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Manganese in PDB 5c3m: Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus

Enzymatic activity of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus

All present enzymatic activity of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus:
3.2.1.86;

Protein crystallography data

The structure of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus, PDB code: 5c3m was solved by T.Cohen, S.Lansky, A.Zehavi, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 3.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.324, 83.198, 151.372, 90.00, 113.61, 90.00
R / Rfree (%) 23 / 30.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus (pdb code 5c3m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus, PDB code: 5c3m:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5c3m

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Manganese binding site 1 out of 4 in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:58.4
occ:1.00
 OH A:TYR316 1.5 65.6 1.0
SG A:CYS172 1.8 60.7 1.0
NE2 A:HIS202 2.3 57.0 1.0
CZ A:TYR316 2.5 72.0 1.0
CB A:CYS172 2.6 56.8 1.0
CE2 A:TYR316 3.0 65.5 1.0
CE1 A:HIS202 3.1 57.6 1.0
CD2 A:HIS202 3.3 53.4 1.0
OD1 A:ASN150 3.4 59.6 1.0
CA A:CYS172 3.5 58.3 1.0
CE1 A:TYR316 3.6 75.0 1.0
ND2 A:ASN201 3.6 56.2 1.0
ND2 A:ASN150 3.8 79.4 1.0
OD1 A:ASN201 3.9 52.9 1.0
CG A:ASN150 4.0 65.4 1.0
CG A:ASN201 4.2 52.0 1.0
ND1 A:HIS202 4.2 55.0 1.0
O A:LEU171 4.3 62.6 1.0
CD2 A:TYR316 4.3 67.1 1.0
CG A:HIS202 4.3 53.4 1.0
C A:CYS172 4.5 56.1 1.0
N A:CYS172 4.5 58.6 1.0
N A:ASN173 4.5 59.8 1.0
CB A:ALA152 4.7 49.3 1.0
CD1 A:TYR316 4.8 69.8 1.0
C A:LEU171 4.8 58.8 1.0
CG2 A:VAL174 4.9 49.3 1.0

Manganese binding site 2 out of 4 in 5c3m

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Manganese binding site 2 out of 4 in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:50.5
occ:1.00
 SG B:CYS172 1.9 56.0 1.0
OH B:TYR316 2.2 62.1 1.0
NE2 B:HIS202 2.3 54.1 1.0
CZ B:TYR316 2.9 61.8 1.0
CB B:CYS172 3.1 50.3 1.0
CE1 B:HIS202 3.1 57.3 1.0
CD2 B:HIS202 3.2 54.0 1.0
CE2 B:TYR316 3.4 60.1 1.0
OD1 B:ASN150 3.7 61.8 1.0
ND2 B:ASN150 3.7 72.6 1.0
CE1 B:TYR316 3.8 60.1 1.0
CA B:CYS172 3.8 57.7 1.0
ND2 B:ASN201 4.1 49.9 1.0
CG B:ASN150 4.1 54.0 1.0
ND1 B:HIS202 4.1 52.5 1.0
CG B:HIS202 4.2 50.7 1.0
O B:LEU171 4.3 52.5 1.0
CD2 B:TYR316 4.6 63.8 1.0
N B:ASN173 4.6 48.0 1.0
C B:CYS172 4.8 49.9 1.0
N B:CYS172 4.8 58.1 1.0
CD1 B:TYR316 4.9 67.2 1.0
OD1 B:ASN201 4.9 50.5 1.0
CG2 B:VAL174 4.9 50.3 1.0
OD1 B:ASN173 4.9 60.9 1.0
CG B:ASN201 4.9 45.1 1.0
CB B:ALA152 5.0 52.7 1.0

Manganese binding site 3 out of 4 in 5c3m

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Manganese binding site 3 out of 4 in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:51.6
occ:1.00
 OH C:TYR316 1.5 60.2 1.0
NE2 C:HIS202 1.8 49.3 1.0
SG C:CYS172 1.8 52.4 1.0
CZ C:TYR316 2.8 62.6 1.0
CE1 C:HIS202 2.8 45.4 1.0
CD2 C:HIS202 2.8 45.2 1.0
CB C:CYS172 3.5 46.4 1.0
CE1 C:TYR316 3.5 61.1 1.0
OD1 C:ASN150 3.5 54.0 1.0
CE2 C:TYR316 3.7 61.2 1.0
ND1 C:HIS202 3.9 40.4 1.0
CG C:HIS202 3.9 43.9 1.0
ND2 C:ASN201 4.1 45.3 1.0
CA C:CYS172 4.1 49.7 1.0
ND2 C:ASN150 4.2 73.5 1.0
CG C:ASN150 4.3 58.3 1.0
OD1 C:ASN201 4.4 49.1 1.0
CG2 C:VAL174 4.5 46.1 1.0
N C:ASN173 4.6 53.4 1.0
CG C:ASN201 4.7 46.6 1.0
OH C:TYR257 4.8 35.1 1.0
O C:LEU171 4.8 49.2 1.0
CD1 C:TYR316 4.9 66.5 1.0
C C:CYS172 5.0 50.2 1.0
CD2 C:TYR316 5.0 65.9 1.0
CE2 C:TYR257 5.0 37.9 1.0

Manganese binding site 4 out of 4 in 5c3m

Go back to Manganese Binding Sites List in 5c3m
Manganese binding site 4 out of 4 in the Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:54.4
occ:1.00
 OH D:TYR316 1.4 60.5 1.0
SG D:CYS172 1.9 54.0 1.0
NE2 D:HIS202 2.0 48.3 1.0
CZ D:TYR316 2.5 60.5 1.0
CD2 D:HIS202 2.9 46.1 1.0
CE1 D:HIS202 3.1 53.8 1.0
CE2 D:TYR316 3.3 59.4 1.0
CB D:CYS172 3.4 47.7 1.0
CE1 D:TYR316 3.4 61.5 1.0
OD1 D:ASN150 3.8 49.6 1.0
ND2 D:ASN201 4.0 45.5 1.0
CG D:HIS202 4.0 45.9 1.0
ND2 D:ASN150 4.0 60.1 1.0
ND1 D:HIS202 4.1 53.1 1.0
CA D:CYS172 4.2 48.2 1.0
OD1 D:ASN173 4.3 57.4 1.0
CG D:ASN150 4.3 53.9 1.0
CG2 D:VAL174 4.4 49.7 1.0
N D:ASN173 4.5 58.8 1.0
CD2 D:TYR316 4.6 62.6 1.0
CD1 D:TYR316 4.6 63.6 1.0
CG D:ASN201 4.9 43.0 1.0
C D:CYS172 4.9 49.6 1.0
OD1 D:ASN201 5.0 47.1 1.0
O D:LEU171 5.0 50.7 1.0

Reference:

T.Cohen, S.Lansky, A.Zehavi, Y.Shoham, G.Shoham. Crystal Structure of GAN4C, A GH4 6-Phospho-Glucosidase From Geobacillus Stearothermophilus To Be Published.
Page generated: Sat Oct 5 23:42:55 2024

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