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Manganese in PDB 5eja: Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min

Enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min

All present enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min:
2.2.1.9;

Protein crystallography data

The structure of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min, PDB code: 5eja was solved by H.G.Song, C.Dong, Y.Z.Chen, Y.R.Sun, Z.H.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.52 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.610, 90.660, 169.458, 76.03, 83.39, 64.41
R / Rfree (%) 17 / 19.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min (pdb code 5eja). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min, PDB code: 5eja:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5eja

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Manganese binding site 1 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:20.0
occ:1.00
 O A:GLY471 2.0 9.1 1.0
O1B A:TD6601 2.1 17.0 1.0
OD1 A:ASN469 2.1 10.0 1.0
OD1 A:ASP442 2.1 12.2 1.0
O1A A:TD6601 2.2 16.8 1.0
O A:HOH895 2.2 15.2 1.0
CG A:ASN469 3.1 12.9 1.0
CG A:ASP442 3.2 14.8 1.0
C A:GLY471 3.3 15.6 1.0
PA A:TD6601 3.3 16.6 1.0
PB A:TD6601 3.3 16.8 1.0
O3A A:TD6601 3.4 16.6 1.0
ND2 A:ASN469 3.5 10.1 1.0
OD2 A:ASP442 3.6 12.1 1.0
N A:ASP442 3.9 9.8 1.0
N A:GLY471 4.0 11.6 1.0
N A:GLY472 4.1 9.2 1.0
CA A:GLY472 4.1 9.0 1.0
N A:GLN473 4.2 10.2 1.0
O7 A:TD6601 4.2 16.7 1.0
N A:ASN469 4.2 9.2 1.0
CA A:GLY471 4.2 13.3 1.0
O A:HOH788 4.3 16.9 1.0
O3B A:TD6601 4.3 16.9 1.0
O2B A:TD6601 4.3 16.8 1.0
O A:VAL467 4.3 11.1 1.0
CB A:ASP442 4.4 9.0 1.0
O2A A:TD6601 4.4 16.5 1.0
CB A:ASN469 4.4 13.5 1.0
N A:LEU443 4.5 8.9 1.0
C A:ASN469 4.6 9.8 1.0
N A:ASN470 4.6 10.8 1.0
CA A:GLY441 4.6 8.3 1.0
CA A:ASP442 4.6 8.5 1.0
CA A:ASN469 4.6 9.3 1.0
C A:GLY441 4.7 12.5 1.0
CG A:GLN473 4.7 10.7 1.0
C A:GLY472 4.7 11.2 1.0
C A:ASN470 5.0 15.0 1.0

Manganese binding site 2 out of 8 in 5eja

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Manganese binding site 2 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:20.3
occ:1.00
 O B:GLY471 2.1 9.4 1.0
OD1 B:ASN469 2.1 10.3 1.0
OD1 B:ASP442 2.1 13.2 1.0
O1B B:TD6601 2.1 18.8 1.0
O B:HOH898 2.1 15.2 1.0
O1A B:TD6601 2.2 18.5 1.0
CG B:ASN469 3.0 13.0 1.0
CG B:ASP442 3.1 12.5 1.0
C B:GLY471 3.3 11.3 1.0
PA B:TD6601 3.3 18.5 1.0
PB B:TD6601 3.4 18.8 1.0
ND2 B:ASN469 3.4 12.6 1.0
O3A B:TD6601 3.5 18.7 1.0
OD2 B:ASP442 3.6 12.8 1.0
N B:ASP442 3.9 9.9 1.0
N B:GLY471 4.0 11.9 1.0
N B:GLN473 4.1 8.7 1.0
N B:GLY472 4.2 12.2 1.0
CA B:GLY472 4.2 8.4 1.0
O7 B:TD6601 4.2 18.3 1.0
N B:ASN469 4.2 9.2 1.0
CA B:GLY471 4.3 13.8 1.0
O B:HOH828 4.3 17.7 1.0
O B:VAL467 4.3 13.1 1.0
O2B B:TD6601 4.4 19.0 1.0
CB B:ASP442 4.4 16.5 1.0
O3B B:TD6601 4.4 18.6 1.0
CB B:ASN469 4.4 10.8 1.0
O2A B:TD6601 4.4 18.5 1.0
C B:ASN469 4.5 11.6 1.0
N B:ASN470 4.6 9.5 1.0
N B:LEU443 4.6 8.5 1.0
CA B:ASN469 4.6 10.7 1.0
CA B:ASP442 4.6 13.3 1.0
CA B:GLY441 4.7 9.1 1.0
CG B:GLN473 4.7 9.1 1.0
C B:GLY472 4.7 12.7 1.0
C B:GLY441 4.7 15.2 1.0
C B:ASN470 5.0 17.1 1.0
O B:ASN469 5.0 15.3 1.0

Manganese binding site 3 out of 8 in 5eja

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Manganese binding site 3 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:24.1
occ:1.00
 O C:GLY471 2.1 11.4 1.0
OD1 C:ASN469 2.1 11.8 1.0
OD1 C:ASP442 2.1 12.5 1.0
O C:HOH863 2.2 18.7 1.0
O1A C:TD6601 2.2 20.9 1.0
O1B C:TD6601 2.2 21.0 1.0
CG C:ASN469 3.1 17.9 1.0
CG C:ASP442 3.2 11.7 1.0
C C:GLY471 3.3 15.5 1.0
PB C:TD6601 3.3 20.8 1.0
PA C:TD6601 3.3 20.7 1.0
O3A C:TD6601 3.4 20.7 1.0
ND2 C:ASN469 3.5 12.2 1.0
OD2 C:ASP442 3.6 13.8 1.0
N C:ASP442 3.8 12.8 1.0
N C:GLY471 4.0 11.8 1.0
O7 C:TD6601 4.1 20.6 1.0
N C:GLN473 4.2 14.2 1.0
N C:GLY472 4.2 11.2 1.0
CA C:GLY472 4.2 11.1 1.0
N C:ASN469 4.2 12.7 1.0
O2B C:TD6601 4.2 20.8 1.0
O C:HOH766 4.2 21.4 1.0
CA C:GLY471 4.3 11.6 1.0
O3B C:TD6601 4.3 20.7 1.0
O C:VAL467 4.3 11.9 1.0
CB C:ASP442 4.4 11.8 1.0
O2A C:TD6601 4.4 20.6 1.0
CB C:ASN469 4.4 12.3 1.0
N C:LEU443 4.5 11.2 1.0
C C:ASN469 4.6 13.0 1.0
CA C:GLY441 4.6 11.3 1.0
CA C:ASP442 4.6 12.0 1.0
N C:ASN470 4.6 13.1 1.0
CA C:ASN469 4.6 12.3 1.0
C C:GLY441 4.7 17.3 1.0
CG C:GLN473 4.7 11.9 1.0
C C:GLY472 4.7 16.8 1.0
C C:ASN470 5.0 16.8 1.0

Manganese binding site 4 out of 8 in 5eja

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Manganese binding site 4 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn602

b:27.1
occ:1.00
 OD1 D:ASN469 2.0 13.7 1.0
OD1 D:ASP442 2.1 13.7 1.0
O D:GLY471 2.1 16.1 1.0
O1B D:TD6601 2.1 23.8 1.0
O1A D:TD6601 2.2 23.5 1.0
O D:HOH782 2.2 22.7 1.0
CG D:ASN469 3.0 19.0 1.0
CG D:ASP442 3.1 16.2 1.0
C D:GLY471 3.3 18.7 1.0
PA D:TD6601 3.3 23.4 1.0
PB D:TD6601 3.4 23.6 1.0
ND2 D:ASN469 3.4 16.6 1.0
O3A D:TD6601 3.5 23.5 1.0
OD2 D:ASP442 3.6 16.1 1.0
N D:ASP442 3.8 14.0 1.0
N D:GLY471 4.0 12.6 1.0
N D:GLN473 4.1 12.4 1.0
N D:GLY472 4.2 13.1 1.0
CA D:GLY472 4.2 13.7 1.0
N D:ASN469 4.2 13.1 1.0
O7 D:TD6601 4.2 23.2 1.0
O D:HOH803 4.2 23.4 1.0
CA D:GLY471 4.2 15.8 1.0
O D:VAL467 4.3 16.0 1.0
O2B D:TD6601 4.3 23.7 1.0
CB D:ASN469 4.3 17.9 1.0
CB D:ASP442 4.3 12.4 1.0
O3B D:TD6601 4.4 23.5 1.0
O2A D:TD6601 4.4 23.2 1.0
C D:ASN469 4.5 15.0 1.0
N D:LEU443 4.5 11.9 1.0
CA D:ASN469 4.6 15.6 1.0
N D:ASN470 4.6 15.1 1.0
CA D:ASP442 4.6 12.2 1.0
CA D:GLY441 4.6 14.8 1.0
CG D:GLN473 4.7 13.1 1.0
C D:GLY441 4.7 15.6 1.0
C D:GLY472 4.7 16.4 1.0
O D:ASN469 4.9 18.9 1.0
C D:ASN470 4.9 19.0 1.0
CB D:GLN473 5.0 15.3 1.0

Manganese binding site 5 out of 8 in 5eja

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Manganese binding site 5 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:20.6
occ:1.00
 O1A E:TD6601 2.1 18.4 1.0
O1B E:TD6601 2.1 18.6 1.0
O E:GLY471 2.1 12.0 1.0
OD1 E:ASN469 2.1 12.1 1.0
OD1 E:ASP442 2.1 12.2 1.0
O E:HOH860 2.2 15.4 1.0
CG E:ASN469 3.1 13.6 1.0
CG E:ASP442 3.2 13.4 1.0
PA E:TD6601 3.2 18.2 1.0
C E:GLY471 3.3 15.7 1.0
PB E:TD6601 3.3 18.4 1.0
O3A E:TD6601 3.4 18.2 1.0
ND2 E:ASN469 3.5 12.3 1.0
OD2 E:ASP442 3.7 14.4 1.0
N E:ASP442 3.8 10.1 1.0
N E:GLY471 4.1 12.2 1.0
O7 E:TD6601 4.1 18.3 1.0
N E:GLY472 4.1 9.7 1.0
CA E:GLY472 4.1 9.5 1.0
N E:GLN473 4.2 11.0 1.0
N E:ASN469 4.2 9.6 1.0
O E:HOH789 4.2 18.2 1.0
CA E:GLY471 4.3 12.5 1.0
O E:VAL467 4.3 12.5 1.0
O2B E:TD6601 4.3 18.4 1.0
O2A E:TD6601 4.3 18.1 1.0
O3B E:TD6601 4.4 18.5 1.0
CB E:ASP442 4.4 10.8 1.0
CB E:ASN469 4.4 10.7 1.0
N E:LEU443 4.5 12.9 1.0
CA E:GLY441 4.6 9.0 1.0
C E:ASN469 4.6 14.0 1.0
CA E:ASP442 4.6 11.0 1.0
N E:ASN470 4.6 13.4 1.0
CA E:ASN469 4.6 13.2 1.0
C E:GLY441 4.7 8.7 1.0
C E:GLY472 4.7 10.9 1.0
CG E:GLN473 4.8 12.8 1.0
CG E:LEU443 5.0 10.1 1.0

Manganese binding site 6 out of 8 in 5eja

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Manganese binding site 6 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn602

b:21.6
occ:1.00
 O F:GLY471 2.1 12.1 1.0
OD1 F:ASP442 2.1 16.4 1.0
OD1 F:ASN469 2.1 11.4 1.0
O1B F:TD6601 2.1 19.2 1.0
O1A F:TD6601 2.1 18.9 1.0
O F:HOH900 2.2 16.4 1.0
CG F:ASN469 3.1 12.5 1.0
CG F:ASP442 3.1 13.5 1.0
C F:GLY471 3.3 11.7 1.0
PA F:TD6601 3.3 18.9 1.0
PB F:TD6601 3.3 19.2 1.0
ND2 F:ASN469 3.5 14.3 1.0
O3A F:TD6601 3.5 19.1 1.0
OD2 F:ASP442 3.6 12.9 1.0
N F:ASP442 3.8 13.9 1.0
N F:GLY471 4.0 13.3 1.0
N F:GLN473 4.1 12.3 1.0
CA F:GLY472 4.1 8.8 1.0
N F:GLY472 4.1 8.7 1.0
O7 F:TD6601 4.2 18.7 1.0
N F:ASN469 4.2 12.2 1.0
CA F:GLY471 4.3 13.6 1.0
O3B F:TD6601 4.3 19.0 1.0
CB F:ASP442 4.3 11.8 1.0
O F:HOH792 4.4 18.9 1.0
O2B F:TD6601 4.4 19.4 1.0
O F:VAL467 4.4 15.1 1.0
CB F:ASN469 4.4 10.1 1.0
O2A F:TD6601 4.4 18.9 1.0
N F:LEU443 4.5 9.1 1.0
C F:ASN469 4.6 13.4 1.0
N F:ASN470 4.6 11.4 1.0
CA F:ASP442 4.6 11.3 1.0
CA F:ASN469 4.6 13.0 1.0
CA F:GLY441 4.6 11.5 1.0
CG F:GLN473 4.6 11.7 1.0
C F:GLY472 4.7 12.8 1.0
C F:GLY441 4.7 12.5 1.0
C F:ASN470 5.0 13.2 1.0
CB F:GLN473 5.0 13.4 1.0

Manganese binding site 7 out of 8 in 5eja

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Manganese binding site 7 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn602

b:23.1
occ:1.00
 O G:GLY471 2.0 11.5 1.0
OD1 G:ASP442 2.1 11.7 1.0
O1A G:TD6601 2.1 21.2 1.0
O1B G:TD6601 2.1 21.3 1.0
OD1 G:ASN469 2.1 11.8 1.0
O G:HOH847 2.2 19.2 1.0
CG G:ASN469 3.1 20.3 1.0
CG G:ASP442 3.1 11.8 1.0
C G:GLY471 3.2 16.7 1.0
PA G:TD6601 3.3 21.0 1.0
PB G:TD6601 3.3 21.1 1.0
O3A G:TD6601 3.4 21.0 1.0
ND2 G:ASN469 3.5 15.8 1.0
OD2 G:ASP442 3.6 11.8 1.0
N G:ASP442 3.8 11.4 1.0
N G:GLY471 4.0 12.4 1.0
N G:GLY472 4.1 11.4 1.0
O7 G:TD6601 4.1 20.9 1.0
CA G:GLY472 4.1 11.2 1.0
N G:GLN473 4.2 12.1 1.0
CA G:GLY471 4.2 16.2 1.0
N G:ASN469 4.3 12.5 1.0
O2B G:TD6601 4.3 21.1 1.0
O G:HOH806 4.3 21.3 1.0
O3B G:TD6601 4.3 21.0 1.0
CB G:ASP442 4.3 11.7 1.0
O2A G:TD6601 4.4 20.9 1.0
O G:VAL467 4.4 12.1 1.0
CB G:ASN469 4.4 13.7 1.0
N G:LEU443 4.5 11.2 1.0
C G:ASN469 4.6 18.0 1.0
CA G:ASP442 4.6 11.5 1.0
CA G:GLY441 4.6 11.2 1.0
N G:ASN470 4.6 13.0 1.0
CA G:ASN469 4.6 12.7 1.0
C G:GLY441 4.7 14.6 1.0
CG G:GLN473 4.7 11.9 1.0
C G:GLY472 4.7 13.0 1.0
C G:ASN470 5.0 12.4 1.0

Manganese binding site 8 out of 8 in 5eja

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Manganese binding site 8 out of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 2 Min and Soaked with Isochorismate For 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn602

b:24.6
occ:1.00
 OD1 H:ASN469 2.0 13.3 1.0
OD1 H:ASP442 2.1 12.8 1.0
O1A H:TD6601 2.1 22.1 1.0
O H:GLY471 2.1 12.3 1.0
O1B H:TD6601 2.1 22.4 1.0
O H:HOH834 2.2 22.1 1.0
CG H:ASN469 3.1 19.2 1.0
CG H:ASP442 3.1 12.3 1.0
C H:GLY471 3.3 13.7 1.0
PA H:TD6601 3.3 22.0 1.0
PB H:TD6601 3.3 22.3 1.0
O3A H:TD6601 3.4 22.1 1.0
ND2 H:ASN469 3.5 19.7 1.0
OD2 H:ASP442 3.6 13.9 1.0
N H:ASP442 3.8 12.2 1.0
N H:GLY471 4.0 12.4 1.0
N H:GLY472 4.2 12.0 1.0
N H:GLN473 4.2 12.7 1.0
O7 H:TD6601 4.2 21.8 1.0
CA H:GLY472 4.2 11.9 1.0
N H:ASN469 4.2 13.4 1.0
CA H:GLY471 4.3 14.4 1.0
O2B H:TD6601 4.3 22.4 1.0
O H:HOH798 4.3 22.2 1.0
O3B H:TD6601 4.3 22.2 1.0
O H:VAL467 4.3 13.0 1.0
O2A H:TD6601 4.3 21.9 1.0
CB H:ASP442 4.4 12.3 1.0
CB H:ASN469 4.4 16.4 1.0
N H:LEU443 4.5 11.8 1.0
C H:ASN469 4.6 17.2 1.0
N H:ASN470 4.6 12.8 1.0
CA H:GLY441 4.6 14.6 1.0
CA H:ASP442 4.6 12.2 1.0
CA H:ASN469 4.6 16.9 1.0
C H:GLY441 4.7 14.9 1.0
CG H:GLN473 4.7 14.7 1.0
C H:GLY472 4.8 14.4 1.0
O H:ASN469 5.0 17.1 1.0
C H:ASN470 5.0 19.4 1.0

Reference:

H.G.Song, C.Dong, M.M.Qin, Y.Z.Chen, Y.R.Sun, J.J.Liu, W.Chan, Z.H.Guo. A Thiamine-Dependent Enzyme Utilizes An Active Tetrahedral Intermediate in Vitamin K Biosynthesis J.Am.Chem.Soc. V. 138 7244 2016.
ISSN: ESSN 1520-5126
PubMed: 27213829
DOI: 10.1021/JACS.6B03437
Page generated: Sun Oct 6 00:04:40 2024

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