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Magnesium in PDB 7uus: The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk

Enzymatic activity of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk

All present enzymatic activity of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk:
1.12.99.6;

Other elements in 7uus:

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

Iron (Fe) 80 atoms
Nickel (Ni) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 7uus

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Magnesium binding site 1 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:9.8
occ:1.00
 O A:VAL462 2.0 8.8 1.0
OE2 A:GLU43 2.0 9.4 1.0
NE2 A:HIS516 2.1 9.0 1.0
CD A:GLU43 3.0 9.4 1.0
CD2 A:HIS516 3.1 9.0 1.0
CE1 A:HIS516 3.1 9.0 1.0
C A:VAL462 3.2 8.8 1.0
OE1 A:GLU43 3.3 9.4 1.0
N A:VAL462 3.7 8.8 1.0
CA A:VAL462 3.9 8.8 1.0
OE2 A:GLU303 3.9 14.0 1.0
OE1 A:GLU303 4.0 14.0 1.0
OE1 A:GLN461 4.1 10.1 1.0
ND1 A:HIS516 4.2 9.0 1.0
N A:VAL463 4.2 8.8 1.0
CG A:HIS516 4.2 9.0 1.0
NZ A:LYS341 4.3 12.5 1.0
CB A:VAL462 4.3 8.8 1.0
CG A:GLU43 4.3 9.4 1.0
CD A:GLU303 4.4 14.0 1.0
CA A:VAL463 4.5 8.8 1.0
CE A:LYS341 4.7 12.5 1.0
C A:GLN461 4.7 10.1 1.0
CD A:LYS341 4.8 12.5 1.0
CG2 A:VAL463 4.8 8.8 1.0

Magnesium binding site 2 out of 8 in 7uus

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Magnesium binding site 2 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:9.8
occ:1.00
 O C:VAL462 2.0 8.8 1.0
OE2 C:GLU43 2.0 9.4 1.0
NE2 C:HIS516 2.1 9.0 1.0
CD C:GLU43 3.0 9.4 1.0
CD2 C:HIS516 3.1 9.0 1.0
CE1 C:HIS516 3.1 9.0 1.0
C C:VAL462 3.2 8.8 1.0
OE1 C:GLU43 3.3 9.4 1.0
N C:VAL462 3.7 8.8 1.0
CA C:VAL462 3.9 8.8 1.0
OE2 C:GLU303 3.9 14.0 1.0
OE1 C:GLU303 4.0 14.0 1.0
OE1 C:GLN461 4.1 10.1 1.0
ND1 C:HIS516 4.2 9.0 1.0
N C:VAL463 4.2 8.9 1.0
CG C:HIS516 4.2 9.0 1.0
NZ C:LYS341 4.2 12.5 1.0
CB C:VAL462 4.3 8.8 1.0
CG C:GLU43 4.3 9.4 1.0
CD C:GLU303 4.4 14.0 1.0
CA C:VAL463 4.5 8.9 1.0
CE C:LYS341 4.7 12.5 1.0
C C:GLN461 4.7 10.1 1.0
CD C:LYS341 4.8 12.5 1.0
CG2 C:VAL463 4.8 8.9 1.0

Magnesium binding site 3 out of 8 in 7uus

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Magnesium binding site 3 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:9.8
occ:1.00
 O E:VAL462 2.0 8.8 1.0
OE2 E:GLU43 2.0 9.4 1.0
NE2 E:HIS516 2.1 9.0 1.0
CD E:GLU43 3.0 9.4 1.0
CD2 E:HIS516 3.1 9.0 1.0
CE1 E:HIS516 3.1 9.0 1.0
C E:VAL462 3.2 8.8 1.0
OE1 E:GLU43 3.3 9.4 1.0
N E:VAL462 3.7 8.8 1.0
CA E:VAL462 3.9 8.8 1.0
OE2 E:GLU303 3.9 14.0 1.0
OE1 E:GLU303 4.0 14.0 1.0
OE1 E:GLN461 4.1 10.1 1.0
ND1 E:HIS516 4.2 9.0 1.0
N E:VAL463 4.2 8.8 1.0
CG E:HIS516 4.2 9.0 1.0
NZ E:LYS341 4.3 12.5 1.0
CB E:VAL462 4.3 8.8 1.0
CG E:GLU43 4.3 9.4 1.0
CD E:GLU303 4.4 14.0 1.0
CA E:VAL463 4.5 8.8 1.0
CE E:LYS341 4.7 12.5 1.0
C E:GLN461 4.7 10.1 1.0
CD E:LYS341 4.8 12.5 1.0
CG2 E:VAL463 4.8 8.8 1.0

Magnesium binding site 4 out of 8 in 7uus

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Magnesium binding site 4 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:9.8
occ:1.00
 O G:VAL462 2.0 8.8 1.0
OE2 G:GLU43 2.0 9.4 1.0
NE2 G:HIS516 2.1 9.0 1.0
CD G:GLU43 3.0 9.4 1.0
CD2 G:HIS516 3.1 9.0 1.0
CE1 G:HIS516 3.1 9.0 1.0
C G:VAL462 3.2 8.8 1.0
OE1 G:GLU43 3.3 9.4 1.0
N G:VAL462 3.7 8.8 1.0
CA G:VAL462 3.9 8.8 1.0
OE2 G:GLU303 3.9 14.0 1.0
OE1 G:GLU303 4.0 14.0 1.0
OE1 G:GLN461 4.1 10.1 1.0
ND1 G:HIS516 4.2 9.0 1.0
N G:VAL463 4.2 8.9 1.0
CG G:HIS516 4.2 9.0 1.0
NZ G:LYS341 4.2 12.5 1.0
CB G:VAL462 4.3 8.8 1.0
CG G:GLU43 4.3 9.4 1.0
CD G:GLU303 4.4 14.0 1.0
CA G:VAL463 4.5 8.9 1.0
CE G:LYS341 4.7 12.5 1.0
C G:GLN461 4.7 10.1 1.0
CD G:LYS341 4.8 12.5 1.0
CG2 G:VAL463 4.8 8.9 1.0

Magnesium binding site 5 out of 8 in 7uus

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Magnesium binding site 5 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg603

b:9.8
occ:1.00
 O I:VAL462 2.0 8.8 1.0
OE2 I:GLU43 2.0 9.4 1.0
NE2 I:HIS516 2.1 9.0 1.0
CD I:GLU43 3.0 9.4 1.0
CD2 I:HIS516 3.1 9.0 1.0
CE1 I:HIS516 3.1 9.0 1.0
C I:VAL462 3.2 8.8 1.0
OE1 I:GLU43 3.3 9.4 1.0
N I:VAL462 3.7 8.8 1.0
CA I:VAL462 3.9 8.8 1.0
OE2 I:GLU303 3.9 14.0 1.0
OE1 I:GLU303 4.0 14.0 1.0
OE1 I:GLN461 4.1 10.1 1.0
ND1 I:HIS516 4.2 9.0 1.0
N I:VAL463 4.2 8.8 1.0
CG I:HIS516 4.2 9.0 1.0
NZ I:LYS341 4.3 12.5 1.0
CB I:VAL462 4.3 8.8 1.0
CG I:GLU43 4.3 9.4 1.0
CD I:GLU303 4.4 14.0 1.0
CA I:VAL463 4.5 8.8 1.0
CE I:LYS341 4.7 12.5 1.0
C I:GLN461 4.7 10.1 1.0
CD I:LYS341 4.8 12.5 1.0
CG2 I:VAL463 4.8 8.8 1.0

Magnesium binding site 6 out of 8 in 7uus

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Magnesium binding site 6 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg603

b:9.8
occ:1.00
 O K:VAL462 2.0 8.8 1.0
OE2 K:GLU43 2.0 9.4 1.0
NE2 K:HIS516 2.1 9.0 1.0
CD K:GLU43 3.0 9.4 1.0
CD2 K:HIS516 3.1 9.0 1.0
CE1 K:HIS516 3.1 9.0 1.0
C K:VAL462 3.2 8.8 1.0
OE1 K:GLU43 3.3 9.4 1.0
N K:VAL462 3.7 8.8 1.0
CA K:VAL462 3.9 8.8 1.0
OE2 K:GLU303 3.9 14.0 1.0
OE1 K:GLU303 4.0 14.0 1.0
OE1 K:GLN461 4.1 10.1 1.0
ND1 K:HIS516 4.2 9.0 1.0
N K:VAL463 4.2 8.8 1.0
CG K:HIS516 4.2 9.0 1.0
NZ K:LYS341 4.3 12.5 1.0
CB K:VAL462 4.3 8.8 1.0
CG K:GLU43 4.3 9.4 1.0
CD K:GLU303 4.4 14.0 1.0
CA K:VAL463 4.5 8.8 1.0
CE K:LYS341 4.7 12.5 1.0
C K:GLN461 4.7 10.1 1.0
CD K:LYS341 4.8 12.5 1.0
CG2 K:VAL463 4.8 8.8 1.0

Magnesium binding site 7 out of 8 in 7uus

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Magnesium binding site 7 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:9.8
occ:1.00
 O M:VAL462 2.0 8.8 1.0
OE2 M:GLU43 2.0 9.4 1.0
NE2 M:HIS516 2.1 9.0 1.0
CD M:GLU43 3.0 9.4 1.0
CD2 M:HIS516 3.1 9.0 1.0
CE1 M:HIS516 3.1 9.0 1.0
C M:VAL462 3.2 8.8 1.0
OE1 M:GLU43 3.3 9.4 1.0
N M:VAL462 3.7 8.8 1.0
CA M:VAL462 3.9 8.8 1.0
OE2 M:GLU303 3.9 14.0 1.0
OE1 M:GLU303 4.0 14.0 1.0
OE1 M:GLN461 4.1 10.1 1.0
ND1 M:HIS516 4.2 9.0 1.0
N M:VAL463 4.2 8.9 1.0
CG M:HIS516 4.2 9.0 1.0
NZ M:LYS341 4.2 12.5 1.0
CB M:VAL462 4.3 8.8 1.0
CG M:GLU43 4.3 9.4 1.0
CD M:GLU303 4.4 14.0 1.0
CA M:VAL463 4.5 8.9 1.0
CE M:LYS341 4.7 12.5 1.0
C M:GLN461 4.7 10.1 1.0
CD M:LYS341 4.8 12.5 1.0
CG2 M:VAL463 4.8 8.9 1.0

Magnesium binding site 8 out of 8 in 7uus

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Magnesium binding site 8 out of 8 in the The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Cryoem Structure of the [Nife]-Hydrogenase Huc From Mycobacterium Smegmatis - Full Complex Focused Refinement of Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg603

b:9.8
occ:1.00
 O O:VAL462 2.0 8.8 1.0
OE2 O:GLU43 2.0 9.4 1.0
NE2 O:HIS516 2.1 9.0 1.0
CD O:GLU43 3.0 9.4 1.0
CD2 O:HIS516 3.1 9.0 1.0
CE1 O:HIS516 3.1 9.0 1.0
C O:VAL462 3.2 8.8 1.0
OE1 O:GLU43 3.3 9.4 1.0
N O:VAL462 3.7 8.8 1.0
CA O:VAL462 3.9 8.8 1.0
OE2 O:GLU303 3.9 14.0 1.0
OE1 O:GLU303 4.0 14.0 1.0
OE1 O:GLN461 4.1 10.1 1.0
ND1 O:HIS516 4.2 9.0 1.0
N O:VAL463 4.2 8.9 1.0
CG O:HIS516 4.2 9.0 1.0
NZ O:LYS341 4.2 12.5 1.0
CB O:VAL462 4.3 8.8 1.0
CG O:GLU43 4.3 9.4 1.0
CD O:GLU303 4.4 14.0 1.0
CA O:VAL463 4.5 8.9 1.0
CE O:LYS341 4.7 12.5 1.0
C O:GLN461 4.7 10.1 1.0
CD O:LYS341 4.8 12.5 1.0
CG2 O:VAL463 4.8 8.9 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.
Page generated: Thu Oct 3 10:13:46 2024

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