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Magnesium in PDB 4hhm: Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk

Enzymatic activity of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk

All present enzymatic activity of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk, PDB code: 4hhm was solved by H.Ben Hlima, J.Riguet, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.500, 137.400, 136.600, 90.00, 90.06, 90.00
R / Rfree (%) 19.7 / 25

Other elements in 4hhm:

The structure of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk also contains other interesting chemical elements:

Cobalt (Co) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk (pdb code 4hhm). 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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk, PDB code: 4hhm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4hhm

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Magnesium binding site 1 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:11.9
occ:1.00
OE2 A:GLU181 2.1 13.2 1.0
OD2 A:ASP287 2.2 20.0 1.0
OD2 A:ASP245 2.2 17.6 1.0
OE1 A:GLU217 2.3 23.7 1.0
O A:HOH2259 2.5 21.0 1.0
O A:HOH2260 2.6 16.2 1.0
CD A:GLU181 2.9 15.7 1.0
OE1 A:GLU181 3.1 12.6 1.0
CD A:GLU217 3.3 22.2 1.0
CG A:ASP287 3.3 20.0 1.0
CG A:ASP245 3.4 18.1 1.0
OE2 A:GLU217 3.8 23.6 1.0
CB A:ASP287 3.8 20.1 1.0
CB A:ASP245 3.9 18.0 1.0
O A:HOH2109 4.0 17.5 1.0
CE1 A:HIS220 4.2 10.3 1.0
CB A:GLU217 4.3 18.5 1.0
OD1 A:ASP287 4.3 22.0 1.0
CG A:GLU217 4.3 19.9 1.0
CG A:GLU181 4.3 15.5 1.0
OD1 A:ASP245 4.4 20.6 1.0
NE2 A:HIS220 4.4 15.1 1.0
ND2 A:ASN215 4.5 14.8 1.0
CO A:CO2001 4.6 47.9 1.0

Magnesium binding site 2 out of 8 in 4hhm

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Magnesium binding site 2 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:18.1
occ:1.00
OE1 B:GLU217 2.1 13.1 1.0
OD2 B:ASP245 2.3 17.6 1.0
OD2 B:ASP287 2.3 23.3 1.0
OE2 B:GLU181 2.4 23.9 1.0
O B:HOH2337 2.5 27.0 1.0
O B:HOH2161 2.7 20.6 1.0
CD B:GLU181 2.9 22.1 1.0
OE1 B:GLU181 3.0 19.4 1.0
CD B:GLU217 3.3 12.8 1.0
CG B:ASP245 3.4 15.5 1.0
CG B:ASP287 3.4 18.8 1.0
CE1 B:HIS220 3.7 13.0 1.0
O B:HOH2190 3.8 50.8 1.0
CB B:ASP245 4.0 14.0 1.0
CB B:ASP287 4.1 18.2 1.0
NE2 B:HIS220 4.1 14.1 1.0
OE2 B:GLU217 4.1 10.1 1.0
CB B:GLU217 4.2 15.6 1.0
CG B:GLU217 4.3 14.3 1.0
CG B:GLU181 4.3 21.5 1.0
O B:HOH2160 4.3 14.5 1.0
OD1 B:ASP245 4.4 17.8 1.0
OD1 B:ASP287 4.4 20.1 1.0
ND1 B:HIS220 4.6 12.4 1.0
CO B:CO2001 4.6 35.2 1.0
ND2 B:ASN215 4.8 16.0 1.0
O B:HOH2251 5.0 12.5 1.0

Magnesium binding site 3 out of 8 in 4hhm

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Magnesium binding site 3 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:15.4
occ:1.00
OE2 C:GLU181 2.2 17.6 1.0
OD2 C:ASP287 2.2 18.0 1.0
OD2 C:ASP245 2.4 26.5 1.0
OE1 C:GLU217 2.4 21.9 1.0
O C:HOH2313 2.6 30.2 1.0
O C:HOH2314 2.7 32.7 1.0
CD C:GLU181 2.9 19.2 1.0
OE1 C:GLU181 3.1 18.9 1.0
CG C:ASP245 3.3 23.6 1.0
CG C:ASP287 3.3 22.2 1.0
CD C:GLU217 3.6 15.9 1.0
CB C:ASP245 3.8 21.7 1.0
CB C:ASP287 3.9 21.2 1.0
O C:HOH2140 4.0 20.4 1.0
OD1 C:ASP245 4.2 23.9 1.0
CE1 C:HIS220 4.2 17.2 1.0
CG C:GLU181 4.3 16.9 1.0
CB C:GLU217 4.4 14.4 1.0
OD1 C:ASP287 4.4 24.0 1.0
NE2 C:HIS220 4.4 18.2 1.0
CG C:GLU217 4.4 15.8 1.0
O C:HOH2143 4.4 35.3 1.0
OE2 C:GLU217 4.5 15.4 1.0
ND2 C:ASN215 4.7 16.5 1.0
CO C:CO2001 4.8 39.3 1.0

Magnesium binding site 4 out of 8 in 4hhm

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Magnesium binding site 4 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:17.9
occ:1.00
OE2 D:GLU181 2.3 22.5 1.0
OD2 D:ASP245 2.3 20.3 1.0
OE1 D:GLU217 2.3 21.1 1.0
OD2 D:ASP287 2.4 17.7 1.0
O D:HOH2254 2.8 27.9 1.0
OE1 D:GLU181 2.9 20.1 1.0
CD D:GLU181 3.0 19.7 1.0
CG D:ASP287 3.2 16.5 1.0
CG D:ASP245 3.5 21.8 1.0
CD D:GLU217 3.6 19.2 1.0
O D:HOH2255 3.6 51.9 1.0
CB D:ASP287 3.9 18.6 1.0
O D:HOH2335 4.1 14.2 1.0
CB D:ASP245 4.1 21.6 1.0
OD1 D:ASP287 4.1 19.9 1.0
CE1 D:HIS220 4.1 12.0 1.0
NE2 D:HIS220 4.3 14.4 1.0
CG D:GLU217 4.3 19.9 1.0
CB D:GLU217 4.4 18.1 1.0
OE2 D:GLU217 4.5 20.9 1.0
OD1 D:ASP245 4.5 23.6 1.0
CG D:GLU181 4.5 20.1 1.0
CO D:CO2001 4.5 40.8 1.0
ND2 D:ASN215 4.8 23.7 1.0
ND1 D:HIS220 4.9 12.5 1.0

Magnesium binding site 5 out of 8 in 4hhm

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Magnesium binding site 5 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2002

b:17.8
occ:1.00
OE2 E:GLU181 2.2 15.7 1.0
OD2 E:ASP287 2.2 21.6 1.0
OD2 E:ASP245 2.2 18.8 1.0
OE1 E:GLU217 2.3 16.8 1.0
O E:HOH2261 2.6 30.4 1.0
O E:HOH2151 2.6 16.5 1.0
CD E:GLU181 3.1 17.4 1.0
CG E:ASP287 3.2 23.2 1.0
OE1 E:GLU181 3.3 14.2 1.0
CG E:ASP245 3.3 15.9 1.0
CD E:GLU217 3.5 13.0 1.0
CB E:ASP287 3.7 21.9 1.0
CB E:ASP245 3.9 15.1 1.0
CE1 E:HIS220 4.1 16.3 1.0
OD1 E:ASP287 4.1 24.1 1.0
CO E:CO2001 4.2 40.2 1.0
CB E:GLU217 4.2 14.4 1.0
CG E:GLU217 4.3 13.2 1.0
O E:HOH2120 4.3 26.5 1.0
OD1 E:ASP245 4.4 17.1 1.0
OE2 E:GLU217 4.4 15.1 1.0
NE2 E:HIS220 4.4 16.9 1.0
CG E:GLU181 4.5 16.7 1.0
O E:HOH2359 4.6 36.5 1.0
ND2 E:ASN215 4.6 11.9 1.0
ND1 E:HIS220 4.9 16.9 1.0

Magnesium binding site 6 out of 8 in 4hhm

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Magnesium binding site 6 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2002

b:21.0
occ:1.00
OE2 F:GLU181 2.3 25.6 1.0
OD2 F:ASP287 2.3 19.9 1.0
OE1 F:GLU217 2.3 21.9 1.0
OD2 F:ASP245 2.4 25.4 1.0
O F:HOH2210 2.5 16.0 1.0
O F:HOH2141 2.6 26.2 1.0
OE1 F:GLU181 2.9 23.9 1.0
CD F:GLU181 2.9 23.1 1.0
CG F:ASP287 3.4 18.4 1.0
O F:HOH2140 3.5 20.3 1.0
CG F:ASP245 3.5 24.1 1.0
CD F:GLU217 3.5 18.3 1.0
CB F:ASP287 4.1 17.7 1.0
CB F:ASP245 4.1 22.8 1.0
CG F:GLU217 4.2 17.5 1.0
CE1 F:HIS220 4.3 16.8 1.0
CG F:GLU181 4.3 20.6 1.0
OD1 F:ASP287 4.3 24.2 1.0
CB F:GLU217 4.4 16.8 1.0
OE2 F:GLU217 4.5 17.8 1.0
NE2 F:HIS220 4.5 19.6 1.0
OD1 F:ASP245 4.5 22.6 1.0
ND2 F:ASN215 4.6 23.5 1.0
CO F:CO2001 4.9 40.1 1.0

Magnesium binding site 7 out of 8 in 4hhm

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Magnesium binding site 7 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2002

b:13.0
occ:1.00
OD2 G:ASP287 2.2 20.0 1.0
OE2 G:GLU181 2.2 16.0 1.0
OD2 G:ASP245 2.4 16.2 1.0
OE1 G:GLU217 2.4 16.7 1.0
O G:HOH2262 2.6 24.2 1.0
O G:HOH2261 2.7 24.2 1.0
CD G:GLU181 3.1 14.7 1.0
CG G:ASP287 3.3 19.5 1.0
OE1 G:GLU181 3.3 13.8 1.0
CG G:ASP245 3.5 15.4 1.0
CD G:GLU217 3.6 19.7 1.0
CB G:ASP287 3.9 19.1 1.0
CB G:ASP245 4.0 14.3 1.0
CE1 G:HIS220 4.1 17.8 1.0
O G:HOH2147 4.1 15.7 1.0
OD1 G:ASP287 4.3 20.2 1.0
CB G:GLU217 4.3 18.2 1.0
NE2 G:HIS220 4.4 18.8 1.0
CO G:CO2001 4.4 40.3 1.0
CG G:GLU217 4.4 19.4 1.0
OE2 G:GLU217 4.5 24.4 1.0
CG G:GLU181 4.5 14.2 1.0
OD1 G:ASP245 4.6 18.1 1.0
ND2 G:ASN215 4.8 15.7 1.0

Magnesium binding site 8 out of 8 in 4hhm

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Magnesium binding site 8 out of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk


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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2002

b:21.7
occ:1.00
OE2 H:GLU181 2.2 19.9 1.0
OD2 H:ASP287 2.3 15.3 1.0
OD2 H:ASP245 2.3 16.2 1.0
OE1 H:GLU217 2.4 16.6 1.0
O H:HOH2276 2.5 16.8 1.0
O H:HOH2387 2.6 30.6 1.0
CD H:GLU181 2.9 18.5 1.0
OE1 H:GLU181 2.9 16.3 1.0
CG H:ASP287 3.4 17.0 1.0
CG H:ASP245 3.5 16.1 1.0
CD H:GLU217 3.7 18.5 1.0
O H:HOH2216 3.9 17.7 1.0
CB H:ASP287 4.0 16.1 1.0
CE1 H:HIS220 4.0 11.0 1.0
CB H:ASP245 4.1 15.1 1.0
CG H:GLU181 4.3 17.9 1.0
NE2 H:HIS220 4.4 11.7 1.0
OD1 H:ASP287 4.4 17.3 1.0
CG H:GLU217 4.5 16.6 1.0
OD1 H:ASP245 4.5 15.9 1.0
OE2 H:GLU217 4.6 20.8 1.0
CB H:GLU217 4.6 14.8 1.0
CO H:CO2001 4.6 37.6 1.0
O H:HOH2236 4.6 28.3 1.0
ND2 H:ASN215 4.7 10.3 1.0
O H:HOH2249 4.9 30.7 1.0

Reference:

H.Ben Hlima, S.Bejar, J.Riguet, R.Haser, N.Aghajari. Identification of Critical Residues For the Activity and Thermostability of Streptomyces Sp. Sk Glucose Isomerase. Appl.Microbiol.Biotechnol. V. 97 9715 2013.
ISSN: ISSN 0175-7598
PubMed: 23463249
DOI: 10.1007/S00253-013-4784-2
Page generated: Fri Aug 16 16:18:32 2024

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