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Cobalt 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:

Magnesium (Mg) 8 atoms

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:47.9
occ:1.00
OE2 A:GLU217 2.0 23.6 1.0
OD2 A:ASP255 2.1 25.7 1.0
OD1 A:ASP257 2.2 21.9 1.0
CG A:ASP255 3.0 27.5 1.0
CG A:ASP257 3.1 21.4 1.0
OD1 A:ASP255 3.1 26.8 1.0
CD A:GLU217 3.2 22.2 1.0
O A:HOH2260 3.2 16.2 1.0
OD2 A:ASP257 3.3 25.0 1.0
NE2 A:HIS220 3.3 15.1 1.0
OE1 A:GLU217 3.7 23.7 1.0
CD2 A:HIS220 3.8 10.7 1.0
ND2 A:ASN247 4.0 16.0 1.0
CG A:GLU217 4.4 19.9 1.0
OD2 A:ASP287 4.4 20.0 1.0
CB A:ASP255 4.4 22.3 1.0
CE1 A:HIS220 4.4 10.3 1.0
CB A:ASP257 4.5 19.3 1.0
OD1 A:ASP287 4.5 22.0 1.0
CG A:ASP287 4.5 20.0 1.0
O A:ASP287 4.5 21.6 1.0
MG A:MG2002 4.6 11.9 1.0
CB A:ALA219 4.9 10.3 1.0
NZ A:LYS289 5.0 28.2 1.0

Cobalt binding site 2 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:35.2
occ:1.00
OD2 B:ASP255 2.1 24.2 1.0
OE2 B:GLU217 2.2 10.1 1.0
OD1 B:ASP257 2.3 19.7 1.0
CG B:ASP255 2.7 26.1 1.0
OD1 B:ASP255 2.8 27.1 1.0
O B:HOH2251 3.0 12.5 1.0
CG B:ASP257 3.1 17.4 1.0
OD2 B:ASP257 3.1 22.8 1.0
CD B:GLU217 3.2 12.8 1.0
NE2 B:HIS220 3.2 14.1 1.0
OE1 B:GLU217 3.5 13.1 1.0
CD2 B:HIS220 3.7 13.8 1.0
O B:HOH2337 4.0 27.0 1.0
ND2 B:ASN247 4.0 6.8 1.0
CB B:ASP255 4.1 21.7 1.0
CE1 B:HIS220 4.3 13.0 1.0
OD2 B:ASP287 4.4 23.3 1.0
CB B:ASP257 4.5 13.6 1.0
CG B:GLU217 4.5 14.3 1.0
MG B:MG2002 4.6 18.1 1.0
CB B:ALA219 4.7 8.3 1.0
CG B:ASP287 4.8 18.8 1.0
O B:HOH2401 4.8 39.6 1.0
NZ B:LYS183 4.9 17.3 1.0
O B:ASP287 4.9 18.9 1.0
O B:HOH2168 4.9 27.9 1.0
OD1 B:ASP287 4.9 20.1 1.0
CG B:HIS220 5.0 14.4 1.0

Cobalt binding site 3 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:39.3
occ:1.00
OD2 C:ASP255 2.1 26.8 1.0
OE2 C:GLU217 2.2 15.4 1.0
OD1 C:ASP257 2.4 27.9 1.0
OD2 C:ASP257 2.9 29.5 1.0
CG C:ASP255 3.0 26.8 1.0
CG C:ASP257 3.0 24.9 1.0
CD C:GLU217 3.0 15.9 1.0
OE1 C:GLU217 3.1 21.9 1.0
O C:HOH2314 3.2 32.7 1.0
OD1 C:ASP255 3.2 29.3 1.0
NE2 C:HIS220 3.5 18.2 1.0
ND2 C:ASN247 3.8 18.7 1.0
CD2 C:HIS220 3.9 15.0 1.0
O C:HOH2315 4.1 29.5 1.0
OD2 C:ASP287 4.3 18.0 1.0
CB C:ASP255 4.3 22.4 1.0
CG C:GLU217 4.4 15.8 1.0
CB C:ASP257 4.4 22.3 1.0
O C:ASP287 4.5 22.6 1.0
CB C:ALA219 4.6 15.4 1.0
CE1 C:HIS220 4.7 17.2 1.0
CG C:ASP287 4.7 22.2 1.0
MG C:MG2002 4.8 15.4 1.0
OD1 C:ASP287 4.9 24.0 1.0
CA C:ASP257 4.9 19.4 1.0

Cobalt binding site 4 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:40.8
occ:1.00
OD1 D:ASP257 2.1 19.1 1.0
OE2 D:GLU217 2.2 20.9 1.0
OD2 D:ASP255 2.2 25.7 1.0
CG D:ASP255 2.9 25.1 1.0
CD D:GLU217 3.0 19.2 1.0
CG D:ASP257 3.0 17.6 1.0
OD1 D:ASP255 3.0 26.0 1.0
OE1 D:GLU217 3.0 21.1 1.0
NE2 D:HIS220 3.2 14.4 1.0
OD2 D:ASP257 3.2 21.7 1.0
CD2 D:HIS220 3.6 11.7 1.0
ND2 D:ASN247 3.9 17.4 1.0
O D:HOH2255 3.9 51.9 1.0
OD1 D:ASP287 4.1 19.9 1.0
CE1 D:HIS220 4.3 12.0 1.0
CB D:ASP255 4.4 20.4 1.0
CB D:ASP257 4.4 16.2 1.0
CG D:GLU217 4.4 19.9 1.0
CG D:ASP287 4.5 16.5 1.0
MG D:MG2002 4.5 17.9 1.0
O D:ASP287 4.6 19.0 1.0
OD2 D:ASP287 4.7 17.7 1.0
CB D:ALA219 4.7 12.2 1.0
NZ D:LYS289 4.9 29.4 1.0
CG D:HIS220 4.9 13.3 1.0
CA D:ASP257 4.9 16.2 1.0

Cobalt binding site 5 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:40.2
occ:1.00
OD2 E:ASP255 2.2 24.0 1.0
OE2 E:GLU217 2.2 15.1 1.0
OD1 E:ASP257 2.3 21.4 1.0
OE1 E:GLU217 2.7 16.8 1.0
O E:HOH2359 2.7 36.5 1.0
CD E:GLU217 2.8 13.0 1.0
NE2 E:HIS220 3.1 16.9 1.0
CG E:ASP255 3.1 25.3 1.0
CG E:ASP257 3.3 21.0 1.0
OD1 E:ASP255 3.4 22.1 1.0
OD2 E:ASP257 3.5 27.5 1.0
CD2 E:HIS220 3.6 14.4 1.0
O E:HOH2261 3.7 30.4 1.0
ND2 E:ASN247 3.9 11.5 1.0
CE1 E:HIS220 4.0 16.3 1.0
MG E:MG2002 4.2 17.8 1.0
CG E:GLU217 4.3 13.2 1.0
OD2 E:ASP287 4.5 21.6 1.0
CB E:ASP255 4.5 18.1 1.0
OD1 E:ASP287 4.5 24.1 1.0
CG E:ASP287 4.6 23.2 1.0
O E:ASP287 4.7 19.0 1.0
CB E:ASP257 4.7 16.2 1.0
CG E:HIS220 4.8 16.3 1.0
ND1 E:HIS220 5.0 16.9 1.0
CB E:ALA219 5.0 8.9 1.0

Cobalt binding site 6 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:40.1
occ:1.00
OE2 F:GLU217 2.0 17.8 1.0
OD1 F:ASP257 2.1 24.1 1.0
OD2 F:ASP255 2.1 21.2 1.0
CG F:ASP255 2.9 25.1 1.0
CD F:GLU217 2.9 18.3 1.0
OD1 F:ASP255 3.0 24.8 1.0
CG F:ASP257 3.0 26.0 1.0
OE1 F:GLU217 3.1 21.9 1.0
OD2 F:ASP257 3.3 29.6 1.0
NE2 F:HIS220 3.5 19.6 1.0
ND2 F:ASN247 3.8 11.4 1.0
CD2 F:HIS220 3.9 16.6 1.0
O F:HOH2210 4.3 16.0 1.0
CG F:GLU217 4.3 17.5 1.0
CB F:ASP257 4.4 24.6 1.0
CB F:ASP255 4.4 21.9 1.0
O F:ASP287 4.5 21.8 1.0
CB F:ALA219 4.5 15.0 1.0
OD1 F:ASP287 4.6 24.2 1.0
CE1 F:HIS220 4.6 16.8 1.0
OD2 F:ASP287 4.7 19.9 1.0
CG F:ASP287 4.7 18.4 1.0
CA F:ASP257 4.8 21.2 1.0
MG F:MG2002 4.9 21.0 1.0

Cobalt binding site 7 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:40.3
occ:1.00
OD1 G:ASP257 2.1 22.5 1.0
OD2 G:ASP255 2.2 20.1 1.0
OE2 G:GLU217 2.3 24.4 1.0
CD G:GLU217 3.0 19.7 1.0
OE1 G:GLU217 3.0 16.7 1.0
CG G:ASP255 3.0 25.2 1.0
CG G:ASP257 3.1 22.9 1.0
OD1 G:ASP255 3.2 23.8 1.0
NE2 G:HIS220 3.3 18.8 1.0
OD2 G:ASP257 3.4 24.3 1.0
ND2 G:ASN247 3.8 19.6 1.0
CD2 G:HIS220 3.8 18.1 1.0
O G:HOH2262 3.9 24.2 1.0
OD2 G:ASP287 4.2 20.0 1.0
MG G:MG2002 4.4 13.0 1.0
CE1 G:HIS220 4.4 17.8 1.0
CG G:GLU217 4.4 19.4 1.0
CB G:ASP257 4.4 19.9 1.0
CB G:ASP255 4.5 19.3 1.0
CG G:ASP287 4.5 19.5 1.0
O G:ASP287 4.5 21.2 1.0
OD1 G:ASP287 4.5 20.2 1.0
CB G:ALA219 4.7 9.1 1.0
CA G:ASP257 4.9 20.6 1.0

Cobalt binding site 8 out of 8 in 4hhm

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Cobalt 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 Cobalt with other atoms in the Co 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:Co2001

b:37.6
occ:1.00
OD2 H:ASP255 2.1 17.7 1.0
OE2 H:GLU217 2.3 20.8 1.0
OD1 H:ASP257 2.3 24.6 1.0
O H:HOH2387 2.8 30.6 1.0
CD H:GLU217 3.0 18.5 1.0
OE1 H:GLU217 3.0 16.6 1.0
CG H:ASP255 3.0 21.9 1.0
CG H:ASP257 3.1 21.8 1.0
O H:HOH2277 3.2 34.6 1.0
OD2 H:ASP257 3.2 25.6 1.0
OD1 H:ASP255 3.2 22.2 1.0
NE2 H:HIS220 3.4 11.7 1.0
ND2 H:ASN247 3.8 11.1 1.0
CD2 H:HIS220 3.9 11.7 1.0
OD2 H:ASP287 4.0 15.3 1.0
CB H:ASP255 4.4 16.6 1.0
CE1 H:HIS220 4.4 11.0 1.0
CG H:GLU217 4.4 16.6 1.0
CB H:ASP257 4.5 17.4 1.0
CG H:ASP287 4.6 17.0 1.0
MG H:MG2002 4.6 21.7 1.0
O H:ASP287 4.6 17.9 1.0
O H:HOH2249 4.7 30.7 1.0
CB H:ALA219 4.8 7.0 1.0
OD1 H:ASP287 4.9 17.3 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: Tue Jul 30 17:09:38 2024

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