Magnesium 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 Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium 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 Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 7utd
Go back to
Magnesium Binding Sites List in 7utd
Magnesium 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 Magnesium with other atoms in the Mg 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: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 10:12:34 2024
|