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Nickel in PDB 5aa5: Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution

Enzymatic activity of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution

All present enzymatic activity of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution:
1.12.99.6;

Protein crystallography data

The structure of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution, PDB code: 5aa5 was solved by C.Schaefer, M.Bommer, S.Hennig, J.H.Jeoung, H.Dobbek, O.Lenz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.965 / 2.497
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.780, 267.971, 144.686, 90.00, 106.58, 90.00
R / Rfree (%) 18.7 / 24.2

Other elements in 5aa5:

The structure of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 78 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution (pdb code 5aa5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution, PDB code: 5aa5:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 5aa5

Go back to Nickel Binding Sites List in 5aa5
Nickel binding site 1 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni701

b:62.5
occ:1.00
 NI C:NFU701 0.0 62.5 1.0
SG C:CYS573 2.2 61.3 1.0
SG C:CYS81 2.2 27.4 1.0
SG C:CYS84 2.3 31.9 1.0
SG C:CYS576 2.4 33.2 1.0
CB C:CYS81 2.7 23.3 1.0
FE C:NFU701 2.9 33.5 1.0
CB C:CYS84 3.6 27.3 1.0
CB C:CYS573 3.6 32.8 1.0
CB C:CYS576 3.6 32.3 1.0
C2 C:NFU701 3.9 60.9 1.0
CG2 C:ILE83 3.9 24.5 1.0
C1 C:NFU701 4.0 26.5 1.0
N C:CYS84 4.1 23.8 1.0
CA C:CYS81 4.2 27.9 1.0
N C:CYS576 4.3 25.0 1.0
CA C:CYS84 4.4 24.4 1.0
C3 C:NFU701 4.4 33.8 1.0
CA C:CYS576 4.5 29.3 1.0
O C:CYS573 4.7 35.4 1.0
N2 C:NFU701 4.8 60.0 1.0
C C:CYS81 4.8 25.9 1.0
CA C:CYS573 4.9 32.2 1.0
N C:ILE83 4.9 22.6 1.0
NH1 C:ARG501 4.9 33.4 1.0
C C:CYS84 4.9 31.1 1.0
N1 C:NFU701 5.0 27.2 1.0

Nickel binding site 2 out of 6 in 5aa5

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Nickel binding site 2 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni701

b:55.8
occ:1.00
 NI E:NFU701 0.0 55.8 1.0
SG E:CYS573 2.2 59.5 1.0
SG E:CYS81 2.2 61.1 1.0
SG E:CYS84 2.3 43.0 1.0
SG E:CYS576 2.4 41.7 1.0
FE E:NFU701 2.9 44.7 1.0
CB E:CYS81 2.9 40.0 1.0
CB E:CYS576 3.5 43.3 1.0
CB E:CYS84 3.7 41.3 1.0
CB E:CYS573 3.7 45.7 1.0
C2 E:NFU701 3.9 65.1 1.0
CG2 E:ILE83 3.9 36.7 1.0
C1 E:NFU701 4.1 47.0 1.0
N E:CYS84 4.1 34.4 1.0
N E:CYS576 4.3 42.0 1.0
CA E:CYS81 4.4 37.7 1.0
CA E:CYS576 4.4 42.8 1.0
C3 E:NFU701 4.4 40.4 1.0
CA E:CYS84 4.5 36.3 1.0
O E:CYS573 4.6 47.1 1.0
N2 E:NFU701 4.7 64.6 1.0
CA E:CYS573 4.9 47.1 1.0
CD E:ARG501 4.9 52.8 1.0
N E:ILE83 4.9 37.9 1.0
NE E:ARG501 5.0 56.6 1.0
C E:CYS81 5.0 37.4 1.0

Nickel binding site 3 out of 6 in 5aa5

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Nickel binding site 3 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni701

b:32.6
occ:1.00
 NI G:NFU701 0.0 32.6 1.0
SG G:CYS573 2.2 51.1 1.0
SG G:CYS81 2.2 29.5 1.0
SG G:CYS84 2.3 23.9 1.0
SG G:CYS576 2.3 25.6 1.0
FE G:NFU701 2.9 26.5 1.0
CB G:CYS81 2.9 17.4 1.0
CB G:CYS84 3.5 17.6 1.0
CB G:CYS573 3.5 15.6 1.0
CB G:CYS576 3.7 18.1 1.0
C2 G:NFU701 3.9 51.0 1.0
N G:CYS84 3.9 17.0 1.0
CG2 G:ILE83 4.0 28.5 1.0
C1 G:NFU701 4.1 45.9 1.0
CA G:CYS84 4.3 17.1 1.0
CA G:CYS81 4.3 24.3 1.0
N G:CYS576 4.3 20.2 1.0
C3 G:NFU701 4.4 39.6 1.0
NH1 G:ARG501 4.4 34.4 1.0
CA G:CYS576 4.6 19.1 1.0
N2 G:NFU701 4.8 50.6 1.0
CA G:CYS573 4.8 16.2 1.0
O G:CYS573 4.8 23.6 1.0
C G:CYS81 4.8 22.3 1.0
N G:ILE83 4.9 16.8 1.0
C G:CYS84 4.9 21.7 1.0
C G:ILE83 4.9 20.1 1.0

Nickel binding site 4 out of 6 in 5aa5

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Nickel binding site 4 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni701

b:59.3
occ:1.00
 NI I:NFU701 0.0 59.3 1.0
SG I:CYS573 2.2 59.3 1.0
SG I:CYS576 2.3 33.7 1.0
SG I:CYS81 2.3 48.1 1.0
SG I:CYS84 2.3 32.9 1.0
CB I:CYS81 2.8 42.5 1.0
FE I:NFU701 2.9 36.1 1.0
CB I:CYS84 3.5 31.3 1.0
CB I:CYS573 3.5 39.5 1.0
CB I:CYS576 3.6 44.9 1.0
C2 I:NFU701 3.9 45.1 1.0
C1 I:NFU701 4.1 53.0 1.0
N I:CYS84 4.1 29.3 1.0
CG2 I:ILE83 4.2 25.8 1.0
CA I:CYS81 4.2 42.1 1.0
CA I:CYS84 4.3 28.1 1.0
N I:CYS576 4.4 40.5 1.0
C3 I:NFU701 4.4 33.8 1.0
CA I:CYS576 4.5 43.9 1.0
O I:CYS573 4.7 43.3 1.0
CA I:CYS573 4.7 36.6 1.0
N2 I:NFU701 4.8 44.3 1.0
C I:CYS84 4.9 29.5 1.0
CD I:ARG501 5.0 40.7 1.0
C I:CYS81 5.0 43.1 1.0
N I:GLY82 5.0 39.2 1.0
N I:ILE83 5.0 25.7 1.0
C I:CYS573 5.0 42.8 1.0
N1 I:NFU701 5.0 52.1 1.0

Nickel binding site 5 out of 6 in 5aa5

Go back to Nickel Binding Sites List in 5aa5
Nickel binding site 5 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ni701

b:57.3
occ:1.00
 NI K:NFU701 0.0 57.3 1.0
SG K:CYS573 2.2 45.5 1.0
SG K:CYS81 2.2 45.8 1.0
SG K:CYS84 2.2 34.5 1.0
SG K:CYS576 2.3 35.0 1.0
CB K:CYS81 2.7 29.9 1.0
FE K:NFU701 2.9 32.1 1.0
CB K:CYS84 3.5 32.6 1.0
CB K:CYS576 3.7 30.9 1.0
CB K:CYS573 3.8 43.0 1.0
C2 K:NFU701 3.9 40.7 1.0
C1 K:NFU701 4.0 48.7 1.0
N K:CYS84 4.1 24.5 1.0
CG2 K:ILE83 4.1 25.2 1.0
CA K:CYS81 4.2 25.0 1.0
CA K:CYS84 4.3 31.6 1.0
N K:CYS576 4.4 30.8 1.0
C3 K:NFU701 4.4 41.5 1.0
CA K:CYS576 4.6 31.1 1.0
O K:CYS573 4.7 35.0 1.0
N2 K:NFU701 4.8 40.7 1.0
C K:CYS81 4.8 29.0 1.0
C K:CYS84 4.9 29.4 1.0
CA K:CYS573 4.9 42.2 1.0
N K:ILE83 4.9 25.7 1.0
N1 K:NFU701 5.0 42.4 1.0

Nickel binding site 6 out of 6 in 5aa5

Go back to Nickel Binding Sites List in 5aa5
Nickel binding site 6 out of 6 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni701

b:72.2
occ:1.00
 NI L:NFU701 0.0 72.2 1.0
SG L:CYS573 2.2 57.7 1.0
SG L:CYS81 2.3 64.5 1.0
SG L:CYS84 2.3 50.6 1.0
SG L:CYS576 2.3 65.0 1.0
FE L:NFU701 2.9 47.1 1.0
CB L:CYS81 2.9 39.0 1.0
CB L:CYS84 3.3 37.4 1.0
CB L:CYS573 3.5 47.7 1.0
CB L:CYS576 3.8 47.6 1.0
CG2 L:ILE83 3.8 37.4 1.0
C2 L:NFU701 3.9 60.9 1.0
N L:CYS84 4.0 40.7 1.0
C1 L:NFU701 4.0 72.2 1.0
CA L:CYS84 4.2 37.4 1.0
CA L:CYS81 4.4 39.8 1.0
N L:CYS576 4.4 52.3 1.0
C3 L:NFU701 4.5 24.2 1.0
O L:CYS573 4.6 48.8 1.0
CA L:CYS576 4.6 51.8 1.0
NH1 L:ARG501 4.7 53.2 1.0
CA L:CYS573 4.7 50.9 1.0
N2 L:NFU701 4.8 60.3 1.0
C L:CYS84 4.9 39.9 1.0
C L:CYS81 4.9 36.8 1.0
C L:ILE83 4.9 37.8 1.0
N L:ILE83 4.9 34.0 1.0
C L:CYS573 4.9 49.4 1.0
N1 L:NFU701 4.9 72.4 1.0
CZ L:ARG501 4.9 56.8 1.0

Reference:

C.Schafer, M.Bommer, S.E.Hennig, J.Jeoung, H.Dobbek, O.Lenz. Structure of An Actinobacterial-Type [Nife]-Hydrogenase Reveals Insight Into O2-Tolerant H2 Oxidation. Structure V. 24 285 2016.
ISSN: ISSN 0969-2126
PubMed: 26749450
DOI: 10.1016/J.STR.2015.11.010
Page generated: Thu Oct 10 06:13:47 2024

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