Magnesium in PDB 5z2r: Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min

Enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min

All present enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min:
2.2.1.9;

Protein crystallography data

The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r was solved by M.M.Qin, Z.H.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.630, 90.750, 172.370, 82.91, 75.71, 64.20
R / Rfree (%) 17 / 20.1

Other elements in 5z2r:

The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min (pdb code 5z2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5z2r

Go back to Magnesium Binding Sites List in 5z2r
Magnesium binding site 1 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:7.1
occ:1.00
O A:HOH747 1.9 35.8 1.0
O A:GLY471 2.0 25.9 1.0
O3B A:TD6601 2.0 13.1 1.0
O2A A:TD6601 2.0 18.7 1.0
OD1 A:ASP442 2.1 25.1 1.0
OD1 A:ASN469 2.1 22.1 1.0
CG A:ASN469 3.0 22.0 1.0
CG A:ASP442 3.1 23.3 1.0
C A:GLY471 3.2 23.6 1.0
PA A:TD6601 3.2 17.4 1.0
PB A:TD6601 3.2 15.0 1.0
O3A A:TD6601 3.4 13.4 1.0
ND2 A:ASN469 3.4 21.9 1.0
OD2 A:ASP442 3.6 23.5 1.0
N A:ASP442 3.9 19.6 1.0
N A:GLY471 4.0 24.0 1.0
N A:GLY472 4.0 22.8 1.0
N A:GLN473 4.1 21.7 1.0
CA A:GLY472 4.1 22.1 1.0
CA A:GLY471 4.1 23.2 1.0
O7 A:TD6601 4.2 18.8 1.0
O1B A:TD6601 4.2 14.9 1.0
O A:HOH717 4.2 15.2 1.0
O2B A:TD6601 4.3 13.1 1.0
O1A A:TD6601 4.3 12.1 1.0
N A:ASN469 4.3 22.3 1.0
CB A:ASP442 4.3 21.9 1.0
CB A:ASN469 4.4 22.3 1.0
O A:VAL467 4.4 20.2 1.0
N A:LEU443 4.5 19.3 1.0
CA A:ASP442 4.6 21.0 1.0
C A:ASN469 4.6 22.9 1.0
C A:GLY472 4.7 21.8 1.0
CA A:ASN469 4.7 22.6 1.0
CA A:GLY441 4.7 18.6 1.0
CG A:GLN473 4.7 23.9 1.0
N A:ASN470 4.7 23.0 1.0
C A:GLY441 4.7 18.9 1.0
C A:ASN470 5.0 24.0 1.0
CB A:GLN473 5.0 23.4 1.0
O A:ASN469 5.0 23.2 1.0

Magnesium binding site 2 out of 7 in 5z2r

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Magnesium binding site 2 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:1.6
occ:1.00
O B:HOH724 1.8 15.7 1.0
O B:GLY471 2.0 18.8 1.0
OD1 B:ASP442 2.0 19.5 1.0
O2A B:TD6601 2.0 20.2 1.0
OD1 B:ASN469 2.1 20.8 1.0
O3B B:TD6601 2.1 21.0 1.0
CG B:ASP442 3.1 20.2 1.0
CG B:ASN469 3.1 21.4 1.0
C B:GLY471 3.2 20.3 1.0
PA B:TD6601 3.2 18.9 1.0
PB B:TD6601 3.3 20.5 1.0
O3A B:TD6601 3.3 18.4 1.0
ND2 B:ASN469 3.6 20.4 1.0
OD2 B:ASP442 3.6 13.8 1.0
N B:ASP442 3.9 20.6 1.0
N B:GLY471 4.0 24.0 1.0
N B:GLY472 4.1 20.9 1.0
CA B:GLY471 4.1 21.4 1.0
CA B:GLY472 4.1 20.8 1.0
O7 B:TD6601 4.2 20.7 1.0
N B:GLN473 4.2 23.0 1.0
O1B B:TD6601 4.3 20.5 1.0
O2B B:TD6601 4.3 18.3 1.0
O1A B:TD6601 4.3 16.8 1.0
N B:ASN469 4.3 23.7 1.0
CB B:ASP442 4.4 18.2 1.0
O B:VAL467 4.4 23.0 1.0
O B:HOH824 4.5 25.4 1.0
CB B:ASN469 4.5 22.4 1.0
N B:LEU443 4.5 16.9 1.0
CA B:GLY441 4.6 18.0 1.0
CA B:ASP442 4.7 18.1 1.0
C B:ASN469 4.7 25.8 1.0
N B:ASN470 4.7 25.4 1.0
CA B:ASN469 4.7 24.0 1.0
C B:GLY441 4.7 20.4 1.0
C B:GLY472 4.8 22.0 1.0
CG B:GLN473 4.8 24.7 1.0
C B:ASN470 4.9 26.9 1.0
CG B:LEU443 5.0 18.7 1.0

Magnesium binding site 3 out of 7 in 5z2r

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Magnesium binding site 3 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:1.0
occ:1.00
O C:GLY471 1.9 17.9 1.0
OD1 C:ASP442 2.0 17.4 1.0
OD1 C:ASN469 2.1 19.1 1.0
O2A C:TD6601 2.1 17.4 1.0
O3B C:TD6601 2.1 17.1 1.0
O C:HOH2955 2.5 28.1 1.0
CG C:ASP442 3.0 16.1 1.0
C C:GLY471 3.1 17.0 1.0
CG C:ASN469 3.2 20.2 1.0
PA C:TD6601 3.2 17.1 1.0
PB C:TD6601 3.2 16.7 1.0
O3A C:TD6601 3.3 16.9 1.0
OD2 C:ASP442 3.5 16.3 1.0
ND2 C:ASN469 3.6 20.5 1.0
N C:ASP442 3.9 14.1 1.0
N C:GLY472 3.9 17.2 1.0
CA C:GLY472 4.0 17.4 1.0
N C:GLY471 4.0 18.7 1.0
N C:GLN473 4.0 20.8 1.0
O7 C:TD6601 4.1 20.5 1.0
CA C:GLY471 4.1 16.9 1.0
O2B C:TD6601 4.2 15.6 1.0
O C:HOH2811 4.2 21.0 1.0
CB C:ASP442 4.3 15.6 1.0
O1B C:TD6601 4.3 12.6 1.0
N C:ASN469 4.3 18.5 1.0
O1A C:TD6601 4.4 14.3 1.0
O C:VAL467 4.4 15.3 1.0
CB C:ASN469 4.5 19.4 1.0
N C:LEU443 4.5 14.0 1.0
C C:GLY472 4.6 19.3 1.0
CA C:ASP442 4.6 14.0 1.0
C C:ASN469 4.7 17.6 1.0
CA C:GLY441 4.7 12.4 1.0
CG C:GLN473 4.7 22.7 1.0
CA C:ASN469 4.7 18.6 1.0
C C:GLY441 4.7 12.6 1.0
N C:ASN470 4.8 18.2 1.0
CG C:LEU443 5.0 13.6 1.0
C C:ASN470 5.0 20.2 1.0
CB C:GLN473 5.0 22.4 1.0

Magnesium binding site 4 out of 7 in 5z2r

Go back to Magnesium Binding Sites List in 5z2r
Magnesium binding site 4 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:1.0
occ:1.00
OD1 D:ASN469 2.0 17.9 1.0
OD1 D:ASP442 2.0 18.7 1.0
O D:GLY471 2.0 20.1 1.0
O2A D:TD6601 2.1 17.4 1.0
O3B D:TD6601 2.1 18.5 1.0
O D:HOH750 2.5 13.6 1.0
CG D:ASN469 3.0 16.8 1.0
CG D:ASP442 3.1 15.3 1.0
C D:GLY471 3.2 18.2 1.0
PA D:TD6601 3.2 17.8 1.0
PB D:TD6601 3.3 18.7 1.0
ND2 D:ASN469 3.4 16.4 1.0
O3A D:TD6601 3.4 17.4 1.0
OD2 D:ASP442 3.6 13.6 1.0
N D:ASP442 3.9 14.8 1.0
N D:GLY471 4.0 17.9 1.0
O D:HOH859 4.0 35.3 1.0
N D:GLY472 4.1 18.4 1.0
N D:GLN473 4.1 21.2 1.0
CA D:GLY472 4.1 18.1 1.0
CA D:GLY471 4.2 17.7 1.0
O7 D:TD6601 4.2 20.4 1.0
O2B D:TD6601 4.2 17.0 1.0
N D:ASN469 4.2 19.0 1.0
CB D:ASN469 4.3 17.4 1.0
CB D:ASP442 4.3 15.0 1.0
O D:VAL467 4.4 19.1 1.0
O1A D:TD6601 4.4 14.1 1.0
O1B D:TD6601 4.4 17.8 1.0
N D:LEU443 4.5 16.3 1.0
C D:ASN469 4.6 19.4 1.0
CA D:ASN469 4.6 18.4 1.0
N D:ASN470 4.6 19.1 1.0
CG D:GLN473 4.7 22.6 1.0
CA D:ASP442 4.7 15.1 1.0
CA D:GLY441 4.7 14.9 1.0
C D:GLY472 4.7 19.1 1.0
C D:GLY441 4.8 15.3 1.0
CG D:LEU443 4.8 19.5 1.0
C D:ASN470 5.0 19.3 1.0

Magnesium binding site 5 out of 7 in 5z2r

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Magnesium binding site 5 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:1.0
occ:1.00
O E:GLY471 1.9 18.6 1.0
O13 E:TDP607 2.0 13.9 1.0
OD1 E:ASP442 2.0 15.4 1.0
O22 E:TDP607 2.0 16.9 1.0
O E:HOH732 2.0 14.4 1.0
OD1 E:ASN469 2.1 18.2 1.0
CG E:ASP442 3.1 15.7 1.0
CG E:ASN469 3.1 17.8 1.0
C E:GLY471 3.1 18.6 1.0
P1 E:TDP607 3.3 14.9 1.0
P2 E:TDP607 3.3 16.6 1.0
ND2 E:ASN469 3.5 16.3 1.0
O11 E:TDP607 3.6 15.2 1.0
OD2 E:ASP442 3.6 17.5 1.0
N E:ASP442 3.9 12.6 1.0
N E:GLY471 3.9 19.1 1.0
N E:GLY472 4.0 18.4 1.0
O E:HOH757 4.0 13.6 1.0
CA E:GLY472 4.1 19.2 1.0
CA E:GLY471 4.1 18.9 1.0
N E:GLN473 4.1 21.2 1.0
O5G E:TDP607 4.1 16.9 1.0
O21 E:TDP607 4.2 16.5 1.0
N E:ASN469 4.2 16.9 1.0
CB E:ASP442 4.3 13.3 1.0
O23 E:TDP607 4.3 15.2 1.0
O E:VAL467 4.3 16.1 1.0
O12 E:TDP607 4.4 12.9 1.0
CB E:ASN469 4.4 18.2 1.0
N E:LEU443 4.5 10.3 1.0
C E:ASN469 4.6 17.3 1.0
CA E:ASP442 4.6 12.3 1.0
N E:ASN470 4.6 17.6 1.0
CA E:ASN469 4.7 17.1 1.0
C E:GLY472 4.7 20.1 1.0
CG E:GLN473 4.7 20.5 1.0
CA E:GLY441 4.7 12.6 1.0
C E:GLY441 4.7 12.5 1.0
C E:ASN470 4.9 19.4 1.0
CG E:LEU443 4.9 9.1 1.0

Magnesium binding site 6 out of 7 in 5z2r

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Magnesium binding site 6 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:1.0
occ:1.00
OD1 F:ASP442 1.9 15.7 1.0
O3B F:TD6601 2.0 18.1 1.0
O F:GLY471 2.1 18.2 1.0
OD1 F:ASN469 2.1 13.5 1.0
O F:HOH727 2.1 18.4 1.0
O2A F:TD6601 2.1 20.4 1.0
CG F:ASP442 3.0 15.3 1.0
CG F:ASN469 3.1 13.0 1.0
PA F:TD6601 3.2 20.2 1.0
C F:GLY471 3.2 19.2 1.0
PB F:TD6601 3.3 18.2 1.0
O3A F:TD6601 3.4 18.4 1.0
ND2 F:ASN469 3.4 11.8 1.0
OD2 F:ASP442 3.5 14.1 1.0
N F:ASP442 3.9 16.8 1.0
N F:GLY471 4.0 18.9 1.0
N F:GLY472 4.1 19.9 1.0
O7 F:TD6601 4.2 22.9 1.0
N F:GLN473 4.2 20.0 1.0
CA F:GLY472 4.2 18.5 1.0
CA F:GLY471 4.2 18.9 1.0
O1B F:TD6601 4.3 19.4 1.0
N F:ASN469 4.3 17.6 1.0
CB F:ASP442 4.3 14.9 1.0
O2B F:TD6601 4.3 16.2 1.0
CB F:ASN469 4.4 15.7 1.0
O F:VAL467 4.4 18.8 1.0
O1A F:TD6601 4.4 19.1 1.0
O F:HOH845 4.5 14.1 1.0
N F:LEU443 4.6 13.4 1.0
C F:ASN469 4.6 16.6 1.0
CA F:ASP442 4.6 15.3 1.0
CA F:ASN469 4.6 16.8 1.0
N F:ASN470 4.7 18.1 1.0
CG F:GLN473 4.7 20.8 1.0
CA F:GLY441 4.7 16.3 1.0
C F:GLY472 4.7 18.6 1.0
C F:GLY441 4.7 16.3 1.0
O F:ASN469 5.0 16.6 1.0
C F:ASN470 5.0 19.1 1.0

Magnesium binding site 7 out of 7 in 5z2r

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Magnesium binding site 7 out of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg602

b:1.4
occ:1.00
OD1 H:ASP442 2.0 17.8 1.0
O H:GLY471 2.0 21.7 1.0
O2A H:TD6601 2.0 24.4 1.0
OD1 H:ASN469 2.0 24.9 1.0
O3B H:TD6601 2.2 24.2 1.0
O H:HOH848 2.6 28.4 1.0
CG H:ASN469 3.1 25.2 1.0
CG H:ASP442 3.1 18.8 1.0
C H:GLY471 3.2 22.6 1.0
PA H:TD6601 3.2 24.3 1.0
PB H:TD6601 3.3 23.1 1.0
O3A H:TD6601 3.3 23.8 1.0
ND2 H:ASN469 3.5 24.5 1.0
OD2 H:ASP442 3.6 19.1 1.0
N H:ASP442 3.8 19.6 1.0
N H:GLY471 4.0 25.0 1.0
N H:GLY472 4.1 23.3 1.0
CA H:GLY471 4.2 23.1 1.0
O7 H:TD6601 4.2 27.6 1.0
CA H:GLY472 4.2 24.0 1.0
N H:GLN473 4.2 26.1 1.0
O2B H:TD6601 4.2 20.0 1.0
N H:ASN469 4.3 24.4 1.0
O H:HOH803 4.3 29.7 1.0
CB H:ASP442 4.3 18.6 1.0
O1B H:TD6601 4.3 24.4 1.0
O1A H:TD6601 4.3 23.2 1.0
O H:VAL467 4.4 22.6 1.0
CB H:ASN469 4.4 25.2 1.0
N H:LEU443 4.5 16.9 1.0
CA H:ASP442 4.6 19.1 1.0
CA H:GLY441 4.6 17.6 1.0
C H:ASN469 4.7 26.2 1.0
CG H:GLN473 4.7 30.1 1.0
C H:GLY441 4.7 18.6 1.0
CA H:ASN469 4.7 25.2 1.0
N H:ASN470 4.7 26.6 1.0
C H:GLY472 4.8 24.7 1.0
C H:ASN470 5.0 26.9 1.0
CG H:LEU443 5.0 19.8 1.0

Reference:

M.M.Qin, H.G.Song, X.Dai, Y.Z.Chen, Z.H.Guo. Two Active Site Arginines Are Critical Determinants of Substrate Binding and Catalysis in Mend: A Thiamine-Dependent Enzyme in Menaquinone Biosynthesis. Biochem. J. V. 475 3651 2018.
ISSN: ESSN 1470-8728
PubMed: 30341164
DOI: 10.1042/BCJ20180548
Page generated: Mon Dec 14 22:16:00 2020

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