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Magnesium in PDB 3hwx: Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp

Enzymatic activity of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp

All present enzymatic activity of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp:
2.2.1.9;

Protein crystallography data

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp, PDB code: 3hwx was solved by A.Priyadarshi, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.353, 90.463, 169.170, 75.99, 83.00, 64.15
R / Rfree (%) 19.7 / 25.3

Other elements in 3hwx:

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp also contains other interesting chemical elements:

Sodium (Na) 15 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp (pdb code 3hwx). 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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp, PDB code: 3hwx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3hwx

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Magnesium binding site 1 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:2.0
occ:1.00
O2A A:TPP601 1.8 3.0 1.0
O A:GLY471 1.9 11.1 1.0
OD1 A:ASN469 2.1 14.2 1.0
O3B A:TPP601 2.2 7.4 1.0
O A:HOH702 2.3 6.1 1.0
OD1 A:ASP442 2.6 16.1 1.0
C A:GLY471 3.0 11.1 1.0
PA A:TPP601 3.2 2.0 1.0
CG A:ASN469 3.2 11.2 1.0
CG A:ASP442 3.3 12.4 1.0
PB A:TPP601 3.4 11.0 1.0
OD2 A:ASP442 3.5 16.7 1.0
O3A A:TPP601 3.7 4.3 1.0
ND2 A:ASN469 3.7 10.2 1.0
N A:ASP442 3.9 8.7 1.0
N A:GLY472 3.9 10.9 1.0
N A:GLY471 3.9 11.0 1.0
O7 A:TPP601 4.0 2.7 1.0
CA A:GLY472 4.0 10.7 1.0
CA A:GLY471 4.0 10.8 1.0
N A:GLN473 4.1 10.9 1.0
O2B A:TPP601 4.2 12.2 1.0
O1A A:TPP601 4.3 2.0 1.0
N A:ASN469 4.4 9.2 1.0
O A:HOH771 4.4 2.0 1.0
CB A:ASP442 4.5 9.6 1.0
N A:LEU443 4.5 6.8 1.0
CB A:ASN469 4.5 9.4 1.0
O A:VAL467 4.6 8.8 1.0
CA A:ASP442 4.6 8.8 1.0
C A:ASN469 4.6 9.3 1.0
O1B A:TPP601 4.6 6.4 1.0
N A:ASN470 4.6 9.4 1.0
C A:GLY472 4.6 10.8 1.0
CA A:GLY441 4.6 8.3 1.0
CG A:GLN473 4.6 11.9 1.0
C A:GLY441 4.7 8.8 1.0
CA A:ASN469 4.7 9.1 1.0
C A:ASN470 4.8 10.4 1.0
O A:ASN469 4.9 9.2 1.0
CB A:GLN473 5.0 11.1 1.0

Magnesium binding site 2 out of 8 in 3hwx

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Magnesium binding site 2 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:2.0
occ:1.00
OD1 B:ASP442 1.9 8.3 1.0
O B:GLY471 1.9 11.9 1.0
O1B B:TPP601 1.9 9.3 1.0
OD1 B:ASN469 2.0 7.9 1.0
O1A B:TPP601 2.1 7.9 1.0
CG B:ASN469 2.9 7.1 1.0
CG B:ASP442 3.1 8.2 1.0
PB B:TPP601 3.2 8.1 1.0
C B:GLY471 3.2 11.1 1.0
PA B:TPP601 3.2 8.6 1.0
ND2 B:ASN469 3.3 2.0 1.0
O3A B:TPP601 3.3 5.7 1.0
OD2 B:ASP442 3.6 8.2 1.0
N B:ASP442 4.0 6.8 1.0
O3B B:TPP601 4.0 6.1 1.0
O7 B:TPP601 4.1 5.3 1.0
N B:GLN473 4.1 9.3 1.0
N B:GLY472 4.1 10.3 1.0
N B:GLY471 4.1 10.8 1.0
O B:VAL467 4.2 8.9 1.0
CA B:GLY471 4.2 10.4 1.0
CA B:GLY472 4.2 9.8 1.0
N B:ASN469 4.3 8.3 1.0
CB B:ASP442 4.3 6.8 1.0
CB B:ASN469 4.3 8.0 1.0
O2A B:TPP601 4.4 6.5 1.0
O2B B:TPP601 4.4 8.2 1.0
N B:LEU443 4.6 6.7 1.0
CA B:ASP442 4.6 6.9 1.0
C B:GLY441 4.6 6.2 1.0
CA B:GLY441 4.7 6.0 1.0
CA B:ASN469 4.7 8.1 1.0
CG B:GLN473 4.7 7.4 1.0
C B:ASN469 4.7 8.6 1.0
C B:GLY472 4.7 9.5 1.0
O B:ASN469 4.9 8.6 1.0
CB B:GLN473 4.9 9.4 1.0

Magnesium binding site 3 out of 8 in 3hwx

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Magnesium binding site 3 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg602

b:2.0
occ:1.00
OD1 I:ASN469 1.8 5.8 1.0
O2A I:TPP601 1.9 6.4 1.0
O I:GLY471 2.0 10.8 1.0
O3B I:TPP601 2.3 8.4 1.0
OD1 I:ASP442 2.5 14.4 1.0
CG I:ASN469 2.9 9.9 1.0
PB I:TPP601 3.2 6.0 1.0
CG I:ASP442 3.2 9.4 1.0
PA I:TPP601 3.2 4.2 1.0
C I:GLY471 3.3 10.6 1.0
ND2 I:ASN469 3.4 8.6 1.0
OD2 I:ASP442 3.4 10.5 1.0
O3A I:TPP601 3.5 2.9 1.0
N I:ASP442 3.9 8.9 1.0
O1B I:TPP601 4.1 5.0 1.0
N I:ASN469 4.1 14.5 1.0
CA I:GLY472 4.1 10.0 1.0
N I:GLY472 4.2 9.8 1.0
N I:GLN473 4.2 10.7 1.0
N I:GLY471 4.2 10.8 1.0
O7 I:TPP601 4.2 8.2 1.0
CB I:ASN469 4.2 13.3 1.0
CA I:GLY471 4.3 10.8 1.0
O2B I:TPP601 4.3 10.3 1.0
O1A I:TPP601 4.3 4.5 1.0
CB I:ASP442 4.5 7.8 1.0
O I:VAL467 4.5 14.4 1.0
N I:ASN470 4.5 12.8 1.0
CA I:ASN469 4.5 13.2 1.0
C I:ASN469 4.6 13.1 1.0
CA I:ASP442 4.7 8.4 1.0
CA I:GLY441 4.7 9.4 1.0
C I:GLY472 4.7 10.1 1.0
N I:LEU443 4.7 7.2 1.0
C I:GLY441 4.7 9.2 1.0
CG I:GLN473 4.9 12.3 1.0
C I:ASN470 5.0 11.6 1.0

Magnesium binding site 4 out of 8 in 3hwx

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Magnesium binding site 4 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg602

b:2.0
occ:1.00
OD1 J:ASN469 1.8 22.0 1.0
O1B J:TPP601 1.9 14.8 1.0
O J:GLY471 2.0 15.1 1.0
OD1 J:ASP442 2.2 6.2 1.0
O1A J:TPP601 2.4 24.1 1.0
CG J:ASN469 2.9 18.1 1.0
C J:GLY471 3.1 15.0 1.0
CG J:ASP442 3.2 10.3 1.0
PB J:TPP601 3.2 16.8 1.0
ND2 J:ASN469 3.4 19.7 1.0
O J:HOH723 3.5 2.0 1.0
PA J:TPP601 3.6 19.6 1.0
O3A J:TPP601 3.6 18.4 1.0
OD2 J:ASP442 3.7 9.1 1.0
N J:GLY471 4.0 16.8 1.0
N J:GLN473 4.0 14.6 1.0
N J:GLY472 4.0 14.0 1.0
N J:ASP442 4.0 10.7 1.0
CA J:GLY472 4.1 14.3 1.0
CA J:GLY471 4.1 15.5 1.0
O2B J:TPP601 4.1 16.7 1.0
N J:ASN469 4.2 16.5 1.0
CB J:ASN469 4.2 16.9 1.0
O3B J:TPP601 4.3 16.7 1.0
O7 J:TPP601 4.4 18.2 1.0
C J:ASN469 4.4 17.2 1.0
CA J:ASN469 4.5 17.0 1.0
CB J:ASP442 4.5 10.2 1.0
CG J:GLN473 4.6 12.8 1.0
C J:GLY472 4.6 14.3 1.0
O J:VAL467 4.6 16.5 1.0
O J:ASN469 4.6 17.5 1.0
N J:LEU443 4.7 9.5 1.0
O2A J:TPP601 4.7 19.5 1.0
N J:ASN470 4.8 17.1 1.0
CA J:ASP442 4.8 10.2 1.0
CA J:GLY441 4.8 11.1 1.0
CB J:GLN473 4.8 14.0 1.0
C J:ASN470 4.9 17.6 1.0
C J:GLY441 4.9 10.9 1.0

Magnesium binding site 5 out of 8 in 3hwx

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Magnesium binding site 5 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg602

b:2.0
occ:1.00
O3B R:TPP601 1.9 2.0 1.0
O R:GLY471 1.9 7.3 1.0
O2A R:TPP601 2.1 4.4 1.0
OD1 R:ASP442 2.1 14.1 1.0
OD1 R:ASN469 2.3 8.8 1.0
PB R:TPP601 3.0 2.0 1.0
CG R:ASP442 3.0 9.8 1.0
PA R:TPP601 3.1 6.0 1.0
CG R:ASN469 3.2 8.3 1.0
C R:GLY471 3.2 7.5 1.0
O3A R:TPP601 3.3 2.0 1.0
OD2 R:ASP442 3.4 12.6 1.0
ND2 R:ASN469 3.5 8.5 1.0
N R:ASP442 3.7 7.5 1.0
O2B R:TPP601 3.9 3.3 1.0
O7 R:TPP601 4.0 4.6 1.0
N R:GLY471 4.1 7.6 1.0
N R:GLY472 4.1 7.0 1.0
CA R:GLY471 4.2 7.1 1.0
O R:VAL467 4.2 9.9 1.0
O1B R:TPP601 4.2 2.0 1.0
CA R:GLY472 4.3 7.7 1.0
N R:GLN473 4.3 9.2 1.0
CB R:ASP442 4.3 7.6 1.0
C R:GLY441 4.3 6.5 1.0
O1A R:TPP601 4.4 3.5 1.0
N R:ASN469 4.4 9.8 1.0
CA R:GLY441 4.4 5.6 1.0
CA R:ASP442 4.5 7.9 1.0
CB R:ASN469 4.6 8.8 1.0
N R:LEU443 4.6 7.7 1.0
CG R:GLN473 4.7 9.2 1.0
N R:ASN470 4.8 8.5 1.0
C R:GLY472 4.9 8.6 1.0
C R:ASN469 4.9 8.8 1.0
CA R:ASN469 4.9 8.7 1.0

Magnesium binding site 6 out of 8 in 3hwx

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Magnesium binding site 6 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg602

b:8.2
occ:1.00
O1B S:TPP601 1.8 3.8 1.0
OD1 S:ASN469 1.9 13.7 1.0
O1A S:TPP601 2.1 2.0 1.0
O S:GLY471 2.2 12.4 1.0
OD1 S:ASP442 2.3 20.3 1.0
CG S:ASN469 2.7 14.0 1.0
ND2 S:ASN469 2.9 16.9 1.0
PB S:TPP601 2.9 5.1 1.0
O3A S:TPP601 3.1 2.0 1.0
CG S:ASP442 3.2 17.0 1.0
PA S:TPP601 3.2 4.3 1.0
C S:GLY471 3.4 12.3 1.0
OD2 S:ASP442 3.6 18.9 1.0
N S:ASP442 3.9 12.9 1.0
O2B S:TPP601 4.0 6.0 1.0
N S:GLN473 4.0 13.8 1.0
O3B S:TPP601 4.0 4.9 1.0
O7 S:TPP601 4.1 4.2 1.0
CB S:ASN469 4.2 12.9 1.0
CA S:GLY472 4.2 12.8 1.0
N S:GLY472 4.2 12.3 1.0
N S:ASN469 4.3 11.5 1.0
N S:GLY471 4.3 11.9 1.0
CA S:GLY471 4.5 11.7 1.0
O2A S:TPP601 4.5 2.0 1.0
CB S:ASP442 4.5 13.9 1.0
CA S:GLY441 4.5 11.7 1.0
O S:VAL467 4.5 7.9 1.0
C S:GLY472 4.6 13.9 1.0
C S:GLY441 4.7 12.3 1.0
CA S:ASN469 4.7 12.3 1.0
CA S:ASP442 4.7 13.4 1.0
N S:LEU443 4.8 12.7 1.0
C S:ASN469 4.8 12.5 1.0
N S:ASN470 4.9 11.9 1.0
CG S:GLN473 4.9 12.6 1.0
CB S:GLN473 4.9 13.9 1.0

Magnesium binding site 7 out of 8 in 3hwx

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Magnesium binding site 7 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg602

b:2.0
occ:1.00
O3B Z:TPP601 2.0 4.3 1.0
O2A Z:TPP601 2.1 12.6 1.0
OD1 Z:ASN469 2.1 6.9 1.0
OD1 Z:ASP442 2.2 18.3 1.0
O Z:GLY471 2.2 16.0 1.0
O Z:HOH876 2.4 23.5 1.0
CG Z:ASP442 3.1 16.7 1.0
CG Z:ASN469 3.1 10.8 1.0
C Z:GLY471 3.1 15.8 1.0
PB Z:TPP601 3.3 10.2 1.0
PA Z:TPP601 3.4 11.7 1.0
OD2 Z:ASP442 3.5 17.2 1.0
ND2 Z:ASN469 3.5 7.7 1.0
O3A Z:TPP601 3.6 10.4 1.0
N Z:GLY471 3.9 15.7 1.0
N Z:GLY472 3.9 15.2 1.0
CA Z:GLY472 4.0 14.8 1.0
N Z:GLN473 4.0 15.3 1.0
CA Z:GLY471 4.0 15.5 1.0
N Z:ASP442 4.0 14.3 1.0
O7 Z:TPP601 4.1 9.4 1.0
O2B Z:TPP601 4.2 10.8 1.0
O Z:HOH692 4.3 2.0 1.0
CB Z:ASP442 4.4 14.9 1.0
O1B Z:TPP601 4.4 8.8 1.0
N Z:LEU443 4.4 14.6 1.0
CB Z:ASN469 4.5 12.9 1.0
CG Z:GLN473 4.5 15.6 1.0
N Z:ASN469 4.5 14.1 1.0
O1A Z:TPP601 4.5 11.3 1.0
C Z:GLY472 4.6 15.2 1.0
N Z:ASN470 4.6 14.8 1.0
CA Z:ASP442 4.7 14.7 1.0
O Z:VAL467 4.7 16.1 1.0
C Z:ASN470 4.8 15.7 1.0
C Z:ASN469 4.8 13.8 1.0
CA Z:ASN469 4.9 13.3 1.0
CA Z:GLY441 4.9 14.1 1.0
C Z:GLY441 4.9 14.2 1.0
CG Z:LEU443 4.9 11.6 1.0
CB Z:GLN473 4.9 15.4 1.0

Magnesium binding site 8 out of 8 in 3hwx

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Magnesium binding site 8 out of 8 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Thdp within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg602

b:2.0
occ:1.00
OD1 1:ASN469 1.7 18.4 1.0
O1B 1:TPP601 1.9 7.9 1.0
O 1:GLY471 1.9 12.8 1.0
O1A 1:TPP601 2.4 7.3 1.0
OD1 1:ASP442 2.7 16.5 1.0
CG 1:ASN469 2.7 17.1 1.0
ND2 1:ASN469 3.1 16.2 1.0
PB 1:TPP601 3.1 6.3 1.0
C 1:GLY471 3.1 13.5 1.0
O3A 1:TPP601 3.3 5.9 1.0
PA 1:TPP601 3.4 4.5 1.0
CG 1:ASP442 3.6 14.4 1.0
N 1:ASP442 3.9 12.0 1.0
N 1:GLY472 4.0 14.1 1.0
O2B 1:TPP601 4.0 3.1 1.0
O 1:VAL467 4.0 15.9 1.0
CA 1:GLY472 4.1 14.8 1.0
CB 1:ASN469 4.1 17.2 1.0
N 1:GLY471 4.1 12.5 1.0
OD2 1:ASP442 4.1 14.6 1.0
O7 1:TPP601 4.1 7.5 1.0
CA 1:GLY471 4.2 12.7 1.0
N 1:GLN473 4.2 15.7 1.0
N 1:ASN469 4.2 17.7 1.0
O3B 1:TPP601 4.2 5.5 1.0
CA 1:ASN469 4.5 16.7 1.0
CB 1:ASP442 4.6 12.4 1.0
O 1:HOH743 4.6 9.3 1.0
O2A 1:TPP601 4.6 5.1 1.0
C 1:ASN469 4.7 15.6 1.0
C 1:GLY472 4.7 15.3 1.0
CA 1:ASP442 4.7 12.2 1.0
N 1:LEU443 4.8 12.1 1.0
CA 1:GLY441 4.8 12.6 1.0
C 1:GLY441 4.8 12.6 1.0
CG 1:GLN473 4.9 15.4 1.0

Reference:

A.Priyadarshi, E.E.Kim, K.Y.Hwang. Structural and Functional Analysis of Vitamin K2 Synthesis Protein Mend. Biochem.Biophys.Res.Commun. V. 388 748 2009.
ISSN: ISSN 0006-291X
PubMed: 19703421
DOI: 10.1016/J.BBRC.2009.08.093
Page generated: Mon Dec 14 08:15:04 2020

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