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Nickel in PDB 7utd: The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk

Enzymatic activity of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk

All present enzymatic activity of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk:
1.12.99.6;

Other elements in 7utd:

The structure of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Iron (Fe) 80 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk (pdb code 7utd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk, PDB code: 7utd:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 7utd

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Nickel binding site 1 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:30.8
occ:1.00
 SG A:CYS62 2.2 7.3 1.0
SG A:CYS510 2.2 11.0 1.0
SG A:CYS513 2.5 9.3 1.0
SG A:CYS65 2.6 7.5 1.0
FE A:FCO602 2.7 11.2 1.0
CB A:CYS62 3.0 7.3 1.0
CB A:CYS510 3.1 11.0 1.0
CB A:CYS513 3.6 9.3 1.0
C1 A:FCO602 3.7 11.2 1.0
CG2 A:ILE64 3.8 7.6 1.0
CB A:CYS65 3.8 7.5 1.0
C2 A:FCO602 3.8 11.2 1.0
N A:CYS65 4.2 7.5 1.0
C3 A:FCO602 4.4 11.2 1.0
N A:CYS513 4.4 9.3 1.0
CD A:ARG443 4.4 10.6 1.0
CA A:CYS62 4.4 7.3 1.0
CA A:CYS513 4.5 9.3 1.0
CG2 A:VAL512 4.5 9.3 1.0
CA A:CYS510 4.5 11.0 1.0
N1 A:FCO602 4.5 11.2 1.0
CA A:CYS65 4.6 7.5 1.0
NH1 A:ARG443 4.6 10.6 1.0
NE A:ARG443 4.7 10.6 1.0
N2 A:FCO602 4.7 11.2 1.0
CZ A:ARG443 4.9 10.6 1.0
C A:CYS62 5.0 7.3 1.0

Nickel binding site 2 out of 8 in 7utd

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Nickel binding site 2 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:31.1
occ:1.00
 SG C:CYS62 2.2 7.3 1.0
SG C:CYS510 2.2 11.0 1.0
SG C:CYS513 2.5 9.3 1.0
SG C:CYS65 2.6 7.5 1.0
FE C:FCO602 2.7 11.2 1.0
CB C:CYS62 3.0 7.3 1.0
CB C:CYS510 3.1 11.0 1.0
CB C:CYS513 3.6 9.3 1.0
C1 C:FCO602 3.7 11.2 1.0
CG2 C:ILE64 3.8 7.6 1.0
CB C:CYS65 3.8 7.5 1.0
C2 C:FCO602 3.8 11.2 1.0
N C:CYS65 4.2 7.5 1.0
C3 C:FCO602 4.4 11.2 1.0
N C:CYS513 4.4 9.3 1.0
CD C:ARG443 4.4 10.6 1.0
CA C:CYS62 4.4 7.3 1.0
CG2 C:VAL512 4.5 9.2 1.0
CA C:CYS513 4.5 9.3 1.0
CA C:CYS510 4.5 11.0 1.0
N1 C:FCO602 4.5 11.2 1.0
CA C:CYS65 4.6 7.5 1.0
NH1 C:ARG443 4.7 10.6 1.0
NE C:ARG443 4.7 10.6 1.0
N2 C:FCO602 4.7 11.2 1.0
CZ C:ARG443 4.9 10.6 1.0
C C:CYS62 5.0 7.3 1.0

Nickel binding site 3 out of 8 in 7utd

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Nickel binding site 3 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni601

b:30.8
occ:1.00
 SG E:CYS62 2.2 7.3 1.0
SG E:CYS510 2.2 11.0 1.0
SG E:CYS513 2.5 9.3 1.0
SG E:CYS65 2.6 7.5 1.0
FE E:FCO602 2.7 11.2 1.0
CB E:CYS62 3.0 7.3 1.0
CB E:CYS510 3.1 11.0 1.0
CB E:CYS513 3.6 9.3 1.0
C1 E:FCO602 3.7 11.2 1.0
CG2 E:ILE64 3.8 7.6 1.0
CB E:CYS65 3.8 7.5 1.0
C2 E:FCO602 3.8 11.2 1.0
N E:CYS65 4.2 7.5 1.0
C3 E:FCO602 4.4 11.2 1.0
N E:CYS513 4.4 9.3 1.0
CD E:ARG443 4.4 10.6 1.0
CA E:CYS62 4.4 7.3 1.0
CA E:CYS513 4.5 9.3 1.0
CG2 E:VAL512 4.5 9.3 1.0
CA E:CYS510 4.5 11.0 1.0
N1 E:FCO602 4.5 11.2 1.0
CA E:CYS65 4.6 7.5 1.0
NH1 E:ARG443 4.6 10.6 1.0
NE E:ARG443 4.7 10.6 1.0
N2 E:FCO602 4.7 11.2 1.0
CZ E:ARG443 4.9 10.6 1.0
C E:CYS62 5.0 7.3 1.0

Nickel binding site 4 out of 8 in 7utd

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Nickel binding site 4 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni601

b:31.1
occ:1.00
 SG G:CYS62 2.2 7.3 1.0
SG G:CYS510 2.2 11.0 1.0
SG G:CYS513 2.5 9.3 1.0
SG G:CYS65 2.6 7.5 1.0
FE G:FCO602 2.7 11.2 1.0
CB G:CYS62 3.0 7.3 1.0
CB G:CYS510 3.1 11.0 1.0
CB G:CYS513 3.6 9.3 1.0
C1 G:FCO602 3.7 11.2 1.0
CG2 G:ILE64 3.8 7.6 1.0
CB G:CYS65 3.8 7.5 1.0
C2 G:FCO602 3.8 11.2 1.0
N G:CYS65 4.2 7.5 1.0
C3 G:FCO602 4.4 11.2 1.0
N G:CYS513 4.4 9.3 1.0
CD G:ARG443 4.4 10.6 1.0
CA G:CYS62 4.4 7.3 1.0
CG2 G:VAL512 4.5 9.2 1.0
CA G:CYS513 4.5 9.3 1.0
CA G:CYS510 4.5 11.0 1.0
N1 G:FCO602 4.5 11.2 1.0
CA G:CYS65 4.6 7.5 1.0
NH1 G:ARG443 4.7 10.6 1.0
NE G:ARG443 4.7 10.6 1.0
N2 G:FCO602 4.7 11.2 1.0
CZ G:ARG443 4.9 10.6 1.0
C G:CYS62 5.0 7.3 1.0

Nickel binding site 5 out of 8 in 7utd

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Nickel binding site 5 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni601

b:30.8
occ:1.00
 SG I:CYS62 2.2 7.3 1.0
SG I:CYS510 2.2 11.0 1.0
SG I:CYS513 2.5 9.3 1.0
SG I:CYS65 2.6 7.5 1.0
FE I:FCO602 2.7 11.2 1.0
CB I:CYS62 3.0 7.3 1.0
CB I:CYS510 3.1 11.0 1.0
CB I:CYS513 3.6 9.3 1.0
C1 I:FCO602 3.7 11.2 1.0
CG2 I:ILE64 3.8 7.6 1.0
CB I:CYS65 3.8 7.5 1.0
C2 I:FCO602 3.8 11.2 1.0
N I:CYS65 4.2 7.5 1.0
C3 I:FCO602 4.4 11.2 1.0
N I:CYS513 4.4 9.3 1.0
CD I:ARG443 4.4 10.6 1.0
CA I:CYS62 4.4 7.3 1.0
CA I:CYS513 4.5 9.3 1.0
CG2 I:VAL512 4.5 9.3 1.0
CA I:CYS510 4.5 11.0 1.0
N1 I:FCO602 4.5 11.2 1.0
CA I:CYS65 4.6 7.5 1.0
NH1 I:ARG443 4.6 10.6 1.0
NE I:ARG443 4.7 10.6 1.0
N2 I:FCO602 4.7 11.2 1.0
CZ I:ARG443 4.9 10.6 1.0
C I:CYS62 5.0 7.3 1.0

Nickel binding site 6 out of 8 in 7utd

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Nickel binding site 6 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ni601

b:30.8
occ:1.00
 SG K:CYS62 2.2 7.3 1.0
SG K:CYS510 2.2 11.0 1.0
SG K:CYS513 2.5 9.3 1.0
SG K:CYS65 2.6 7.5 1.0
FE K:FCO602 2.7 11.2 1.0
CB K:CYS62 3.0 7.3 1.0
CB K:CYS510 3.1 11.0 1.0
CB K:CYS513 3.6 9.3 1.0
C1 K:FCO602 3.7 11.2 1.0
CG2 K:ILE64 3.8 7.6 1.0
CB K:CYS65 3.8 7.5 1.0
C2 K:FCO602 3.8 11.2 1.0
N K:CYS65 4.2 7.5 1.0
C3 K:FCO602 4.4 11.2 1.0
N K:CYS513 4.4 9.3 1.0
CD K:ARG443 4.4 10.6 1.0
CA K:CYS62 4.4 7.3 1.0
CA K:CYS513 4.5 9.3 1.0
CG2 K:VAL512 4.5 9.3 1.0
CA K:CYS510 4.5 11.0 1.0
N1 K:FCO602 4.5 11.2 1.0
CA K:CYS65 4.6 7.5 1.0
NH1 K:ARG443 4.6 10.6 1.0
NE K:ARG443 4.7 10.6 1.0
N2 K:FCO602 4.7 11.2 1.0
CZ K:ARG443 4.9 10.6 1.0
C K:CYS62 5.0 7.3 1.0

Nickel binding site 7 out of 8 in 7utd

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Nickel binding site 7 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni601

b:31.1
occ:1.00
 SG M:CYS62 2.2 7.3 1.0
SG M:CYS510 2.2 11.0 1.0
SG M:CYS513 2.5 9.3 1.0
SG M:CYS65 2.6 7.5 1.0
FE M:FCO602 2.7 11.2 1.0
CB M:CYS62 3.0 7.3 1.0
CB M:CYS510 3.1 11.0 1.0
CB M:CYS513 3.6 9.3 1.0
C1 M:FCO602 3.7 11.2 1.0
CG2 M:ILE64 3.8 7.6 1.0
CB M:CYS65 3.8 7.5 1.0
C2 M:FCO602 3.8 11.2 1.0
N M:CYS65 4.2 7.5 1.0
C3 M:FCO602 4.4 11.2 1.0
N M:CYS513 4.4 9.3 1.0
CD M:ARG443 4.4 10.6 1.0
CA M:CYS62 4.4 7.3 1.0
CG2 M:VAL512 4.5 9.2 1.0
CA M:CYS513 4.5 9.3 1.0
CA M:CYS510 4.5 11.0 1.0
N1 M:FCO602 4.5 11.2 1.0
CA M:CYS65 4.6 7.5 1.0
NH1 M:ARG443 4.7 10.6 1.0
NE M:ARG443 4.7 10.6 1.0
N2 M:FCO602 4.7 11.2 1.0
CZ M:ARG443 4.9 10.6 1.0
C M:CYS62 5.0 7.3 1.0

Nickel binding site 8 out of 8 in 7utd

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Nickel binding site 8 out of 8 in the The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of The 2.19-Angstrom Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Complex Minus Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni601

b:31.1
occ:1.00
 SG O:CYS62 2.2 7.3 1.0
SG O:CYS510 2.2 11.0 1.0
SG O:CYS513 2.5 9.3 1.0
SG O:CYS65 2.6 7.5 1.0
FE O:FCO602 2.7 11.2 1.0
CB O:CYS62 3.0 7.3 1.0
CB O:CYS510 3.1 11.0 1.0
CB O:CYS513 3.6 9.3 1.0
C1 O:FCO602 3.7 11.2 1.0
CG2 O:ILE64 3.8 7.6 1.0
CB O:CYS65 3.8 7.5 1.0
C2 O:FCO602 3.8 11.2 1.0
N O:CYS65 4.2 7.5 1.0
C3 O:FCO602 4.4 11.2 1.0
N O:CYS513 4.4 9.3 1.0
CD O:ARG443 4.4 10.6 1.0
CA O:CYS62 4.4 7.3 1.0
CG2 O:VAL512 4.5 9.2 1.0
CA O:CYS513 4.5 9.3 1.0
CA O:CYS510 4.5 11.0 1.0
N1 O:FCO602 4.5 11.2 1.0
CA O:CYS65 4.6 7.5 1.0
NH1 O:ARG443 4.7 10.6 1.0
NE O:ARG443 4.7 10.6 1.0
N2 O:FCO602 4.7 11.2 1.0
CZ O:ARG443 4.9 10.6 1.0
C O:CYS62 5.0 7.3 1.0

Reference:

R.Grinter, A.Kropp, H.Venugopal, M.Senger, J.Badley, P.Cabotaje, S.T.Stripp, C.K.Barlow, M.Belousoff, G.M.Cook, R.B.Schittenhelm, S.Khalid, G.Berggren, G.Greening. An Oxygen-Insensitive, Quinone-Transporting Hydrogenase Enables Bacteria to Extract Energy From Air To Be Published.
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