R:LEU495 4.0 9.7 0.5
OE2 R:GLU334 4.0 10.2 0.5
CB R:LEU495 4.1 7.4 0.5
O R:HOH3263 4.1 6.8 0.5
CA R:LEU495 4.1 8.4 0.5
CG R:GLU53 4.1 10.1 0.5
OE1 R:GLN494 4.1 11.8 0.5
OE1 R:GLU334 4.2 11.1 0.5
O R:HOH2212 4.2 9.6 0.5
O R:HOH2246 4.2 8.1 0.5
CB R:LEU495 4.3 10.6 0.5
ND1 R:HIS549 4.3 10.1 0.5
NZ R:LYS372 4.3 10.5 0.5
N R:VAL496 4.4 10.0 0.5
CG R:HIS549 4.4 9.2 0.5
O R:VAL548 4.4 7.5 0.5
CG R:GLU53 4.5 10.1 0.5
CD R:GLU334 4.5 9.7 0.5
OE1 R:GLN494 4.6 9.2 0.5
CD R:LYS372 4.6 8.4 0.5
CE R:LYS372 4.6 9.1 0.5
CA R:VAL496 4.7 8.6 0.5
NZ R:LYS372 4.7 7.0 0.5
OE2 R:GLU334 4.7 7.4 0.5
C R:GLN494 4.8 10.7 0.5
N R:VAL496 4.8 8.4 0.5
O R:HOH3041 4.8 9.4 0.5
CE R:LYS372 4.9 7.5 0.5
OE1 R:GLU334 5.0 8.1 0.5

Magnesium binding site 4 out of 5 in 4urh

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Magnesium binding site 4 out of 5 in the High-Resolution Structure of Partially Oxidized 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 High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1552

b:7.7
occ:0.50
 MG R:MG1552 0.0 7.7 0.5
MG R:MG1552 0.8 8.9 0.5
O R:HOH2040 1.3 10.8 0.5
O R:HOH2203 2.0 7.9 0.5
O R:HOH3040 2.0 8.8 0.5
O R:HOH3039 2.0 7.7 0.5
O R:HOH3203 2.1 6.8 0.5
O R:LEU495 2.1 9.3 0.5
OE2 R:GLU53 2.1 9.5 0.5
O R:LEU495 2.2 7.9 0.5
O R:HOH2039 2.3 10.1 0.5
OE2 R:GLU53 2.5 10.1 0.5
NE2 R:HIS549 3.0 9.2 0.5
CD R:GLU53 3.1 10.5 0.5
C R:LEU495 3.3 9.7 0.5
C R:LEU495 3.4 9.3 0.5
OE1 R:GLU53 3.4 9.7 0.5
OE2 R:GLU334 3.4 10.2 0.5
OE1 R:GLU334 3.4 11.1 0.5
CD R:GLU53 3.6 12.1 0.5
CE1 R:HIS549 3.8 10.2 0.5
N R:LEU495 3.8 8.4 0.5
OE1 R:GLN494 3.8 11.8 0.5
CD R:GLU334 3.8 9.7 0.5
N R:LEU495 3.8 9.7 0.5
OE1 R:GLU53 3.9 11.4 0.5
NZ R:LYS372 4.0 10.5 0.5
CA R:LEU495 4.0 8.4 0.5
OE2 R:GLU334 4.1 7.4 0.5
CD2 R:HIS549 4.1 11.3 0.5
OE1 R:GLN494 4.1 9.2 0.5
CA R:LEU495 4.1 9.7 0.5
OE1 R:GLU334 4.2 8.1 0.5
O R:HOH3228 4.2 8.7 0.5
O R:HOH3263 4.2 6.8 0.5
N R:VAL496 4.2 10.0 0.5
CD R:LYS372 4.2 8.4 0.5
NZ R:LYS372 4.2 7.0 0.5
CB R:LEU495 4.3 7.4 0.5
CE R:LYS372 4.4 9.1 0.5
CA R:VAL496 4.4 8.6 0.5
CG2 R:VAL496 4.4 9.8 0.5
CG R:GLU53 4.4 10.1 0.5
N R:VAL496 4.5 8.4 0.5
O R:HOH2246 4.5 8.1 0.5
CD R:LYS372 4.6 7.8 0.5
CD R:GLU334 4.6 9.4 0.5
CE R:LYS372 4.6 7.5 0.5
CB R:LEU495 4.6 10.6 0.5
C R:GLN494 4.7 10.7 0.5
O R:HOH2212 4.7 9.6 0.5
C R:GLN494 4.7 8.2 0.5
CA R:VAL496 4.7 7.8 0.5
CB R:GLN494 4.8 10.9 0.5
CD R:GLN494 4.9 11.6 0.5
CG R:GLU53 4.9 10.1 0.5
CA R:GLN494 4.9 10.7 0.5
ND1 R:HIS549 5.0 10.1 0.5

Magnesium binding site 5 out of 5 in 4urh

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Magnesium binding site 5 out of 5 in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1552

b:12.4
occ:1.00
 O S:HOH2032 2.0 14.5 1.0
O S:HOH2193 2.0 14.2 1.0
O S:HOH2031 2.1 14.8 1.0
O S:LEU495 2.1 12.6 1.0
OE2 S:GLU53 2.2 13.7 1.0
NE2 S:HIS549 2.2 11.1 1.0
CE1 S:HIS549 3.1 10.7 1.0
CD S:GLU53 3.1 12.7 1.0
CD2 S:HIS549 3.2 11.8 1.0
C S:LEU495 3.3 13.2 1.0
OE1 S:GLU53 3.4 14.5 1.0
N S:LEU495 3.7 14.2 1.0
CA S:LEU495 4.0 12.6 1.0
OE2 S:GLU334 4.0 16.8 1.0
OE1 S:GLN494 4.1 18.8 1.0
OE1 S:GLU334 4.2 16.1 1.0
NZ S:LYS372 4.2 17.0 1.0
O S:HOH2199 4.2 14.6 1.0
O S:HOH2228 4.2 13.8 1.0
ND1 S:HIS549 4.3 11.7 1.0
CB S:LEU495 4.3 11.8 1.0
N S:VAL496 4.4 14.1 1.0
CG S:HIS549 4.4 10.9 1.0
CG S:GLU53 4.5 12.0 1.0
CD S:GLU334 4.6 15.8 1.0
CE S:LYS372 4.6 15.6 1.0
CA S:VAL496 4.6 12.8 1.0
CD S:LYS372 4.6 14.9 1.0
C S:GLN494 4.8 13.4 1.0

Reference:

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9
Page generated: Tue Aug 20 04:57:06 2024

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