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Magnesium in PDB 3i6e: Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.

Enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.

All present enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.:
5.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi., PDB code: 3i6e 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) 24.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.135, 135.358, 113.024, 90.00, 103.18, 90.00
R / Rfree (%) 23.5 / 26.3

Other elements in 3i6e:

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. (pdb code 3i6e). 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 Ruegeria Pomeroyi., PDB code: 3i6e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3i6e

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Magnesium binding site 1 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg386

b:36.3
occ:1.00
 OE2 A:GLU224 1.9 35.7 1.0
O A:HOH1013 1.9 40.0 1.0
O A:HOH1012 2.0 30.8 1.0
OD2 A:ASP249 2.1 29.9 1.0
O A:HOH1011 2.1 36.4 1.0
OD2 A:ASP198 2.2 31.9 1.0
CD A:GLU224 2.9 34.8 1.0
CG A:ASP198 3.1 31.1 1.0
CG A:ASP249 3.1 30.1 1.0
OD1 A:ASP198 3.3 28.4 1.0
O A:HOH1015 3.3 30.4 1.0
CB A:ASP249 3.6 26.7 1.0
CG A:GLU224 3.7 35.7 1.0
OE1 A:GLU224 3.8 35.2 1.0
O A:HOH1014 4.1 41.1 1.0
NZ A:LYS168 4.1 34.4 1.0
NZ A:LYS273 4.1 22.7 1.0
OE1 A:GLU250 4.2 30.2 1.0
OD1 A:ASP249 4.2 29.6 1.0
OD1 A:ASN200 4.5 47.0 1.0
ND2 A:ASN200 4.5 44.9 1.0
CB A:ASP198 4.5 29.3 1.0
CB A:GLU224 4.5 31.8 1.0
CG A:ASN200 4.6 41.6 1.0
CE A:LYS273 4.7 22.3 1.0
OE2 A:GLU250 4.8 37.1 1.0
CD A:GLU250 4.8 35.1 1.0
O A:HOH519 5.0 32.2 1.0

Magnesium binding site 2 out of 8 in 3i6e

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Magnesium binding site 2 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg386

b:36.8
occ:1.00
 O B:HOH1022 1.9 31.1 1.0
OE2 B:GLU224 1.9 34.0 1.0
O B:HOH1021 2.0 40.8 1.0
OD2 B:ASP249 2.1 31.2 1.0
OD2 B:ASP198 2.2 31.7 1.0
CD B:GLU224 2.8 32.4 1.0
CG B:ASP198 3.1 30.3 1.0
O B:HOH1023 3.1 41.3 1.0
CG B:ASP249 3.1 28.3 1.0
OD1 B:ASP198 3.3 30.6 1.0
O B:HOH1025 3.4 30.4 1.0
CB B:ASP249 3.5 25.0 1.0
CG B:GLU224 3.6 31.7 1.0
OE1 B:GLU224 3.7 31.7 1.0
ND2 B:ASN200 4.0 37.6 1.0
OE1 B:GLU250 4.0 30.9 1.0
O B:HOH1024 4.0 40.1 1.0
NZ B:LYS273 4.0 22.8 1.0
NZ B:LYS168 4.1 32.4 1.0
OD1 B:ASP249 4.2 23.7 1.0
CB B:GLU224 4.5 26.5 1.0
CB B:ASP198 4.5 28.6 1.0
CE B:LYS273 4.7 23.0 1.0
CD B:GLU250 4.8 34.3 1.0
CG B:ASN200 4.8 39.2 1.0
O B:HOH422 4.9 31.2 1.0
OE2 B:GLU250 4.9 39.1 1.0
OG B:SER271 5.0 29.7 1.0

Magnesium binding site 3 out of 8 in 3i6e

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Magnesium binding site 3 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg386

b:40.7
occ:1.00
 OE2 C:GLU224 2.0 33.1 1.0
O C:HOH1033 2.0 44.1 1.0
O C:HOH1032 2.0 37.8 1.0
OD2 C:ASP249 2.2 31.5 1.0
OD2 C:ASP198 2.2 34.6 1.0
O C:HOH1031 2.2 42.2 1.0
CD C:GLU224 2.9 33.3 1.0
CG C:ASP198 3.1 33.6 1.0
CG C:ASP249 3.2 31.8 1.0
OD1 C:ASP198 3.3 34.0 1.0
O C:HOH1035 3.5 27.6 1.0
CB C:ASP249 3.6 28.8 1.0
OE1 C:GLU224 3.7 36.1 1.0
CG C:GLU224 3.8 32.5 1.0
NZ C:LYS168 4.0 32.5 1.0
ND2 C:ASN200 4.0 38.8 1.0
NZ C:LYS273 4.0 26.8 1.0
OE1 C:GLU250 4.1 34.4 1.0
OD1 C:ASP249 4.3 28.2 1.0
CB C:ASP198 4.5 31.6 1.0
CB C:GLU224 4.5 30.1 1.0
OE2 C:GLU250 4.7 39.9 1.0
CE C:LYS273 4.7 26.1 1.0
CG C:ASN200 4.7 37.9 1.0
CD C:GLU250 4.7 37.5 1.0

Magnesium binding site 4 out of 8 in 3i6e

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Magnesium binding site 4 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg386

b:38.0
occ:1.00
 OE2 D:GLU224 1.8 35.6 1.0
O D:HOH1042 1.9 29.8 1.0
O D:HOH1041 2.0 36.1 1.0
OD2 D:ASP249 2.1 28.8 1.0
OD2 D:ASP198 2.3 31.7 1.0
O D:HOH1043 2.3 39.2 1.0
CD D:GLU224 2.9 35.3 1.0
CG D:ASP249 3.1 28.6 1.0
CG D:ASP198 3.2 29.1 1.0
OD1 D:ASP198 3.3 26.7 1.0
CB D:ASP249 3.5 27.8 1.0
O D:HOH394 3.5 30.1 1.0
OE1 D:GLU224 3.7 36.5 1.0
CG D:GLU224 3.7 35.0 1.0
NZ D:LYS273 3.9 24.8 1.0
O D:HOH1044 4.0 40.1 1.0
NZ D:LYS168 4.1 32.2 1.0
OE1 D:GLU250 4.1 28.4 1.0
OD1 D:ASP249 4.2 24.4 1.0
ND2 D:ASN200 4.2 41.1 1.0
CB D:GLU224 4.5 30.5 1.0
CB D:ASP198 4.6 28.2 1.0
OE2 D:GLU250 4.6 34.9 1.0
CE D:LYS273 4.6 24.6 1.0
CD D:GLU250 4.6 31.4 1.0
CG D:ASN200 4.7 39.4 1.0
OG D:SER271 4.9 29.1 1.0
OD1 D:ASN200 4.9 42.3 1.0
CA D:ASP249 5.0 25.5 1.0
O D:HOH701 5.0 34.0 1.0

Magnesium binding site 5 out of 8 in 3i6e

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Magnesium binding site 5 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg386

b:36.2
occ:1.00
 OE2 E:GLU224 1.9 30.1 1.0
O E:HOH1051 2.0 37.6 1.0
O E:HOH1052 2.0 29.8 1.0
O E:HOH1053 2.1 42.0 1.0
OD2 E:ASP249 2.1 28.8 1.0
OD2 E:ASP198 2.2 33.7 1.0
CD E:GLU224 3.0 34.2 1.0
CG E:ASP249 3.1 28.9 1.0
CG E:ASP198 3.2 30.7 1.0
O E:HOH1055 3.3 29.1 1.0
OD1 E:ASP198 3.4 30.0 1.0
CB E:ASP249 3.6 26.5 1.0
OE1 E:GLU224 3.7 35.4 1.0
CG E:GLU224 3.8 32.8 1.0
O E:HOH1054 3.9 43.4 1.0
NZ E:LYS168 3.9 32.4 1.0
NZ E:LYS273 4.0 27.0 1.0
OE1 E:GLU250 4.2 34.4 1.0
OD1 E:ASP249 4.3 28.3 1.0
ND2 E:ASN200 4.4 42.5 1.0
CB E:GLU224 4.5 31.5 1.0
CB E:ASP198 4.5 30.7 1.0
OE2 E:GLU250 4.5 38.7 1.0
CE E:LYS273 4.6 25.4 1.0
CD E:GLU250 4.7 35.7 1.0
CG E:ASN200 4.8 41.1 1.0
OG E:SER271 4.9 30.0 1.0
OD1 E:ASN200 5.0 44.7 1.0

Magnesium binding site 6 out of 8 in 3i6e

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Magnesium binding site 6 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg386

b:33.6
occ:1.00
 OE2 F:GLU224 1.8 34.1 1.0
O F:HOH1062 1.9 29.3 1.0
OD2 F:ASP249 2.1 29.2 1.0
O F:HOH1061 2.1 34.5 1.0
OD2 F:ASP198 2.3 30.5 1.0
CD F:GLU224 2.9 32.0 1.0
CG F:ASP249 3.1 27.6 1.0
CG F:ASP198 3.1 30.5 1.0
O F:HOH1065 3.2 33.5 1.0
OD1 F:ASP198 3.3 27.1 1.0
CB F:ASP249 3.5 25.1 1.0
CG F:GLU224 3.7 33.1 1.0
OE1 F:GLU224 3.8 32.0 1.0
ND2 F:ASN200 3.9 38.0 1.0
NZ F:LYS168 4.1 37.7 1.0
OE1 F:GLU250 4.1 32.0 1.0
NZ F:LYS273 4.1 22.3 1.0
OD1 F:ASP249 4.2 25.7 1.0
O F:HOH1064 4.3 41.0 1.0
CB F:GLU224 4.5 28.4 1.0
CB F:ASP198 4.6 25.5 1.0
CE F:LYS273 4.7 23.6 1.0
CD F:GLU250 4.7 35.5 1.0
CG F:ASN200 4.7 35.5 1.0
OE2 F:GLU250 4.9 38.6 1.0
OG F:SER271 4.9 28.7 1.0
CA F:ASP249 5.0 23.1 1.0

Magnesium binding site 7 out of 8 in 3i6e

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Magnesium binding site 7 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg386

b:30.2
occ:1.00
 OE2 G:GLU224 2.0 26.8 1.0
O G:HOH1072 2.0 25.0 1.0
O G:HOH1071 2.0 32.4 1.0
OD2 G:ASP249 2.2 28.2 1.0
OD2 G:ASP198 2.2 25.4 1.0
O G:HOH1073 2.4 38.0 1.0
CD G:GLU224 3.0 30.4 1.0
CG G:ASP198 3.1 23.7 1.0
CG G:ASP249 3.2 25.6 1.0
OD1 G:ASP198 3.2 24.0 1.0
O G:HOH1075 3.5 30.4 1.0
CB G:ASP249 3.6 20.7 1.0
CG G:GLU224 3.7 29.5 1.0
OE1 G:GLU224 3.8 31.3 1.0
O G:HOH1074 3.9 46.2 1.0
NZ G:LYS273 3.9 20.0 1.0
NZ G:LYS168 4.0 25.2 1.0
OE1 G:GLU250 4.1 24.5 1.0
ND2 G:ASN200 4.2 36.9 1.0
OD1 G:ASP249 4.3 21.5 1.0
CB G:ASP198 4.5 21.2 1.0
CG G:ASN200 4.6 35.2 1.0
CB G:GLU224 4.6 24.7 1.0
CE G:LYS273 4.7 18.8 1.0
CD G:GLU250 4.7 28.2 1.0
OD1 G:ASN200 4.8 38.3 1.0
OE2 G:GLU250 4.8 31.8 1.0

Magnesium binding site 8 out of 8 in 3i6e

Go back to Magnesium Binding Sites List in 3i6e
Magnesium binding site 8 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


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 Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg386

b:39.1
occ:1.00
 OD2 H:ASP249 2.0 32.3 1.0
O H:HOH1081 2.1 34.0 1.0
O H:HOH1082 2.2 30.5 1.0
OE2 H:GLU224 2.2 34.9 1.0
OD2 H:ASP198 2.3 32.9 1.0
O H:HOH1083 2.4 40.9 1.0
O H:HOH1085 3.0 35.2 1.0
CG H:ASP249 3.1 30.3 1.0
CG H:ASP198 3.2 31.9 1.0
CD H:GLU224 3.3 35.5 1.0
OD1 H:ASP198 3.4 30.4 1.0
CB H:ASP249 3.5 28.6 1.0
OE1 H:GLU224 3.9 36.6 1.0
NZ H:LYS273 4.0 25.9 1.0
NZ H:LYS168 4.0 34.3 1.0
OD1 H:ASP249 4.1 26.1 1.0
OE1 H:GLU250 4.2 35.0 1.0
O H:HOH1084 4.2 34.8 1.0
CB H:GLU224 4.3 30.0 1.0
CG H:GLU224 4.4 32.8 1.0
ND2 H:ASN200 4.5 40.1 1.0
CE H:LYS273 4.5 25.1 1.0
CB H:ASP198 4.6 29.6 1.0
OG H:SER271 4.7 29.7 1.0
CD H:GLU250 4.9 36.5 1.0
OE2 H:GLU250 4.9 41.0 1.0
CB H:SER271 5.0 26.9 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 Ruegeria Pomeroyi. To Be Published.
Page generated: Wed Aug 14 15:58:15 2024

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