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Magnesium in PDB 1yrq: Structure of the Ready Oxidized Form of [Nife]-Hydrogenase

Enzymatic activity of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase

All present enzymatic activity of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq was solved by A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, 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) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.500, 99.700, 183.200, 90.00, 91.80, 90.00
R / Rfree (%) 17.1 / 22

Other elements in 1yrq:

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 12 atoms
Iron (Fe) 144 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase (pdb code 1yrq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1yrq

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Magnesium binding site 1 out of 6 in the Structure of the Ready Oxidized Form of [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 Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg553

b:8.3
occ:1.00
 O H:HOH555 2.0 3.1 1.0
O H:HOH554 2.0 2.2 1.0
O H:HOH556 2.1 5.6 1.0
O H:LEU495 2.1 9.1 1.0
OE1 H:GLU53 2.2 13.8 1.0
NE2 H:HIS549 2.2 7.5 1.0
CD H:GLU53 3.1 12.0 1.0
CE1 H:HIS549 3.1 10.2 1.0
CD2 H:HIS549 3.3 6.5 1.0
C H:LEU495 3.3 8.0 1.0
OE2 H:GLU53 3.3 8.6 1.0
N H:LEU495 3.8 7.6 1.0
CA H:LEU495 4.0 8.0 1.0
OE2 H:GLU334 4.1 9.2 1.0
OE1 H:GLU334 4.1 12.2 1.0
OE1 H:GLN494 4.2 12.8 1.0
O H:HOH771 4.2 3.5 1.0
NZ H:LYS372 4.2 8.1 1.0
ND1 H:HIS549 4.3 9.8 1.0
CB H:LEU495 4.3 8.3 1.0
O H:HOH568 4.3 5.7 1.0
N H:VAL496 4.4 7.9 1.0
CG H:HIS549 4.4 11.3 1.0
CG H:GLU53 4.5 9.6 1.0
CD H:LYS372 4.5 5.0 1.0
CE H:LYS372 4.5 8.9 1.0
CD H:GLU334 4.6 8.7 1.0
CA H:VAL496 4.6 6.2 1.0
C H:GLN494 4.7 9.1 1.0
CA H:GLN494 5.0 8.4 1.0

Magnesium binding site 2 out of 6 in 1yrq

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Magnesium binding site 2 out of 6 in the Structure of the Ready Oxidized Form of [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 Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg553

b:6.5
occ:1.00
 OE1 I:GLU53 2.0 3.6 1.0
O I:HOH555 2.1 8.2 1.0
O I:HOH556 2.1 5.7 1.0
O I:LEU495 2.2 7.1 1.0
O I:HOH554 2.2 3.0 1.0
NE2 I:HIS549 2.2 6.5 1.0
CD I:GLU53 3.0 4.3 1.0
CE1 I:HIS549 3.1 7.8 1.0
CD2 I:HIS549 3.3 4.0 1.0
C I:LEU495 3.3 8.1 1.0
OE2 I:GLU53 3.3 5.7 1.0
N I:LEU495 3.6 9.8 1.0
CA I:LEU495 3.9 8.6 1.0
OE1 I:GLN494 4.2 8.6 1.0
CB I:LEU495 4.2 10.0 1.0
OE2 I:GLU334 4.2 6.3 1.0
ND1 I:HIS549 4.3 8.8 1.0
OE1 I:GLU334 4.3 10.6 1.0
O I:HOH748 4.4 4.6 1.0
CG I:HIS549 4.4 5.4 1.0
CG I:GLU53 4.4 3.3 1.0
N I:VAL496 4.4 8.8 1.0
O I:HOH569 4.5 7.2 1.0
NZ I:LYS372 4.6 8.3 1.0
C I:GLN494 4.6 7.8 1.0
CD I:LYS372 4.6 7.3 1.0
CA I:VAL496 4.7 6.8 1.0
CD I:GLU334 4.7 7.1 1.0
CA I:GLN494 4.9 6.8 1.0
CE I:LYS372 4.9 8.9 1.0

Magnesium binding site 3 out of 6 in 1yrq

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Magnesium binding site 3 out of 6 in the Structure of the Ready Oxidized Form of [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 Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg553

b:5.4
occ:1.00
 OE1 J:GLU53 2.1 10.3 1.0
O J:LEU495 2.1 6.7 1.0
O J:HOH555 2.1 4.5 1.0
O J:HOH556 2.1 6.5 1.0
O J:HOH554 2.2 4.7 1.0
NE2 J:HIS549 2.2 5.0 1.0
CE1 J:HIS549 3.0 9.4 1.0
CD J:GLU53 3.1 10.8 1.0
C J:LEU495 3.3 7.4 1.0
CD2 J:HIS549 3.3 4.7 1.0
OE2 J:GLU53 3.4 11.9 1.0
N J:LEU495 3.7 5.8 1.0
CA J:LEU495 3.9 7.0 1.0
O J:HOH740 4.1 7.3 1.0
OE1 J:GLN494 4.1 10.6 1.0
OE1 J:GLU334 4.1 11.2 1.0
OE2 J:GLU334 4.1 13.1 1.0
O J:HOH569 4.2 7.7 1.0
CB J:LEU495 4.2 5.9 1.0
ND1 J:HIS549 4.2 6.8 1.0
NZ J:LYS372 4.2 8.5 1.0
CG J:HIS549 4.3 5.6 1.0
N J:VAL496 4.4 7.5 1.0
CG J:GLU53 4.4 8.0 1.0
CD J:LYS372 4.5 4.8 1.0
CD J:GLU334 4.6 11.8 1.0
CE J:LYS372 4.7 7.1 1.0
CA J:VAL496 4.7 7.1 1.0
C J:GLN494 4.8 6.1 1.0

Magnesium binding site 4 out of 6 in 1yrq

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Magnesium binding site 4 out of 6 in the Structure of the Ready Oxidized Form of [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 Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg553

b:3.3
occ:1.00
 O K:HOH555 2.1 7.5 1.0
OE1 K:GLU53 2.1 7.3 1.0
O K:HOH554 2.1 8.9 1.0
O K:HOH556 2.1 4.9 1.0
O K:LEU495 2.2 5.1 1.0
NE2 K:HIS549 2.2 7.8 1.0
CD K:GLU53 3.0 7.2 1.0
CD2 K:HIS549 3.1 6.5 1.0
CE1 K:HIS549 3.1 7.2 1.0
C K:LEU495 3.3 7.0 1.0
OE2 K:GLU53 3.3 6.0 1.0
N K:LEU495 3.8 5.2 1.0
CA K:LEU495 4.0 6.6 1.0
OE2 K:GLU334 4.1 11.0 1.0
OE1 K:GLU334 4.1 12.2 1.0
O K:HOH775 4.2 2.0 1.0
CB K:LEU495 4.2 5.6 1.0
OE1 K:GLN494 4.2 16.2 1.0
ND1 K:HIS549 4.3 8.0 1.0
CG K:HIS549 4.3 7.3 1.0
O K:HOH570 4.3 5.2 1.0
CG K:GLU53 4.4 5.3 1.0
N K:VAL496 4.4 6.6 1.0
NZ K:LYS372 4.5 2.0 1.0
CD K:GLU334 4.6 11.0 1.0
CD K:LYS372 4.6 4.5 1.0
CA K:VAL496 4.7 7.6 1.0
C K:GLN494 4.8 7.7 1.0
CE K:LYS372 4.9 2.0 1.0

Magnesium binding site 5 out of 6 in 1yrq

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Magnesium binding site 5 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg553

b:8.1
occ:1.00
 O M:HOH556 2.0 7.3 1.0
O M:LEU495 2.1 12.3 1.0
O M:HOH555 2.1 9.0 1.0
O M:HOH554 2.1 11.4 1.0
OE1 M:GLU53 2.2 8.0 1.0
NE2 M:HIS549 2.2 6.5 1.0
CD2 M:HIS549 3.1 7.2 1.0
CD M:GLU53 3.2 9.3 1.0
CE1 M:HIS549 3.2 7.0 1.0
C M:LEU495 3.2 11.0 1.0
OE2 M:GLU53 3.5 7.5 1.0
N M:LEU495 3.7 11.4 1.0
CA M:LEU495 3.9 10.5 1.0
OE1 M:GLN494 4.1 14.4 1.0
OE2 M:GLU334 4.1 10.8 1.0
OE1 M:GLU334 4.1 8.7 1.0
O M:HOH713 4.1 8.9 1.0
CB M:LEU495 4.1 10.6 1.0
ND1 M:HIS549 4.3 5.9 1.0
CG M:HIS549 4.3 7.9 1.0
O M:HOH572 4.3 18.3 1.0
N M:VAL496 4.3 7.5 1.0
CG M:GLU53 4.5 11.1 1.0
CD M:GLU334 4.6 12.2 1.0
NZ M:LYS372 4.6 2.0 1.0
CA M:VAL496 4.6 8.2 1.0
C M:GLN494 4.7 12.1 1.0
CD M:LYS372 4.7 3.5 1.0
CE M:LYS372 4.8 3.9 1.0
CG2 M:VAL496 5.0 4.5 1.0

Magnesium binding site 6 out of 6 in 1yrq

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Magnesium binding site 6 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg553

b:8.8
occ:0.59
 O N:HOH554 2.1 7.0 0.6
O N:HOH556 2.1 7.8 0.6
O N:HOH555 2.1 8.2 0.6
OE1 N:GLU53 2.1 7.4 0.6
NE2 N:HIS549 2.1 7.7 0.6
O N:LEU495 2.2 9.6 0.6
CE1 N:HIS549 3.0 8.7 0.6
CD N:GLU53 3.2 8.9 0.6
CD2 N:HIS549 3.2 8.2 0.6
C N:LEU495 3.3 9.6 0.6
OE2 N:GLU53 3.5 6.3 0.6
N N:LEU495 3.8 10.5 0.6
CA N:LEU495 3.9 10.5 0.6
OE2 N:GLU334 4.0 10.2 0.6
CB N:LEU495 4.2 9.9 0.6
ND1 N:HIS549 4.2 8.9 0.6
O N:HOH563 4.3 8.6 0.6
CG N:HIS549 4.3 9.0 0.6
OE1 N:GLN494 4.4 10.8 0.6
NZ N:LYS372 4.4 7.0 0.6
O N:HOH568 4.4 9.9 0.6
OE1 N:GLU334 4.4 8.9 0.6
N N:VAL496 4.4 9.5 0.6
CD N:LYS372 4.4 7.7 0.6
CG N:GLU53 4.5 9.5 0.6
CE N:LYS372 4.5 8.7 0.6
CD N:GLU334 4.6 8.9 0.6
CA N:VAL496 4.7 10.2 0.6
C N:GLN494 4.8 9.5 0.6

Reference:

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X
Page generated: Tue Aug 13 19:52:23 2024

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