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Magnesium in PDB 4h2h: Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)

Protein crystallography data

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h was solved by M.W.Vetting, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.68 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.035, 152.824, 113.027, 90.00, 105.20, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 4h2h:

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iodine (I) 61 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) (pdb code 4h2h). 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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4h2h

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Magnesium binding site 1 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.6
occ:1.00
 OD2 A:ASP241 2.0 12.4 1.0
O A:HOH550 2.1 17.7 1.0
OE2 A:GLU218 2.1 15.3 1.0
OD2 A:ASP193 2.2 17.1 1.0
O11 A:0XW403 2.3 27.4 1.0
O10 A:0XW403 2.5 25.6 1.0
C09 A:0XW403 2.8 25.7 1.0
CD A:GLU218 3.0 19.1 1.0
CG A:ASP241 3.2 13.9 1.0
CG A:ASP193 3.2 18.8 1.0
OD1 A:ASP193 3.5 18.2 1.0
NE2 A:GLN161 3.6 17.7 1.0
CB A:ASP241 3.7 10.6 1.0
CG A:GLU218 3.8 13.7 1.0
OE1 A:GLU218 3.9 18.3 1.0
O A:HOH575 3.9 16.1 1.0
ND2 A:ASN195 4.0 33.2 1.0
OH A:TYR56 4.1 29.1 1.0
NZ A:LYS163 4.1 33.3 1.0
NZ A:LYS265 4.2 14.3 0.3
OD1 A:ASP241 4.2 15.5 1.0
C08 A:0XW403 4.2 30.0 1.0
OE1 A:GLU242 4.2 14.4 1.0
CB A:ASP193 4.4 14.7 1.0
NZ A:LYS265 4.5 9.4 0.7
CD A:GLN161 4.5 19.6 1.0
CG A:ASN195 4.8 32.2 1.0
OE1 A:GLN161 4.8 23.1 1.0
CD A:GLU242 4.9 25.7 1.0
CE A:LYS265 5.0 20.0 0.3
OE2 A:GLU242 5.0 26.3 1.0

Magnesium binding site 2 out of 8 in 4h2h

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Magnesium binding site 2 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:15.5
occ:1.00
 OD2 B:ASP241 2.1 15.6 1.0
OE2 B:GLU218 2.1 16.2 1.0
O B:HOH551 2.1 18.5 1.0
OD2 B:ASP193 2.1 16.9 1.0
O10 B:0XW403 2.3 24.2 1.0
O11 B:0XW403 2.5 24.9 1.0
C09 B:0XW403 2.8 28.3 1.0
CD B:GLU218 3.0 22.2 1.0
CG B:ASP193 3.1 18.8 1.0
CG B:ASP241 3.2 15.6 1.0
NE2 B:GLN161 3.5 22.1 1.0
OD1 B:ASP193 3.6 17.4 1.0
CB B:ASP241 3.7 9.2 1.0
CG B:GLU218 3.7 14.4 1.0
OE1 B:GLU218 3.9 19.3 1.0
ND2 B:ASN195 3.9 33.8 1.0
O B:HOH542 4.0 16.8 1.0
OH B:TYR56 4.2 36.5 1.0
OD1 B:ASP241 4.2 18.3 1.0
C08 B:0XW403 4.3 31.2 1.0
OE1 B:GLU242 4.3 14.9 1.0
CB B:ASP193 4.4 15.1 1.0
NZ B:LYS163 4.4 37.3 1.0
CD B:GLN161 4.4 24.0 1.0
NZ B:LYS265 4.5 7.9 0.6
NZ B:LYS265 4.5 15.2 0.5
OE1 B:GLN161 4.8 25.2 1.0
CG B:ASN195 4.8 33.8 1.0
CD B:GLU242 4.8 23.9 1.0
OE2 B:GLU242 4.8 28.5 1.0
CB B:GLU218 5.0 12.9 1.0

Magnesium binding site 3 out of 8 in 4h2h

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Magnesium binding site 3 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:14.9
occ:1.00
 OE2 C:GLU218 2.0 14.6 1.0
OD2 C:ASP241 2.1 15.8 1.0
O C:HOH514 2.1 18.2 1.0
OD2 C:ASP193 2.1 15.3 1.0
O10 C:0XW402 2.2 32.4 1.0
O11 C:0XW402 2.5 23.9 1.0
C09 C:0XW402 2.7 32.2 1.0
CD C:GLU218 3.0 15.9 1.0
CG C:ASP193 3.1 15.2 1.0
CG C:ASP241 3.2 15.8 1.0
OD1 C:ASP193 3.5 16.4 1.0
NE2 C:GLN161 3.6 17.1 1.0
CB C:ASP241 3.7 12.0 1.0
CG C:GLU218 3.8 12.3 1.0
OE1 C:GLU218 3.9 15.6 1.0
ND2 C:ASN195 3.9 27.6 1.0
O C:HOH561 3.9 17.3 1.0
OH C:TYR56 4.0 34.1 1.0
NZ C:LYS163 4.0 31.6 1.0
C08 C:0XW402 4.2 36.5 1.0
OE1 C:GLU242 4.3 13.3 1.0
OD1 C:ASP241 4.3 17.9 1.0
CB C:ASP193 4.4 12.9 1.0
NZ C:LYS265 4.5 33.5 1.0
CD C:GLN161 4.5 16.6 1.0
O C:HOH610 4.5 18.7 1.0
CG C:ASN195 4.7 25.6 1.0
OE1 C:GLN161 4.8 20.6 1.0
CD C:GLU242 4.9 20.7 1.0
OD1 C:ASN195 4.9 25.2 1.0
OE2 C:GLU242 5.0 22.7 1.0
CB C:GLU218 5.0 11.5 1.0

Magnesium binding site 4 out of 8 in 4h2h

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Magnesium binding site 4 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:17.6
occ:1.00
 OE2 D:GLU218 2.0 15.1 1.0
O D:HOH524 2.1 20.9 1.0
OD2 D:ASP241 2.1 19.6 1.0
OD2 D:ASP193 2.2 18.5 1.0
O10 D:0XW402 2.3 24.4 1.0
O11 D:0XW402 2.4 29.3 1.0
C09 D:0XW402 2.7 28.7 1.0
CD D:GLU218 3.0 20.9 1.0
CG D:ASP193 3.2 18.2 1.0
CG D:ASP241 3.2 17.8 1.0
NE2 D:GLN161 3.5 22.5 1.0
OD1 D:ASP193 3.6 20.0 1.0
CB D:ASP241 3.7 12.2 1.0
CG D:GLU218 3.8 17.8 1.0
OE1 D:GLU218 3.9 22.6 1.0
O D:HOH570 3.9 23.0 1.0
ND2 D:ASN195 4.0 32.1 1.0
OH D:TYR56 4.0 31.3 1.0
NZ D:LYS163 4.0 27.0 1.0
C08 D:0XW402 4.2 35.7 1.0
OD1 D:ASP241 4.3 20.8 1.0
OE1 D:GLU242 4.3 16.3 1.0
CD D:GLN161 4.4 21.1 1.0
CB D:ASP193 4.4 16.0 1.0
NZ D:LYS265 4.5 30.0 1.0
O D:HOH542 4.5 21.6 1.0
OE1 D:GLN161 4.6 21.9 1.0
CG D:ASN195 4.8 31.5 1.0
CD D:GLU242 4.9 19.9 1.0
OE2 D:GLU242 4.9 22.6 1.0
CB D:GLU218 5.0 14.8 1.0

Magnesium binding site 5 out of 8 in 4h2h

Go back to Magnesium Binding Sites List in 4h2h
Magnesium binding site 5 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:18.4
occ:1.00
 OD2 E:ASP241 2.1 19.6 1.0
O E:HOH738 2.1 17.9 1.0
OE2 E:GLU218 2.1 18.4 1.0
OD2 E:ASP193 2.1 20.4 1.0
O11 E:0XW402 2.3 39.8 1.0
O10 E:0XW402 2.5 39.9 1.0
C09 E:0XW402 2.8 39.9 1.0
CD E:GLU218 3.0 23.9 1.0
CG E:ASP193 3.1 23.7 1.0
CG E:ASP241 3.2 18.4 1.0
OD1 E:ASP193 3.5 19.8 1.0
NE2 E:GLN161 3.6 29.5 1.0
CB E:ASP241 3.7 12.1 1.0
CG E:GLU218 3.7 16.2 1.0
OE1 E:GLU218 3.9 24.5 1.0
O E:HOH580 3.9 24.1 1.0
OH E:TYR56 4.1 44.4 1.0
NZ E:LYS163 4.2 41.2 1.0
OE1 E:GLU242 4.2 15.3 1.0
OD1 E:ASP241 4.2 17.5 1.0
C08 E:0XW402 4.3 40.6 1.0
CB E:ASP193 4.5 25.3 1.0
CD E:GLN161 4.5 27.6 1.0
O E:HOH617 4.5 27.9 1.0
OE2 E:GLU242 4.6 34.2 1.0
CD E:GLU242 4.7 26.6 1.0
NZ E:LYS265 4.7 39.5 1.0
OE1 E:GLN161 4.8 28.4 1.0
CB E:GLU218 4.9 14.5 1.0

Magnesium binding site 6 out of 8 in 4h2h

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Magnesium binding site 6 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:15.3
occ:1.00
 OE2 F:GLU218 2.1 16.4 1.0
OD2 F:ASP241 2.1 15.9 1.0
O F:HOH571 2.1 20.7 1.0
OD2 F:ASP193 2.2 17.3 1.0
O11 F:0XW402 2.4 32.4 1.0
O10 F:0XW402 2.5 29.7 1.0
C09 F:0XW402 2.8 33.0 1.0
CD F:GLU218 3.0 16.1 1.0
CG F:ASP193 3.2 16.2 1.0
CG F:ASP241 3.2 15.8 1.0
OD1 F:ASP193 3.5 16.5 1.0
NE2 F:GLN161 3.6 17.9 1.0
CB F:ASP241 3.7 12.3 1.0
CG F:GLU218 3.8 10.8 1.0
NZ F:LYS163 3.9 36.7 1.0
OE1 F:GLU218 3.9 16.2 1.0
O F:HOH521 3.9 19.4 1.0
ND2 F:ASN195 4.1 36.9 1.0
OH F:TYR56 4.1 45.9 1.0
OE1 F:GLU242 4.2 17.3 1.0
OD1 F:ASP241 4.2 18.2 1.0
C08 F:0XW402 4.3 35.5 1.0
NZ F:LYS265 4.4 32.9 1.0
O F:HOH585 4.4 25.0 1.0
CB F:ASP193 4.4 13.2 1.0
CD F:GLN161 4.5 19.5 1.0
CG F:ASN195 4.8 34.3 1.0
OE1 F:GLN161 4.8 21.6 1.0
CD F:GLU242 4.8 23.8 1.0
OE2 F:GLU242 4.9 25.1 1.0
OD1 F:ASN195 5.0 30.7 1.0
CB F:GLU218 5.0 12.5 1.0

Magnesium binding site 7 out of 8 in 4h2h

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Magnesium binding site 7 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:17.5
occ:1.00
 O G:HOH517 2.1 21.8 1.0
OE2 G:GLU218 2.1 20.1 1.0
OD2 G:ASP241 2.1 20.4 1.0
OD2 G:ASP193 2.2 22.2 1.0
O11 G:0XW402 2.2 23.8 1.0
O10 G:0XW402 2.2 27.4 1.0
C09 G:0XW402 2.5 31.2 1.0
CD G:GLU218 3.0 24.2 1.0
CG G:ASP193 3.2 24.6 1.0
CG G:ASP241 3.3 19.0 1.0
NE2 G:GLN161 3.5 20.2 1.0
OD1 G:ASP193 3.5 21.1 1.0
CB G:ASP241 3.7 13.3 1.0
CG G:GLU218 3.8 20.0 1.0
OE1 G:GLU218 3.9 24.5 1.0
ND2 G:ASN195 3.9 23.5 1.0
NZ G:LYS163 3.9 30.4 1.0
OH G:TYR56 4.0 33.4 1.0
O G:HOH572 4.0 23.6 1.0
C08 G:0XW402 4.0 40.3 1.0
OE1 G:GLU242 4.3 16.1 1.0
OD1 G:ASP241 4.3 21.0 1.0
CD G:GLN161 4.4 23.6 1.0
NZ G:LYS265 4.4 33.1 1.0
O G:HOH540 4.4 25.5 1.0
CB G:ASP193 4.5 22.3 1.0
OE1 G:GLN161 4.6 29.7 1.0
CG G:ASN195 4.7 25.9 1.0
OD1 G:ASN195 4.9 26.2 1.0
C07 G:0XW402 4.9 36.7 1.0
CD G:GLU242 5.0 22.2 1.0

Magnesium binding site 8 out of 8 in 4h2h

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Magnesium binding site 8 out of 8 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:16.6
occ:1.00
 OE2 H:GLU218 2.0 18.6 1.0
O H:HOH515 2.1 18.1 1.0
OD2 H:ASP241 2.1 15.6 1.0
OD2 H:ASP193 2.1 16.9 1.0
O10 H:0XW402 2.2 27.6 1.0
O11 H:0XW402 2.3 28.9 1.0
C09 H:0XW402 2.6 32.1 1.0
CD H:GLU218 3.0 21.5 1.0
CG H:ASP193 3.1 21.2 1.0
CG H:ASP241 3.2 16.5 1.0
OD1 H:ASP193 3.5 19.3 1.0
NE2 H:GLN161 3.5 20.4 1.0
CB H:ASP241 3.7 13.9 1.0
CG H:GLU218 3.8 18.7 1.0
OE1 H:GLU218 3.9 18.9 1.0
ND2 H:ASN195 3.9 25.1 1.0
O H:HOH533 3.9 19.3 1.0
NZ H:LYS163 4.0 27.2 1.0
OH H:TYR56 4.0 32.5 1.0
C08 H:0XW402 4.1 37.9 1.0
OD1 H:ASP241 4.3 18.7 1.0
OE1 H:GLU242 4.3 14.8 1.0
CD H:GLN161 4.4 23.8 1.0
CB H:ASP193 4.4 18.8 1.0
NZ H:LYS265 4.4 33.0 1.0
O H:HOH727 4.5 22.1 1.0
OE1 H:GLN161 4.6 26.7 1.0
CG H:ASN195 4.8 25.0 1.0
OD1 H:ASN195 5.0 25.5 1.0
CD H:GLU242 5.0 22.7 1.0

Reference:

S.Zhao, R.Kumar, A.Sakai, M.W.Vetting, B.M.Wood, S.Brown, J.B.Bonanno, B.S.Hillerich, R.D.Seidel, P.C.Babbitt, S.C.Almo, J.V.Sweedler, J.A.Gerlt, J.E.Cronan, M.P.Jacobson. Discovery of New Enzymes and Metabolic Pathways By Using Structure and Genome Context. Nature V. 502 698 2013.
ISSN: ISSN 0028-0836
PubMed: 24056934
DOI: 10.1038/NATURE12576
Page generated: Mon Dec 14 17:08:37 2020

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