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Manganese in PDB 6vc6: 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+

Enzymatic activity of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+

All present enzymatic activity of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+:
3.2.1.122;

Protein crystallography data

The structure of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+, PDB code: 6vc6 was solved by R.Wu, Y.Kim, M.Endres, J.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.460, 62.257, 160.706, 90.00, 90.35, 90.00
R / Rfree (%) 19.6 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ (pdb code 6vc6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+, PDB code: 6vc6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6vc6

Go back to Manganese Binding Sites List in 6vc6
Manganese binding site 1 out of 4 in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:39.6
occ:1.00
 SG A:CYS170 2.2 45.1 1.0
NE2 A:HIS200 2.2 38.8 1.0
O3 A:G6P502 2.3 41.1 1.0
O7N A:NAD503 2.4 39.0 1.0
O2 A:G6P502 2.5 42.2 1.0
CE1 A:HIS200 2.9 36.0 1.0
C2 A:G6P502 3.0 41.0 1.0
C7N A:NAD503 3.0 41.8 1.0
C3 A:G6P502 3.1 37.0 1.0
CD2 A:HIS200 3.3 36.8 1.0
CB A:CYS170 3.3 34.1 1.0
N7N A:NAD503 3.5 37.9 1.0
C3N A:NAD503 4.0 42.6 1.0
ND1 A:HIS200 4.0 37.4 1.0
CA A:CYS170 4.1 38.4 1.0
OD1 A:ASN199 4.2 38.0 1.0
CG A:HIS200 4.3 37.1 1.0
ND2 A:ASN147 4.3 39.9 1.0
OD2 A:ASP171 4.3 39.0 1.0
N A:ASP171 4.4 45.5 1.0
OD1 A:ASN147 4.4 36.7 1.0
C4 A:G6P502 4.4 44.5 1.0
ND2 A:ASN199 4.5 34.9 1.0
C1 A:G6P502 4.5 41.1 1.0
C4N A:NAD503 4.6 42.7 1.0
CB A:GLN172 4.6 38.8 1.0
C A:CYS170 4.7 42.3 1.0
N A:GLN172 4.7 39.5 1.0
CG A:ASN199 4.8 40.4 1.0
CG A:ASN147 4.8 42.5 1.0
C2N A:NAD503 4.9 39.6 1.0
O1 A:G6P502 5.0 46.7 1.0

Manganese binding site 2 out of 4 in 6vc6

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Manganese binding site 2 out of 4 in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:34.0
occ:1.00
 NE2 B:HIS200 2.2 36.8 1.0
O3 B:G6P502 2.3 36.3 1.0
O B:HOH657 2.3 37.4 1.0
O7N B:NAD503 2.4 39.0 1.0
O2 B:G6P502 2.4 40.0 1.0
SG B:CYS170 2.5 38.6 1.0
C2 B:G6P502 2.9 40.6 1.0
CE1 B:HIS200 3.0 38.9 1.0
C7N B:NAD503 3.0 40.3 1.0
C3 B:G6P502 3.1 42.1 1.0
CD2 B:HIS200 3.2 35.5 1.0
CB B:CYS170 3.4 34.1 1.0
N7N B:NAD503 3.5 38.4 1.0
C3N B:NAD503 4.0 42.2 1.0
ND1 B:HIS200 4.2 39.5 1.0
CA B:CYS170 4.2 40.0 1.0
OD2 B:ASP171 4.2 44.7 1.0
ND2 B:ASN147 4.3 38.8 1.0
ND2 B:ASN199 4.3 35.4 1.0
CG B:HIS200 4.3 40.7 1.0
C1 B:G6P502 4.4 42.6 1.0
C4 B:G6P502 4.4 44.7 1.0
OD1 B:ASN147 4.4 39.4 1.0
N B:ASP171 4.4 38.1 1.0
OD1 B:ASN199 4.5 36.0 1.0
C4N B:NAD503 4.6 44.4 1.0
CB B:GLN172 4.6 38.7 1.0
N B:GLN172 4.7 36.8 1.0
C B:CYS170 4.7 41.2 1.0
CG B:ASN147 4.8 42.3 1.0
CG B:ASN199 4.9 39.9 1.0
C2N B:NAD503 4.9 38.2 1.0
O1 B:G6P502 5.0 57.0 1.0

Manganese binding site 3 out of 4 in 6vc6

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Manganese binding site 3 out of 4 in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:36.9
occ:1.00
 O C:HOH637 2.1 40.9 1.0
NE2 C:HIS200 2.2 37.6 1.0
O3 C:G6P502 2.2 42.8 1.0
SG C:CYS170 2.4 42.3 1.0
O7N C:NAD503 2.4 47.9 1.0
O2 C:G6P502 2.5 40.2 1.0
C2 C:G6P502 3.0 44.7 1.0
CE1 C:HIS200 3.0 37.4 1.0
C7N C:NAD503 3.0 46.1 1.0
C3 C:G6P502 3.0 41.8 1.0
CD2 C:HIS200 3.3 33.7 1.0
N7N C:NAD503 3.4 44.0 1.0
CB C:CYS170 3.5 42.3 1.0
C3N C:NAD503 4.1 46.0 1.0
OD2 C:ASP171 4.2 49.1 1.0
ND1 C:HIS200 4.2 36.4 1.0
CA C:CYS170 4.2 44.4 1.0
ND2 C:ASN199 4.3 36.0 1.0
ND2 C:ASN147 4.3 43.1 1.0
CG C:HIS200 4.3 41.8 1.0
OD1 C:ASN147 4.3 40.7 1.0
C4 C:G6P502 4.4 44.6 1.0
N C:ASP171 4.4 44.9 1.0
C1 C:G6P502 4.5 42.3 1.0
OD1 C:ASN199 4.5 43.8 1.0
CB C:GLN172 4.6 42.8 1.0
C4N C:NAD503 4.6 49.3 1.0
N C:GLN172 4.7 44.5 1.0
C C:CYS170 4.8 42.5 1.0
CG C:ASN147 4.8 46.8 1.0
CG C:ASN199 4.9 41.9 1.0
C2N C:NAD503 4.9 43.9 1.0

Manganese binding site 4 out of 4 in 6vc6

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Manganese binding site 4 out of 4 in the 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha- Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:44.0
occ:1.00
 O3 D:G6P502 2.1 47.6 1.0
NE2 D:HIS200 2.1 50.5 1.0
O D:HOH613 2.2 42.9 1.0
SG D:CYS170 2.4 42.9 1.0
O2 D:G6P502 2.5 46.9 1.0
O7N D:NAD503 2.6 48.8 1.0
CE1 D:HIS200 2.9 46.5 1.0
C2 D:G6P502 2.9 48.5 1.0
C3 D:G6P502 2.9 49.8 1.0
C7N D:NAD503 3.1 51.0 1.0
CD2 D:HIS200 3.2 40.4 1.0
CB D:CYS170 3.5 43.9 1.0
N7N D:NAD503 3.5 53.9 1.0
C3N D:NAD503 4.0 50.2 1.0
ND1 D:HIS200 4.1 41.8 1.0
OD1 D:ASN147 4.1 46.7 1.0
OD2 D:ASP171 4.2 52.0 1.0
ND2 D:ASN147 4.2 46.0 1.0
CG D:HIS200 4.3 43.8 1.0
C4 D:G6P502 4.3 52.7 1.0
ND2 D:ASN199 4.3 38.6 1.0
CA D:CYS170 4.3 47.8 1.0
C1 D:G6P502 4.4 47.5 1.0
N D:ASP171 4.5 47.9 1.0
OD1 D:ASN199 4.5 44.0 1.0
C4N D:NAD503 4.6 51.3 1.0
CB D:GLN172 4.6 47.6 1.0
CG D:ASN147 4.6 47.1 1.0
N D:GLN172 4.7 44.9 1.0
C D:CYS170 4.8 47.4 1.0
CG D:ASN199 4.9 41.4 1.0
C2N D:NAD503 4.9 50.1 1.0
O4 D:G6P502 4.9 48.0 1.0
O1 D:G6P502 5.0 65.2 1.0

Reference:

R.Wu, Y.Kim, M.Endres, A.Joachimiak. 2.1 Angstrom Resolution Crystal Structure of 6-Phospho-Alpha-Glucosidase From Gut Microorganisms in Complex with Nad and MN2+ To Be Published.
Page generated: Sun Oct 6 07:28:43 2024

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