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Magnesium in PDB 3i4k: Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum

Enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum

All present enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum:
5.5.1.1; 5.5.1.7;

Protein crystallography data

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum, PDB code: 3i4k was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.541, 156.709, 202.952, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum (pdb code 3i4k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum, PDB code: 3i4k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3i4k

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Magnesium binding site 1 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg385

b:28.3
occ:1.00
 OD2 A:ASP251 2.0 37.1 1.0
O A:HOH961 2.1 33.5 1.0
OE2 A:GLU226 2.2 33.1 1.0
OXT A:ACY384 2.2 34.0 1.0
OD2 A:ASP200 2.3 35.9 1.0
O A:ACY384 2.3 32.5 1.0
C A:ACY384 2.6 34.0 1.0
CD A:GLU226 3.0 28.7 1.0
CG A:ASP251 3.2 32.8 1.0
CG A:ASP200 3.3 34.5 1.0
OD1 A:ASP200 3.6 35.0 1.0
CB A:ASP251 3.7 32.1 1.0
NZ A:LYS169 3.7 32.1 1.0
OE1 A:GLU226 3.8 28.6 1.0
CG A:GLU226 3.8 31.3 1.0
OE2 A:GLU252 4.0 43.8 1.0
OD1 A:ASN202 4.0 36.9 1.0
NZ A:LYS275 4.1 27.9 1.0
CH3 A:ACY384 4.1 34.9 1.0
OD1 A:ASP251 4.2 32.3 1.0
CE A:LYS169 4.6 28.4 1.0
CB A:ASP200 4.6 34.3 1.0
NE1 A:TRP61 4.6 34.2 1.0
CG A:ASN202 4.7 36.5 1.0
CD A:GLU252 4.9 40.0 1.0
CE A:LYS275 4.9 28.5 1.0

Magnesium binding site 2 out of 8 in 3i4k

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Magnesium binding site 2 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg385

b:25.9
occ:1.00
 OE2 B:GLU226 1.9 31.3 1.0
O B:HOH962 2.0 31.0 1.0
OD2 B:ASP251 2.1 33.7 1.0
O B:ACY384 2.2 29.1 1.0
OXT B:ACY384 2.2 29.8 1.0
OD2 B:ASP200 2.4 32.8 1.0
C B:ACY384 2.5 28.4 1.0
CD B:GLU226 3.0 34.4 1.0
CG B:ASP251 3.2 33.4 1.0
CG B:ASP200 3.4 33.6 1.0
CB B:ASP251 3.6 29.8 1.0
NZ B:LYS169 3.7 48.4 1.0
OE1 B:GLU226 3.7 37.0 1.0
OD1 B:ASP200 3.7 32.1 1.0
OD1 B:ASN202 3.9 36.9 1.0
OE2 B:GLU252 3.9 35.3 1.0
NZ B:LYS275 4.0 29.5 1.0
CH3 B:ACY384 4.0 28.6 1.0
CG B:GLU226 4.1 33.5 1.0
OD1 B:ASP251 4.3 28.1 1.0
O B:HOH386 4.3 37.3 1.0
NE1 B:TRP61 4.7 34.5 1.0
CB B:ASP200 4.7 32.9 1.0
CE B:LYS169 4.7 47.5 1.0
CE B:LYS275 4.7 27.7 1.0
CG B:ASN202 4.8 36.7 1.0
CD B:GLU252 4.9 36.1 1.0

Magnesium binding site 3 out of 8 in 3i4k

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Magnesium binding site 3 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg385

b:31.8
occ:1.00
 OE2 C:GLU226 1.9 38.9 1.0
O C:ACY384 2.2 40.5 1.0
OD2 C:ASP251 2.2 38.6 1.0
OXT C:ACY384 2.2 41.4 1.0
O C:HOH963 2.2 42.0 1.0
OD2 C:ASP200 2.3 44.0 1.0
C C:ACY384 2.5 40.4 1.0
CD C:GLU226 3.0 37.2 1.0
CG C:ASP251 3.2 35.1 1.0
CG C:ASP200 3.3 46.7 1.0
OD1 C:ASP200 3.6 45.4 1.0
CB C:ASP251 3.7 33.6 1.0
NZ C:LYS169 3.8 40.6 1.0
OE1 C:GLU226 3.8 36.8 1.0
OE2 C:GLU252 3.8 49.7 1.0
OD1 C:ASN202 3.8 43.4 1.0
CH3 C:ACY384 4.0 40.6 1.0
CG C:GLU226 4.0 36.7 1.0
NZ C:LYS275 4.1 36.0 1.0
OD1 C:ASP251 4.3 32.3 1.0
CE C:LYS169 4.6 41.5 1.0
NE1 C:TRP61 4.6 43.3 1.0
CB C:ASP200 4.6 45.4 1.0
CG C:ASN202 4.7 44.2 1.0
CE C:LYS275 4.8 29.5 1.0
CD C:GLU252 4.8 45.9 1.0
CZ2 C:TRP61 4.9 41.2 1.0

Magnesium binding site 4 out of 8 in 3i4k

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Magnesium binding site 4 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg385

b:33.1
occ:1.00
 O D:HOH964 2.0 37.0 1.0
OE2 D:GLU226 2.0 38.0 1.0
OD2 D:ASP251 2.1 35.9 1.0
OXT D:ACY384 2.2 46.1 1.0
O D:ACY384 2.3 44.8 1.0
OD2 D:ASP200 2.3 36.3 1.0
C D:ACY384 2.6 46.8 1.0
CD D:GLU226 3.1 39.9 1.0
CG D:ASP251 3.1 34.2 1.0
CG D:ASP200 3.4 36.6 1.0
CB D:ASP251 3.6 32.9 1.0
OD1 D:ASP200 3.8 37.8 1.0
OE2 D:GLU252 3.8 44.5 1.0
OE1 D:GLU226 3.8 39.8 1.0
NZ D:LYS169 3.9 41.5 1.0
OD1 D:ASN202 3.9 43.8 1.0
NZ D:LYS275 4.0 38.5 1.0
CG D:GLU226 4.0 38.5 1.0
CH3 D:ACY384 4.1 45.1 1.0
OD1 D:ASP251 4.2 28.9 1.0
O D:HOH396 4.4 39.4 1.0
CB D:ASP200 4.7 38.5 1.0
CG D:ASN202 4.8 44.1 1.0
NE1 D:TRP61 4.8 42.3 1.0
CE D:LYS275 4.8 39.9 1.0
CE D:LYS169 4.8 41.7 1.0
CD D:GLU252 4.9 42.0 1.0

Magnesium binding site 5 out of 8 in 3i4k

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Magnesium binding site 5 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg385

b:24.7
occ:1.00
 O E:HOH965 1.9 29.6 1.0
OE2 E:GLU226 1.9 31.7 1.0
OD2 E:ASP251 2.1 33.8 1.0
O E:ACY384 2.2 31.6 1.0
OXT E:ACY384 2.2 32.4 1.0
OD2 E:ASP200 2.4 34.9 1.0
C E:ACY384 2.5 32.8 1.0
CD E:GLU226 3.0 34.6 1.0
CG E:ASP251 3.2 34.4 1.0
CG E:ASP200 3.3 35.8 1.0
OD1 E:ASP200 3.6 31.3 1.0
CB E:ASP251 3.6 30.8 1.0
OD1 E:ASN202 3.9 32.2 1.0
OE1 E:GLU226 3.9 33.6 1.0
OE2 E:GLU252 3.9 32.4 1.0
CG E:GLU226 3.9 32.2 1.0
NZ E:LYS169 4.0 35.1 1.0
CH3 E:ACY384 4.0 31.3 1.0
NZ E:LYS275 4.1 29.2 1.0
O E:HOH407 4.1 41.2 1.0
OD1 E:ASP251 4.3 33.6 1.0
NE1 E:TRP61 4.5 30.9 1.0
CB E:ASP200 4.6 33.4 1.0
CG E:ASN202 4.6 32.6 1.0
CE E:LYS169 4.7 34.5 1.0
CD E:GLU252 4.9 35.3 1.0
CE E:LYS275 4.9 30.4 1.0
ND2 E:ASN202 5.0 30.8 1.0
OE1 E:GLU252 5.0 35.5 1.0

Magnesium binding site 6 out of 8 in 3i4k

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Magnesium binding site 6 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg385

b:31.2
occ:1.00
 OE2 F:GLU226 2.0 38.1 1.0
O F:HOH966 2.0 36.1 1.0
OXT F:ACY384 2.0 39.6 1.0
OD2 F:ASP251 2.1 38.2 1.0
OD2 F:ASP200 2.2 36.6 1.0
O F:ACY384 2.5 40.4 1.0
C F:ACY384 2.6 40.7 1.0
CD F:GLU226 3.0 37.8 1.0
CG F:ASP251 3.2 36.7 1.0
CG F:ASP200 3.2 37.2 1.0
OD1 F:ASP200 3.5 39.2 1.0
CB F:ASP251 3.7 34.1 1.0
OE2 F:GLU252 3.7 45.0 1.0
NZ F:LYS169 3.7 46.8 1.0
OE1 F:GLU226 3.8 35.2 1.0
CG F:GLU226 3.9 36.7 1.0
OD1 F:ASN202 3.9 43.8 1.0
NZ F:LYS275 4.0 29.8 1.0
CH3 F:ACY384 4.1 39.2 1.0
OD1 F:ASP251 4.3 35.9 1.0
CB F:ASP200 4.5 37.5 1.0
CE F:LYS169 4.6 45.2 1.0
CG F:ASN202 4.7 40.5 1.0
CD F:GLU252 4.7 41.2 1.0
NE1 F:TRP61 4.8 39.4 1.0
CE F:LYS275 4.9 28.3 1.0

Magnesium binding site 7 out of 8 in 3i4k

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Magnesium binding site 7 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg385

b:38.4
occ:1.00
 OD2 G:ASP251 1.8 39.7 1.0
OE2 G:GLU226 2.0 42.5 1.0
O G:HOH967 2.1 45.0 1.0
O G:ACY384 2.2 49.3 1.0
OXT G:ACY384 2.3 48.4 1.0
OD2 G:ASP200 2.3 42.9 1.0
C G:ACY384 2.6 50.5 1.0
CG G:ASP251 3.0 38.0 1.0
CD G:GLU226 3.2 44.5 1.0
CG G:ASP200 3.4 44.2 1.0
CB G:ASP251 3.6 38.0 1.0
OE2 G:GLU252 3.7 49.7 1.0
OD1 G:ASP200 3.8 47.7 1.0
NZ G:LYS275 3.9 34.7 1.0
NZ G:LYS169 3.9 52.8 1.0
OE1 G:GLU226 4.0 46.5 1.0
OD1 G:ASP251 4.0 33.0 1.0
OD1 G:ASN202 4.0 46.2 1.0
CG G:GLU226 4.1 42.8 1.0
CH3 G:ACY384 4.1 49.8 1.0
NE1 G:TRP61 4.5 43.7 1.0
CB G:ASP200 4.7 47.4 1.0
CD G:GLU252 4.8 49.2 1.0
CE G:LYS169 4.8 51.5 1.0
CE G:LYS275 4.8 35.8 1.0
CG G:ASN202 4.8 45.5 1.0
CZ2 G:TRP61 5.0 42.4 1.0

Magnesium binding site 8 out of 8 in 3i4k

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Magnesium binding site 8 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg385

b:35.4
occ:1.00
 OE2 H:GLU226 1.9 38.0 1.0
OD2 H:ASP251 1.9 36.3 1.0
O H:HOH968 2.0 40.2 1.0
OXT H:ACY384 2.1 41.3 1.0
O H:ACY384 2.2 45.3 1.0
OD2 H:ASP200 2.4 39.4 1.0
C H:ACY384 2.5 45.3 1.0
CG H:ASP251 3.0 36.7 1.0
CD H:GLU226 3.1 36.5 1.0
CG H:ASP200 3.4 40.1 1.0
CB H:ASP251 3.7 33.2 1.0
OE1 H:GLU226 3.8 37.5 1.0
OD1 H:ASP200 3.8 39.4 1.0
OE2 H:GLU252 3.8 45.5 1.0
NZ H:LYS169 3.9 45.6 1.0
NZ H:LYS275 3.9 36.9 1.0
OD1 H:ASN202 3.9 48.3 1.0
CH3 H:ACY384 4.0 42.0 1.0
OD1 H:ASP251 4.1 36.1 1.0
CG H:GLU226 4.1 37.2 1.0
CB H:ASP200 4.7 39.7 1.0
CE H:LYS275 4.7 34.4 1.0
CE H:LYS169 4.7 46.9 1.0
NE1 H:TRP61 4.8 38.4 1.0
CD H:GLU252 4.8 42.0 1.0
CG H:ASN202 4.9 45.3 1.0
CZ2 H:TRP61 4.9 33.9 1.0
OE1 H:GLU252 5.0 41.7 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo. Crystal Structure of Muconate Lactonizing Enzyme From Corynebacterium Glutamicum To Be Published.
Page generated: Wed Aug 14 15:35:57 2024

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