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Manganese in PDB 1up6: Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate

Enzymatic activity of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate

All present enzymatic activity of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate:
3.2.1.6;

Protein crystallography data

The structure of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate, PDB code: 1up6 was solved by A.Varrot, V.L.Yip, S.G.Withers, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.438, 179.438, 282.911, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate (pdb code 1up6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate, PDB code: 1up6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1up6

Go back to Manganese Binding Sites List in 1up6
Manganese binding site 1 out of 5 in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1417

b:35.2
occ:0.50
 O3 A:G6P1418 2.2 25.3 0.5
O2 A:G6P1418 2.2 27.7 0.5
O7N A:NAD1416 2.2 18.9 0.5
SG A:CYS162 2.7 30.8 1.0
NE2 A:HIS192 2.8 24.5 1.0
C7N A:NAD1416 2.9 17.8 0.5
C3 A:G6P1418 2.9 25.9 0.5
C2 A:G6P1418 3.0 26.3 0.5
ND2 A:ASN163 3.2 25.8 1.0
N7N A:NAD1416 3.4 14.7 0.5
CE1 A:HIS192 3.4 25.7 1.0
N A:ASN163 3.7 23.2 1.0
CB A:CYS162 3.8 24.6 1.0
C3N A:NAD1416 3.9 18.4 0.5
CD2 A:HIS192 3.9 25.1 1.0
CA A:CYS162 4.0 23.4 1.0
C4 A:G6P1418 4.3 24.8 0.5
C A:CYS162 4.3 23.2 1.0
ND2 A:ASN140 4.4 27.2 1.0
C1 A:G6P1418 4.4 27.4 0.5
CG A:ASN163 4.4 24.8 1.0
C4N A:NAD1416 4.4 18.1 0.5
CG1 A:VAL164 4.6 24.5 1.0
ND1 A:HIS192 4.6 27.4 1.0
ND2 A:ASN191 4.7 20.4 1.0
CA A:ASN163 4.8 22.4 1.0
C2N A:NAD1416 4.8 18.3 0.5
O4 A:G6P1418 4.8 27.3 0.5
CG A:HIS192 4.9 23.4 1.0
N A:VAL164 4.9 22.3 1.0
OD1 A:ASN191 4.9 25.9 1.0
CB A:ASN163 4.9 23.4 1.0

Manganese binding site 2 out of 5 in 1up6

Go back to Manganese Binding Sites List in 1up6
Manganese binding site 2 out of 5 in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1419

b:35.1
occ:0.50
 O A:ILE37 2.0 20.5 1.0
MN A:MN1420 2.5 42.4 1.0
O A:HOH2135 2.5 39.5 1.0
C A:ILE37 3.1 19.5 1.0
O A:HOH2136 3.4 43.9 1.0
N A:GLU39 3.5 20.3 1.0
N A:ASP38 4.0 19.2 1.0
CB A:GLU39 4.0 20.9 1.0
CA A:ASP38 4.1 19.8 1.0
CA A:ILE37 4.1 19.1 1.0
C A:ASP38 4.3 20.0 1.0
CA A:GLU39 4.4 20.4 1.0
O A:ASP36 4.5 17.7 1.0

Manganese binding site 3 out of 5 in 1up6

Go back to Manganese Binding Sites List in 1up6
Manganese binding site 3 out of 5 in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1420

b:42.4
occ:1.00
 O A:ILE37 2.2 20.5 1.0
MN A:MN1419 2.5 35.1 0.5
O A:HOH2136 3.1 43.9 1.0
C A:ILE37 3.2 19.5 1.0
N A:ASP38 4.0 19.2 1.0
CA A:ASP38 4.1 19.8 1.0
CA A:ILE37 4.2 19.1 1.0
CB A:ILE37 4.4 19.2 1.0
O A:HOH2135 4.7 39.5 1.0
N A:GLU39 4.8 20.3 1.0
CG1 A:ILE37 5.0 19.8 1.0

Manganese binding site 4 out of 5 in 1up6

Go back to Manganese Binding Sites List in 1up6
Manganese binding site 4 out of 5 in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1417

b:36.0
occ:0.50
 O2 C:G6P1418 2.1 20.6 0.5
O7N C:NAD1416 2.4 17.9 0.5
SG C:CYS162 2.4 28.6 1.0
O3 C:G6P1418 2.5 17.4 0.5
NE2 C:HIS192 2.5 25.6 1.0
C7N C:NAD1416 2.8 17.3 0.5
N7N C:NAD1416 3.0 14.6 0.5
C2 C:G6P1418 3.0 21.2 0.5
CE1 C:HIS192 3.1 26.8 1.0
C3 C:G6P1418 3.2 20.6 0.5
ND2 C:ASN163 3.5 24.5 1.0
CB C:CYS162 3.5 24.6 1.0
CD2 C:HIS192 3.6 25.4 1.0
N C:ASN163 3.9 22.9 1.0
CA C:CYS162 3.9 23.5 1.0
C3N C:NAD1416 4.0 17.7 0.5
ND2 C:ASN191 4.2 22.4 1.0
ND1 C:HIS192 4.2 25.8 1.0
C C:CYS162 4.4 23.4 1.0
C1 C:G6P1418 4.4 22.6 0.5
CG1 C:VAL164 4.4 23.4 1.0
ND2 C:ASN140 4.5 26.3 1.0
CG C:HIS192 4.5 24.4 1.0
CG C:ASN163 4.6 24.5 1.0
C4 C:G6P1418 4.6 21.0 0.5
OD1 C:ASN140 4.7 25.5 1.0
C4N C:NAD1416 4.7 17.4 0.5
OD1 C:ASN191 4.8 28.0 1.0
O1 C:G6P1418 4.9 24.1 0.5
C2N C:NAD1416 4.9 17.5 0.5
CG C:ASN191 4.9 21.6 1.0
N C:VAL164 5.0 22.5 1.0
CA C:ASN163 5.0 22.5 1.0

Manganese binding site 5 out of 5 in 1up6

Go back to Manganese Binding Sites List in 1up6
Manganese binding site 5 out of 5 in the Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the 6-Phospho-Beta Glucosidase From Thermotoga Maritima at 2.55 Angstrom Resolution in the Tetragonal Form with Manganese, Nad+ and Glucose-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1417

b:45.6
occ:0.50
 O7N G:NAD1416 2.4 17.2 0.5
SG G:CYS162 2.4 27.6 1.0
NE2 G:HIS192 2.4 28.6 1.0
C7N G:NAD1416 2.9 16.8 0.5
N7N G:NAD1416 3.0 16.6 0.5
CE1 G:HIS192 3.1 29.0 1.0
ND2 G:ASN163 3.3 25.1 1.0
CD2 G:HIS192 3.5 27.6 1.0
CB G:CYS162 3.7 22.9 1.0
CA G:CYS162 4.0 22.4 1.0
N G:ASN163 4.0 22.5 1.0
C3N G:NAD1416 4.1 17.5 0.5
ND2 G:ASN191 4.2 20.5 1.0
OD1 G:ASN140 4.2 25.3 1.0
ND1 G:HIS192 4.3 28.5 1.0
ND2 G:ASN140 4.3 25.1 1.0
CG1 G:VAL164 4.5 22.5 1.0
CG G:HIS192 4.5 25.0 1.0
C G:CYS162 4.5 22.5 1.0
CG G:ASN163 4.5 24.1 1.0
CG G:ASN140 4.7 23.5 1.0
C2N G:NAD1416 4.9 17.8 0.5
C4N G:NAD1416 4.9 17.4 0.5
OD1 G:ASN191 4.9 24.8 1.0

Reference:

V.L.Yip, A.Varrot, G.J.Davies, S.S.Rajan, X.Yang, J.Thompson, W.F.Anderson, S.G.Withers. An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps By A Family 4 Beta-Glycosidase From Thermotoga Maritima. J.Am.Chem.Soc. V. 126 8354 2004.
ISSN: ISSN 0002-7863
PubMed: 15237973
DOI: 10.1021/JA047632W
Page generated: Sat Oct 5 12:38:39 2024

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