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Manganese in PDB 5ej8: Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min

Enzymatic activity of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min

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

Protein crystallography data

The structure of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min, PDB code: 5ej8 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) 27.65 / 1.34
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.660, 90.760, 169.340, 83.25, 76.03, 64.32
R / Rfree (%) 13.3 / 16.4

Other elements in 5ej8:

The structure of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min also contains other interesting chemical elements:

Magnesium (Mg) 15 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min (pdb code 5ej8). 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 Structure Soaked with 2-Ketoglutarate For 2 Min, PDB code: 5ej8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5ej8

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Manganese binding site 1 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:11.1
occ:0.55
MG A:MG603 0.3 6.7 0.5
O A:GLY471 2.0 11.7 1.0
O3B A:TD6601 2.1 9.1 1.0
OD1 A:ASN469 2.1 9.2 1.0
O1A A:TD6601 2.1 9.0 1.0
OD1 A:ASP442 2.2 9.6 1.0
O A:HOH901 2.2 9.7 1.0
HD21 A:ASN469 3.1 12.1 1.0
CG A:ASN469 3.1 9.8 1.0
H A:ASP442 3.2 10.6 1.0
C A:GLY471 3.2 11.5 1.0
CG A:ASP442 3.2 9.1 1.0
H A:GLN473 3.3 11.1 1.0
PB A:TD6601 3.3 9.5 1.0
PA A:TD6601 3.3 8.8 1.0
HA2 A:GLY472 3.4 10.4 1.0
O3A A:TD6601 3.4 8.6 1.0
ND2 A:ASN469 3.4 10.1 1.0
H A:ASN469 3.5 12.1 1.0
H A:GLY471 3.5 13.5 1.0
OD2 A:ASP442 3.7 10.4 1.0
H A:LEU443 3.8 9.8 1.0
HG2 A:GLN473 3.8 12.9 1.0
N A:ASP442 4.0 8.8 1.0
N A:GLY471 4.0 11.3 1.0
N A:GLN473 4.1 9.3 1.0
N A:GLY472 4.1 8.4 1.0
CA A:GLY472 4.1 8.6 1.0
HA3 A:GLY441 4.1 12.6 1.0
O7 A:TD6601 4.1 9.3 1.0
HG A:LEU443 4.2 12.0 1.0
CA A:GLY471 4.2 11.0 1.0
O A:HOH796 4.2 12.0 1.0
O1B A:TD6601 4.3 10.5 1.0
HD22 A:ASN469 4.3 12.1 1.0
O2B A:TD6601 4.3 10.5 1.0
N A:ASN469 4.3 10.1 1.0
CB A:ASN469 4.4 11.7 1.0
O A:VAL467 4.4 10.3 1.0
CB A:ASP442 4.4 8.0 1.0
O2A A:TD6601 4.5 9.8 1.0
HB2 A:GLN473 4.5 12.7 1.0
H A:ASN470 4.5 12.5 1.0
C A:ASN469 4.6 10.4 1.0
N A:ASN470 4.6 10.4 1.0
N A:LEU443 4.6 8.1 1.0
HA2 A:GLY441 4.6 12.6 1.0
CG A:GLN473 4.6 10.7 1.0
C A:GLY472 4.6 8.8 1.0
CA A:ASN469 4.6 11.1 1.0
CA A:ASP442 4.7 8.2 1.0
HB3 A:ASP442 4.7 9.7 1.0
HA2 A:GLY471 4.7 13.2 1.0
CA A:GLY441 4.7 10.5 1.0
HA A:ASN468 4.8 12.0 1.0
HG3 A:GLN473 4.8 12.9 1.0
C A:GLY441 4.8 9.1 1.0
HA3 A:GLY472 4.9 10.4 1.0
H A:GLY472 4.9 10.1 1.0
HB2 A:ASN469 4.9 14.0 1.0
HB3 A:ASN469 4.9 14.0 1.0
HA3 A:GLY471 4.9 13.2 1.0
CB A:GLN473 4.9 10.5 1.0
C A:ASN470 5.0 10.6 1.0
O A:ASN469 5.0 10.8 1.0

Manganese binding site 2 out of 8 in 5ej8

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Manganese binding site 2 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:16.3
occ:0.64
MG B:MG604 0.0 2.0 0.4
O B:GLY471 2.0 10.9 1.0
O1A B:TD6602 2.1 11.0 1.0
OD1 B:ASN469 2.1 10.7 1.0
O1B B:TD6602 2.1 9.7 1.0
OD1 B:ASP442 2.1 10.5 1.0
O B:HOH794 2.2 10.7 1.0
CG B:ASN469 3.1 10.0 1.0
HD21 B:ASN469 3.1 12.1 1.0
H B:ASP442 3.2 12.4 1.0
CG B:ASP442 3.2 10.3 1.0
C B:GLY471 3.2 10.0 1.0
PA B:TD6602 3.3 9.5 1.0
PB B:TD6602 3.3 9.8 1.0
H B:GLN473 3.3 12.5 1.0
O3A B:TD6602 3.4 11.4 1.0
HA2 B:GLY472 3.4 12.7 1.0
ND2 B:ASN469 3.5 10.1 1.0
H B:ASN469 3.5 11.8 1.0
H B:GLY471 3.5 12.3 1.0
OD2 B:ASP442 3.6 10.8 1.0
H B:LEU443 3.7 10.7 1.0
N B:ASP442 3.9 10.3 1.0
HG2 B:GLN473 3.9 15.1 1.0
N B:GLY471 4.0 10.2 1.0
HA3 B:GLY441 4.1 12.2 1.0
N B:GLY472 4.1 10.1 1.0
HG B:LEU443 4.1 13.9 1.0
N B:GLN473 4.1 10.4 1.0
O7 B:TD6602 4.1 9.9 1.0
CA B:GLY472 4.1 10.6 1.0
CA B:GLY471 4.2 10.3 1.0
O B:HOH802 4.3 12.0 1.0
N B:ASN469 4.3 9.8 1.0
O3B B:TD6602 4.3 10.1 1.0
HD22 B:ASN469 4.3 12.1 1.0
O B:VAL467 4.3 10.9 1.0
O2B B:TD6602 4.3 10.3 1.0
CB B:ASP442 4.4 10.7 1.0
CB B:ASN469 4.4 10.4 1.0
O2A B:TD6602 4.4 12.5 1.0
H B:ASN470 4.5 13.1 1.0
N B:LEU443 4.5 8.9 1.0
C B:ASN469 4.6 11.1 1.0
HB2 B:GLN473 4.6 13.4 1.0
HA2 B:GLY441 4.6 12.2 1.0
N B:ASN470 4.6 10.9 1.0
CA B:ASN469 4.6 10.8 1.0
CA B:ASP442 4.6 10.8 1.0
HB3 B:ASP442 4.6 12.8 1.0
CA B:GLY441 4.7 10.2 1.0
C B:GLY472 4.7 10.6 1.0
HA2 B:GLY471 4.7 12.4 1.0
HA B:ASN468 4.7 13.0 1.0
C B:GLY441 4.7 8.8 1.0
CG B:GLN473 4.7 12.6 1.0
HB3 B:ASN469 4.9 12.5 1.0
HG3 B:GLN473 4.9 15.1 1.0
H B:GLY472 4.9 12.1 1.0
HA3 B:GLY472 5.0 12.7 1.0
HA3 B:GLY471 5.0 12.4 1.0
HB2 B:ASN469 5.0 12.5 1.0
C B:ASN470 5.0 10.8 1.0

Manganese binding site 3 out of 8 in 5ej8

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Manganese binding site 3 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn603

b:15.7
occ:0.41
MG C:MG604 0.1 5.2 0.6
O1A C:TD6602 2.0 10.3 1.0
O1B C:TD6602 2.1 10.8 1.0
OD1 C:ASP442 2.1 11.2 1.0
O C:HOH859 2.1 11.8 1.0
O C:GLY471 2.1 11.6 1.0
OD1 C:ASN469 2.1 11.8 1.0
H C:ASP442 3.0 12.5 1.0
CG C:ASN469 3.1 11.9 1.0
HD21 C:ASN469 3.1 14.7 1.0
CG C:ASP442 3.1 11.3 1.0
PA C:TD6602 3.3 9.6 1.0
PB C:TD6602 3.3 10.5 1.0
C C:GLY471 3.3 11.8 1.0
O3A C:TD6602 3.4 10.3 1.0
H C:GLN473 3.4 12.5 1.0
H C:ASN469 3.5 15.3 1.0
HA2 C:GLY472 3.5 13.9 1.0
ND2 C:ASN469 3.5 12.2 1.0
H C:GLY471 3.6 13.4 1.0
OD2 C:ASP442 3.6 12.2 1.0
H C:LEU443 3.7 11.7 1.0
N C:ASP442 3.8 10.4 1.0
HG2 C:GLN473 3.9 16.4 1.0
HA3 C:GLY441 4.0 12.3 1.0
N C:GLY471 4.1 11.2 1.0
O7 C:TD6602 4.1 10.4 1.0
HG C:LEU443 4.1 13.8 1.0
N C:GLN473 4.2 10.4 1.0
N C:GLY472 4.2 11.2 1.0
CA C:GLY472 4.2 11.6 1.0
O C:HOH800 4.2 13.9 1.0
N C:ASN469 4.3 12.7 1.0
CA C:GLY471 4.3 10.9 1.0
O C:VAL467 4.3 12.0 1.0
O3B C:TD6602 4.3 11.0 1.0
CB C:ASP442 4.3 10.9 1.0
HD22 C:ASN469 4.3 14.7 1.0
O2B C:TD6602 4.3 11.4 1.0
O2A C:TD6602 4.4 10.1 1.0
CB C:ASN469 4.4 12.5 1.0
HA2 C:GLY441 4.5 12.3 1.0
N C:LEU443 4.5 9.7 1.0
H C:ASN470 4.5 14.1 1.0
CA C:ASP442 4.5 10.7 1.0
CA C:GLY441 4.5 10.3 1.0
HB2 C:GLN473 4.6 13.6 1.0
HB3 C:ASP442 4.6 13.1 1.0
C C:ASN469 4.6 11.9 1.0
C C:GLY441 4.6 9.8 1.0
N C:ASN470 4.6 11.8 1.0
CA C:ASN469 4.7 13.2 1.0
HA C:ASN468 4.7 16.2 1.0
CG C:GLN473 4.7 13.7 1.0
HA2 C:GLY471 4.7 13.1 1.0
C C:GLY472 4.7 11.6 1.0
HG3 C:GLN473 4.9 16.4 1.0
HB3 C:ASN469 4.9 15.0 1.0
HB2 C:LEU443 5.0 12.5 1.0
HB2 C:ASN469 5.0 15.0 1.0
HA3 C:GLY472 5.0 13.9 1.0

Manganese binding site 4 out of 8 in 5ej8

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Manganese binding site 4 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn603

b:16.1
occ:0.47
MG D:MG604 0.1 7.4 0.5
O1A D:TD6602 2.1 10.9 1.0
O D:GLY471 2.1 12.0 1.0
OD1 D:ASN469 2.1 12.7 1.0
OD1 D:ASP442 2.1 13.2 1.0
O1B D:TD6602 2.1 12.4 1.0
O D:HOH870 2.2 12.3 1.0
H D:ASP442 3.1 14.2 1.0
HD21 D:ASN469 3.1 15.3 1.0
CG D:ASN469 3.1 12.8 1.0
CG D:ASP442 3.1 13.5 1.0
PA D:TD6602 3.2 11.8 1.0
C D:GLY471 3.3 12.1 1.0
PB D:TD6602 3.3 12.7 1.0
H D:GLN473 3.4 15.1 1.0
O3A D:TD6602 3.4 12.4 1.0
ND2 D:ASN469 3.5 12.8 1.0
H D:ASN469 3.5 16.7 1.0
HA2 D:GLY472 3.5 14.9 1.0
H D:GLY471 3.5 16.3 1.0
OD2 D:ASP442 3.6 14.1 1.0
H D:LEU443 3.7 14.9 1.0
N D:ASP442 3.8 11.8 1.0
HG2 D:GLN473 3.9 16.8 1.0
HA3 D:GLY441 4.0 14.8 1.0
N D:GLY471 4.0 13.6 1.0
HG D:LEU443 4.1 15.5 1.0
O7 D:TD6602 4.1 11.2 1.0
N D:GLN473 4.2 12.6 1.0
N D:GLY472 4.2 12.8 1.0
CA D:GLY472 4.2 12.4 1.0
O D:HOH825 4.2 14.9 1.0
CA D:GLY471 4.3 12.9 1.0
N D:ASN469 4.3 13.9 1.0
HD22 D:ASN469 4.3 15.3 1.0
O3B D:TD6602 4.3 13.2 1.0
O D:VAL467 4.3 13.2 1.0
O2A D:TD6602 4.3 11.1 1.0
CB D:ASP442 4.4 12.2 1.0
O2B D:TD6602 4.4 14.0 1.0
CB D:ASN469 4.4 13.8 1.0
H D:ASN470 4.5 16.1 1.0
HA2 D:GLY441 4.5 14.8 1.0
N D:LEU443 4.5 12.5 1.0
HB2 D:GLN473 4.5 16.5 1.0
C D:ASN469 4.6 12.6 1.0
CA D:ASP442 4.6 11.6 1.0
CA D:GLY441 4.6 12.4 1.0
N D:ASN470 4.6 13.4 1.0
HB3 D:ASP442 4.6 14.6 1.0
CA D:ASN469 4.7 13.7 1.0
C D:GLY441 4.7 11.9 1.0
CG D:GLN473 4.7 14.0 1.0
HA D:ASN468 4.7 16.5 1.0
HA2 D:GLY471 4.7 15.5 1.0
C D:GLY472 4.7 12.1 1.0
HG3 D:GLN473 4.8 16.8 1.0
HB3 D:ASN469 4.9 16.5 1.0
HB2 D:ASN469 5.0 16.5 1.0
H D:GLY472 5.0 15.3 1.0

Manganese binding site 5 out of 8 in 5ej8

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Manganese binding site 5 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:11.6
occ:0.47
MG E:MG603 0.2 8.8 0.5
O E:GLY471 2.0 10.9 1.0
O1A E:TD6601 2.1 8.1 1.0
OD1 E:ASN469 2.1 10.1 1.0
O1B E:TD6601 2.1 9.4 1.0
OD1 E:ASP442 2.2 10.7 1.0
O E:HOH783 2.2 9.6 1.0
HD21 E:ASN469 3.1 13.1 1.0
CG E:ASN469 3.1 9.1 1.0
H E:ASP442 3.2 10.9 1.0
CG E:ASP442 3.2 9.5 1.0
C E:GLY471 3.2 10.5 1.0
PA E:TD6601 3.3 8.8 1.0
PB E:TD6601 3.3 9.8 1.0
H E:GLN473 3.3 12.8 1.0
O3A E:TD6601 3.4 9.5 1.0
HA2 E:GLY472 3.4 11.9 1.0
ND2 E:ASN469 3.4 10.9 1.0
H E:ASN469 3.5 13.4 1.0
H E:GLY471 3.5 12.7 1.0
OD2 E:ASP442 3.6 11.8 1.0
H E:LEU443 3.7 11.9 1.0
HG2 E:GLN473 3.8 15.5 1.0
N E:ASP442 3.9 9.1 1.0
N E:GLY471 4.0 10.6 1.0
HA3 E:GLY441 4.1 12.2 1.0
N E:GLY472 4.1 9.3 1.0
CA E:GLY472 4.1 9.9 1.0
O7 E:TD6601 4.1 8.2 1.0
N E:GLN473 4.1 10.7 1.0
HG E:LEU443 4.1 11.5 1.0
CA E:GLY471 4.2 10.3 1.0
O3B E:TD6601 4.3 9.8 1.0
O E:HOH876 4.3 12.9 1.0
HD22 E:ASN469 4.3 13.1 1.0
N E:ASN469 4.3 11.2 1.0
O2B E:TD6601 4.4 11.2 1.0
O E:VAL467 4.4 10.9 1.0
CB E:ASP442 4.4 10.7 1.0
CB E:ASN469 4.4 10.3 1.0
O2A E:TD6601 4.4 9.4 1.0
HB2 E:GLN473 4.5 13.1 1.0
H E:ASN470 4.5 13.1 1.0
N E:LEU443 4.6 9.9 1.0
C E:ASN469 4.6 9.8 1.0
HA2 E:GLY441 4.6 12.2 1.0
N E:ASN470 4.6 10.9 1.0
CA E:ASN469 4.6 10.6 1.0
CA E:ASP442 4.7 9.7 1.0
HB3 E:ASP442 4.7 12.9 1.0
CA E:GLY441 4.7 10.2 1.0
HA2 E:GLY471 4.7 12.4 1.0
CG E:GLN473 4.7 12.9 1.0
C E:GLY472 4.7 9.3 1.0
HA E:ASN468 4.7 13.0 1.0
C E:GLY441 4.8 9.9 1.0
HG3 E:GLN473 4.8 15.5 1.0
HA3 E:GLY472 4.9 11.9 1.0
HB3 E:ASN469 4.9 12.4 1.0
H E:GLY472 4.9 11.2 1.0
HB2 E:ASN469 4.9 12.4 1.0
HA3 E:GLY471 4.9 12.4 1.0
C E:ASN470 5.0 11.3 1.0
CB E:GLN473 5.0 10.9 1.0
HB2 E:LEU443 5.0 10.8 1.0

Manganese binding site 6 out of 8 in 5ej8

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Manganese binding site 6 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn603

b:11.1
occ:0.51
MG F:MG604 0.1 10.4 0.5
O F:GLY471 2.1 9.6 1.0
O1A F:TD6602 2.1 10.1 1.0
OD1 F:ASP442 2.1 11.1 1.0
OD1 F:ASN469 2.1 11.4 1.0
O1B F:TD6602 2.2 9.6 1.0
O F:HOH820 2.2 24.7 1.0
CG F:ASN469 3.1 9.1 1.0
H F:ASP442 3.1 9.7 1.0
CG F:ASP442 3.1 10.3 1.0
HD21 F:ASN469 3.2 13.6 1.0
C F:GLY471 3.3 8.6 1.0
PA F:TD6602 3.3 9.2 1.0
PB F:TD6602 3.4 9.5 1.0
O3A F:TD6602 3.4 8.3 1.0
H F:GLN473 3.4 12.0 1.0
H F:ASN469 3.5 13.1 1.0
HA2 F:GLY472 3.5 11.4 1.0
ND2 F:ASN469 3.5 11.3 1.0
H F:GLY471 3.5 12.8 1.0
OD2 F:ASP442 3.6 11.1 1.0
H F:LEU443 3.7 10.9 1.0
N F:ASP442 3.9 8.0 1.0
HG2 F:GLN473 3.9 15.6 1.0
HA3 F:GLY441 4.0 10.4 1.0
N F:GLY471 4.0 10.7 1.0
HG F:LEU443 4.1 12.8 1.0
O7 F:TD6602 4.1 9.3 1.0
N F:GLY472 4.1 10.4 1.0
N F:GLN473 4.2 10.0 1.0
CA F:GLY472 4.2 9.5 1.0
O F:HOH757 4.2 11.3 1.0
CA F:GLY471 4.2 11.0 1.0
N F:ASN469 4.3 10.9 1.0
O F:VAL467 4.3 11.6 1.0
CB F:ASP442 4.3 9.4 1.0
O2B F:TD6602 4.3 10.3 1.0
HD22 F:ASN469 4.3 13.6 1.0
O3B F:TD6602 4.4 10.4 1.0
O2A F:TD6602 4.4 8.9 1.0
CB F:ASN469 4.4 10.6 1.0
H F:ASN470 4.5 11.7 1.0
N F:LEU443 4.5 9.1 1.0
HA2 F:GLY441 4.5 10.4 1.0
C F:ASN469 4.6 10.3 1.0
CA F:ASP442 4.6 9.5 1.0
N F:ASN470 4.6 9.8 1.0
HB3 F:ASP442 4.6 11.2 1.0
HB2 F:GLN473 4.6 14.7 1.0
CA F:GLY441 4.6 8.6 1.0
CA F:ASN469 4.6 9.8 1.0
HA2 F:GLY471 4.7 13.2 1.0
HA F:ASN468 4.7 11.2 1.0
C F:GLY441 4.7 8.7 1.0
C F:GLY472 4.7 10.1 1.0
CG F:GLN473 4.8 13.0 1.0
HB3 F:ASN469 4.9 12.7 1.0
H F:GLY472 5.0 12.5 1.0
HB2 F:ASN469 5.0 12.7 1.0
HA3 F:GLY472 5.0 11.4 1.0
HA3 F:GLY471 5.0 13.2 1.0
HG3 F:GLN473 5.0 15.6 1.0
HB2 F:LEU443 5.0 11.2 1.0
C F:ASN470 5.0 10.9 1.0

Manganese binding site 7 out of 8 in 5ej8

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Manganese binding site 7 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn602

b:14.7
occ:0.45
MG G:MG603 0.1 6.7 0.6
OD1 G:ASN469 2.1 11.6 1.0
O G:GLY471 2.1 10.9 1.0
OD1 G:ASP442 2.1 11.0 1.0
O1B G:TD6601 2.1 10.9 1.0
O1A G:TD6601 2.1 10.5 1.0
O G:HOH818 2.2 11.6 1.0
CG G:ASN469 3.0 12.0 1.0
HD21 G:ASN469 3.1 15.0 1.0
H G:ASP442 3.1 13.0 1.0
CG G:ASP442 3.1 10.8 1.0
C G:GLY471 3.3 10.9 1.0
PA G:TD6601 3.3 10.4 1.0
H G:GLN473 3.3 14.7 1.0
PB G:TD6601 3.3 10.9 1.0
O3A G:TD6601 3.4 10.2 1.0
ND2 G:ASN469 3.4 12.5 1.0
H G:ASN469 3.4 13.7 1.0
HA2 G:GLY472 3.5 13.3 1.0
H G:GLY471 3.6 13.7 1.0
OD2 G:ASP442 3.6 13.1 1.0
H G:LEU443 3.7 11.0 1.0
N G:ASP442 3.9 10.9 1.0
HG2 G:GLN473 3.9 19.0 1.0
HA3 G:GLY441 4.0 12.3 1.0
N G:GLY471 4.1 11.4 1.0
N G:GLN473 4.1 12.2 1.0
N G:GLY472 4.2 11.2 1.0
O7 G:TD6601 4.2 9.6 1.0
HG G:LEU443 4.2 13.7 1.0
CA G:GLY472 4.2 11.1 1.0
N G:ASN469 4.2 11.4 1.0
CA G:GLY471 4.3 12.4 1.0
O G:HOH817 4.3 13.2 1.0
HD22 G:ASN469 4.3 15.0 1.0
O3B G:TD6601 4.3 11.9 1.0
O2B G:TD6601 4.3 11.1 1.0
O G:VAL467 4.3 12.6 1.0
CB G:ASP442 4.3 9.8 1.0
CB G:ASN469 4.4 11.4 1.0
O2A G:TD6601 4.4 10.8 1.0
H G:ASN470 4.5 14.6 1.0
HA2 G:GLY441 4.5 12.3 1.0
N G:LEU443 4.5 9.2 1.0
C G:ASN469 4.6 12.1 1.0
HB2 G:GLN473 4.6 16.1 1.0
CA G:ASP442 4.6 9.3 1.0
CA G:ASN469 4.6 11.5 1.0
N G:ASN470 4.6 12.1 1.0
HB3 G:ASP442 4.6 11.8 1.0
CA G:GLY441 4.6 10.2 1.0
HA G:ASN468 4.7 14.2 1.0
CG G:GLN473 4.7 15.8 1.0
C G:GLY441 4.7 9.9 1.0
C G:GLY472 4.7 12.2 1.0
HA2 G:GLY471 4.7 14.9 1.0
HG3 G:GLN473 4.9 19.0 1.0
HB3 G:ASN469 4.9 13.7 1.0
HB2 G:ASN469 4.9 13.7 1.0
H G:GLY472 5.0 13.4 1.0
HA3 G:GLY471 5.0 14.9 1.0
C G:ASN470 5.0 12.1 1.0

Manganese binding site 8 out of 8 in 5ej8

Go back to Manganese Binding Sites List in 5ej8
Manganese binding site 8 out of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 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 Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn603

b:13.5
occ:0.52
MG H:MG604 0.2 6.8 0.5
O1A H:TD6602 2.0 10.7 1.0
O1B H:TD6602 2.1 9.4 1.0
O H:GLY471 2.1 11.7 1.0
OD1 H:ASP442 2.1 10.2 1.0
OD1 H:ASN469 2.2 11.8 1.0
O H:HOH830 2.2 10.2 1.0
H H:ASP442 3.1 12.6 1.0
HD21 H:ASN469 3.1 13.2 1.0
CG H:ASN469 3.1 11.0 1.0
CG H:ASP442 3.2 10.0 1.0
PA H:TD6602 3.2 10.3 1.0
PB H:TD6602 3.3 10.2 1.0
C H:GLY471 3.3 11.6 1.0
O3A H:TD6602 3.3 9.4 1.0
H H:GLN473 3.3 12.8 1.0
HA2 H:GLY472 3.4 14.0 1.0
ND2 H:ASN469 3.5 11.0 1.0
H H:ASN469 3.5 14.1 1.0
H H:GLY471 3.6 14.2 1.0
OD2 H:ASP442 3.6 11.6 1.0
H H:LEU443 3.7 11.9 1.0
N H:ASP442 3.8 10.5 1.0
HG2 H:GLN473 4.0 16.1 1.0
HA3 H:GLY441 4.0 11.9 1.0
O7 H:TD6602 4.1 9.6 1.0
N H:GLY471 4.1 11.8 1.0
HG H:LEU443 4.1 13.9 1.0
N H:GLN473 4.1 10.7 1.0
CA H:GLY472 4.2 11.6 1.0
N H:GLY472 4.2 10.8 1.0
O3B H:TD6602 4.3 10.5 1.0
O H:HOH802 4.3 13.3 1.0
CA H:GLY471 4.3 11.1 1.0
O2B H:TD6602 4.3 10.8 1.0
N H:ASN469 4.3 11.8 1.0
O H:VAL467 4.3 10.7 1.0
HD22 H:ASN469 4.4 13.2 1.0
CB H:ASP442 4.4 10.7 1.0
O2A H:TD6602 4.4 9.6 1.0
N H:LEU443 4.5 9.9 1.0
CB H:ASN469 4.5 10.7 1.0
HA2 H:GLY441 4.5 11.9 1.0
H H:ASN470 4.5 14.3 1.0
HB2 H:GLN473 4.6 15.3 1.0
CA H:GLY441 4.6 9.9 1.0
CA H:ASP442 4.6 10.9 1.0
HB3 H:ASP442 4.6 12.9 1.0
C H:GLY441 4.7 9.4 1.0
N H:ASN470 4.7 11.9 1.0
C H:ASN469 4.7 10.8 1.0
C H:GLY472 4.7 11.2 1.0
CA H:ASN469 4.7 12.7 1.0
HA H:ASN468 4.7 13.5 1.0
HA2 H:GLY471 4.7 13.3 1.0
CG H:GLN473 4.8 13.4 1.0
HA3 H:GLY472 4.9 14.0 1.0
HB2 H:LEU443 4.9 13.3 1.0
HG3 H:GLN473 5.0 16.1 1.0
H H:GLY472 5.0 13.0 1.0
HB3 H:ASN469 5.0 12.8 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: Tue Dec 15 04:38:21 2020

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