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Manganese in PDB 2bo8: Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase

Protein crystallography data

The structure of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase, PDB code: 2bo8 was solved by J.Flint, E.Taylor, M.Yang, D.N.Bolam, L.E.Tailford, C.Martinez-Fleites, E.J.Dodson, B.G.Davis, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.12 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 405.094, 161.430, 108.708, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.6

Other elements in 2bo8:

The structure of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase (pdb code 2bo8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase, PDB code: 2bo8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 2bo8

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Manganese binding site 1 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:80.4
occ:1.00
 O2A A:GDX400 2.0 65.8 1.0
OD2 A:ASP102 2.2 61.9 1.0
O A:HOH2078 2.4 30.1 1.0
ND1 A:HIS217 2.6 84.6 1.0
O3B A:GDX400 2.7 66.8 1.0
O A:HOH2077 2.7 41.4 1.0
CG A:ASP102 3.1 60.9 1.0
PA A:GDX400 3.1 63.8 1.0
O3A A:GDX400 3.2 60.4 1.0
CE1 A:HIS217 3.2 83.9 1.0
OD1 A:ASP102 3.2 60.8 1.0
PB A:GDX400 3.3 63.0 1.0
CG A:HIS217 3.4 82.5 1.0
CB A:HIS217 3.8 81.6 1.0
O2B A:GDX400 3.9 63.5 1.0
O5D A:GDX400 4.1 63.4 1.0
O1A A:GDX400 4.1 63.4 1.0
NE2 A:HIS217 4.1 84.0 1.0
CD2 A:HIS217 4.2 82.9 1.0
C5D A:GDX400 4.3 62.1 1.0
OD2 A:ASP100 4.4 63.4 1.0
NH2 A:ARG218 4.4 82.3 1.0
N A:ARG218 4.5 83.1 1.0
CB A:ASP102 4.6 60.5 1.0
CB A:ARG218 4.7 83.3 1.0
O A:ARG218 4.8 83.6 1.0
NH1 A:ARG218 4.8 82.7 1.0
O1B A:GDX400 4.8 62.4 1.0
NZ A:LYS215 4.8 79.5 1.0
CZ A:ARG218 4.8 82.6 1.0
CE A:LYS215 4.8 77.0 1.0

Manganese binding site 2 out of 10 in 2bo8

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Manganese binding site 2 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:82.5
occ:1.00
 O2A B:GDX400 2.0 65.2 1.0
OD2 B:ASP102 2.4 62.6 1.0
ND1 B:HIS217 2.5 84.5 1.0
O3B B:GDX400 2.7 66.7 1.0
PA B:GDX400 2.9 63.3 1.0
O3A B:GDX400 3.0 60.9 1.0
CE1 B:HIS217 3.2 83.7 1.0
CG B:ASP102 3.2 60.8 1.0
OD1 B:ASP102 3.2 60.4 1.0
PB B:GDX400 3.2 61.9 1.0
CG B:HIS217 3.4 83.0 1.0
CB B:HIS217 3.8 81.9 1.0
O2B B:GDX400 3.9 63.4 1.0
O1A B:GDX400 3.9 63.5 1.0
O5D B:GDX400 4.0 64.1 1.0
NE2 B:HIS217 4.2 84.2 1.0
CD2 B:HIS217 4.3 83.3 1.0
C5D B:GDX400 4.4 61.6 1.0
OD2 B:ASP100 4.4 63.6 1.0
NH2 B:ARG218 4.4 82.4 1.0
N B:ARG218 4.5 83.1 1.0
CB B:ASP102 4.6 60.2 1.0
O1B B:GDX400 4.7 62.9 1.0
CB B:ARG218 4.7 83.5 1.0
CE B:LYS215 4.8 77.8 1.0
NH1 B:ARG218 4.8 82.7 1.0
O B:ARG218 4.8 83.5 1.0
CZ B:ARG218 4.8 82.5 1.0
NZ B:LYS215 4.9 79.6 1.0

Manganese binding site 3 out of 10 in 2bo8

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Manganese binding site 3 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:80.3
occ:1.00
 O2A C:GDX400 2.0 65.4 1.0
OD2 C:ASP102 2.3 62.5 1.0
ND1 C:HIS217 2.5 84.4 1.0
O C:HOH2038 2.6 68.0 1.0
O3B C:GDX400 2.7 66.4 1.0
PA C:GDX400 3.1 63.3 1.0
CE1 C:HIS217 3.1 83.8 1.0
CG C:ASP102 3.2 61.2 1.0
O3A C:GDX400 3.3 61.5 1.0
PB C:GDX400 3.3 63.2 1.0
OD1 C:ASP102 3.3 60.6 1.0
CG C:HIS217 3.3 82.8 1.0
CB C:HIS217 3.8 81.8 1.0
O2B C:GDX400 3.8 63.6 1.0
O1A C:GDX400 4.0 63.4 1.0
NE2 C:HIS217 4.1 83.6 1.0
O5D C:GDX400 4.2 63.7 1.0
CD2 C:HIS217 4.2 82.9 1.0
N C:ARG218 4.3 82.9 1.0
NH2 C:ARG218 4.4 82.1 1.0
OD2 C:ASP100 4.4 62.8 1.0
C5D C:GDX400 4.5 62.5 1.0
O C:ARG218 4.5 83.4 1.0
CB C:ARG218 4.6 83.2 1.0
CB C:ASP102 4.6 60.7 1.0
NH1 C:ARG218 4.6 82.2 1.0
CZ C:ARG218 4.7 82.3 1.0
O1B C:GDX400 4.8 62.8 1.0
CE C:LYS215 4.8 77.2 1.0
OH C:TYR220 4.9 82.2 1.0
NZ C:LYS215 4.9 79.1 1.0
CA C:ARG218 4.9 83.3 1.0
C C:HIS217 5.0 82.4 1.0
CA C:HIS217 5.0 81.9 1.0

Manganese binding site 4 out of 10 in 2bo8

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Manganese binding site 4 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn500

b:80.7
occ:1.00
 O2A D:GDX400 1.9 65.2 1.0
OD2 D:ASP102 2.5 62.4 1.0
ND1 D:HIS217 2.5 84.5 1.0
O3B D:GDX400 2.5 66.4 1.0
PA D:GDX400 3.1 64.3 1.0
CE1 D:HIS217 3.1 83.7 1.0
O3A D:GDX400 3.2 61.2 1.0
PB D:GDX400 3.2 62.6 1.0
CG D:ASP102 3.3 61.2 1.0
CG D:HIS217 3.4 82.8 1.0
OD1 D:ASP102 3.4 60.8 1.0
CB D:HIS217 3.9 81.8 1.0
O2B D:GDX400 3.9 63.3 1.0
NE2 D:HIS217 4.1 83.8 1.0
O1A D:GDX400 4.1 63.3 1.0
O5D D:GDX400 4.1 63.5 1.0
OD2 D:ASP100 4.2 62.8 1.0
CD2 D:HIS217 4.2 83.1 1.0
C5D D:GDX400 4.3 62.0 1.0
NH2 D:ARG218 4.5 82.1 1.0
N D:ARG218 4.6 83.0 1.0
O1B D:GDX400 4.6 62.4 1.0
O D:ARG218 4.7 83.5 1.0
CB D:ASP102 4.7 60.9 1.0
CE D:LYS215 4.7 77.5 1.0
CB D:ARG218 4.8 83.2 1.0
NH1 D:ARG218 4.8 82.5 1.0
NZ D:LYS215 4.8 79.0 1.0
OH D:TYR220 4.8 82.0 1.0
CZ D:ARG218 4.9 82.5 1.0

Manganese binding site 5 out of 10 in 2bo8

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Manganese binding site 5 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn500

b:79.6
occ:1.00
 O E:HOH2034 2.1 51.6 1.0
ND1 E:HIS217 2.2 84.4 1.0
O2A E:GDX400 2.2 65.3 1.0
OD2 E:ASP102 2.4 62.5 1.0
O3B E:GDX400 2.4 66.8 1.0
CE1 E:HIS217 2.9 83.7 1.0
CG E:HIS217 3.2 82.6 1.0
PB E:GDX400 3.3 61.6 1.0
CG E:ASP102 3.3 61.0 1.0
PA E:GDX400 3.4 63.3 1.0
OD1 E:ASP102 3.5 60.5 1.0
O3A E:GDX400 3.5 60.8 1.0
CB E:HIS217 3.7 81.5 1.0
O2B E:GDX400 3.8 62.8 1.0
NE2 E:HIS217 4.0 83.5 1.0
CD2 E:HIS217 4.1 82.7 1.0
N E:ARG218 4.3 83.0 1.0
O1A E:GDX400 4.3 63.4 1.0
O E:ARG218 4.3 83.2 1.0
O5D E:GDX400 4.5 63.3 1.0
OD2 E:ASP100 4.5 62.9 1.0
CB E:ARG218 4.5 83.0 1.0
NH2 E:ARG218 4.6 82.0 1.0
NH1 E:ARG218 4.7 82.6 1.0
C5D E:GDX400 4.7 62.0 1.0
O1B E:GDX400 4.7 62.4 1.0
CB E:ASP102 4.7 60.7 1.0
OH E:TYR220 4.8 82.0 1.0
C E:HIS217 4.8 82.3 1.0
CA E:ARG218 4.8 83.0 1.0
CE E:LYS215 4.8 77.0 1.0
CA E:HIS217 4.9 81.9 1.0
CZ E:ARG218 4.9 82.2 1.0
NZ E:LYS215 5.0 79.4 1.0

Manganese binding site 6 out of 10 in 2bo8

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Manganese binding site 6 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn500

b:80.3
occ:1.00
 O2A F:GDX400 1.9 64.8 1.0
OD2 F:ASP102 2.3 62.5 1.0
ND1 F:HIS217 2.4 84.1 1.0
O3B F:GDX400 2.6 66.2 1.0
PA F:GDX400 3.1 63.1 1.0
CE1 F:HIS217 3.1 83.7 1.0
CG F:ASP102 3.2 61.2 1.0
OD1 F:ASP102 3.3 60.8 1.0
PB F:GDX400 3.3 63.2 1.0
O3A F:GDX400 3.3 61.5 1.0
CG F:HIS217 3.3 82.7 1.0
CB F:HIS217 3.8 81.9 1.0
O2B F:GDX400 3.9 63.3 1.0
O1A F:GDX400 4.1 63.5 1.0
NE2 F:HIS217 4.1 83.6 1.0
O5D F:GDX400 4.2 63.3 1.0
CD2 F:HIS217 4.2 82.9 1.0
C5D F:GDX400 4.4 62.4 1.0
OD2 F:ASP100 4.4 62.7 1.0
N F:ARG218 4.5 82.8 1.0
NH2 F:ARG218 4.5 82.1 1.0
O F:ARG218 4.6 83.4 1.0
CB F:ASP102 4.6 61.0 1.0
CB F:ARG218 4.7 83.2 1.0
NH1 F:ARG218 4.7 82.4 1.0
O1B F:GDX400 4.8 62.5 1.0
CZ F:ARG218 4.8 82.4 1.0
OH F:TYR220 4.8 82.3 1.0
CE F:LYS215 4.8 77.4 1.0
NZ F:LYS215 4.9 79.2 1.0

Manganese binding site 7 out of 10 in 2bo8

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Manganese binding site 7 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn500

b:79.9
occ:1.00
 O2A G:GDX400 2.0 65.2 1.0
OD2 G:ASP102 2.2 62.4 1.0
ND1 G:HIS217 2.4 84.4 1.0
O3B G:GDX400 2.6 66.5 1.0
CG G:ASP102 3.0 61.3 1.0
OD1 G:ASP102 3.1 61.1 1.0
CE1 G:HIS217 3.1 83.8 1.0
PA G:GDX400 3.2 64.2 1.0
CG G:HIS217 3.3 82.8 1.0
PB G:GDX400 3.4 63.5 1.0
O3A G:GDX400 3.4 61.7 1.0
CB G:HIS217 3.7 81.9 1.0
O2B G:GDX400 4.0 63.2 1.0
NE2 G:HIS217 4.1 83.7 1.0
O1A G:GDX400 4.2 63.5 1.0
CD2 G:HIS217 4.2 83.0 1.0
N G:ARG218 4.3 82.8 1.0
O5D G:GDX400 4.4 63.5 1.0
OD2 G:ASP100 4.4 63.0 1.0
NH2 G:ARG218 4.4 82.2 1.0
CB G:ASP102 4.5 61.0 1.0
CB G:ARG218 4.5 83.1 1.0
C5D G:GDX400 4.5 62.6 1.0
O G:ARG218 4.5 83.6 1.0
NH1 G:ARG218 4.7 82.5 1.0
CZ G:ARG218 4.8 82.5 1.0
CE G:LYS215 4.9 77.6 1.0
CA G:ARG218 4.9 83.2 1.0
O1B G:GDX400 4.9 63.2 1.0
C G:HIS217 4.9 82.4 1.0
OH G:TYR220 4.9 82.3 1.0
CA G:HIS217 4.9 81.8 1.0
NZ G:LYS215 5.0 79.2 1.0

Manganese binding site 8 out of 10 in 2bo8

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Manganese binding site 8 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn500

b:80.0
occ:1.00
 ND1 H:HIS217 2.2 84.4 1.0
O2A H:GDX400 2.3 64.9 1.0
OD2 H:ASP102 2.4 62.5 1.0
O3B H:GDX400 2.5 66.2 1.0
CE1 H:HIS217 2.9 83.9 1.0
CG H:HIS217 3.2 82.7 1.0
CG H:ASP102 3.2 61.2 1.0
OD1 H:ASP102 3.3 60.5 1.0
PB H:GDX400 3.3 62.8 1.0
PA H:GDX400 3.4 63.0 1.0
O3A H:GDX400 3.4 61.4 1.0
CB H:HIS217 3.7 81.8 1.0
O2B H:GDX400 3.9 63.5 1.0
NE2 H:HIS217 4.0 83.8 1.0
CD2 H:HIS217 4.1 82.7 1.0
N H:ARG218 4.3 82.7 1.0
O H:ARG218 4.4 83.3 1.0
O1A H:GDX400 4.4 63.1 1.0
O5D H:GDX400 4.4 63.6 1.0
OD2 H:ASP100 4.6 62.4 1.0
CB H:ARG218 4.6 83.1 1.0
C5D H:GDX400 4.6 62.4 1.0
NH2 H:ARG218 4.7 82.1 1.0
NZ H:LYS215 4.7 79.5 1.0
CE H:LYS215 4.7 77.3 1.0
CB H:ASP102 4.7 60.8 1.0
OH H:TYR220 4.8 82.3 1.0
NH1 H:ARG218 4.8 82.2 1.0
O1B H:GDX400 4.8 62.9 1.0
C H:HIS217 4.8 82.4 1.0
CA H:HIS217 4.9 81.9 1.0
CA H:ARG218 4.9 83.2 1.0
CZ H:ARG218 4.9 82.3 1.0

Manganese binding site 9 out of 10 in 2bo8

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Manganese binding site 9 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn500

b:80.8
occ:1.00
 O2A I:GDX400 2.2 65.0 1.0
ND1 I:HIS217 2.3 84.4 1.0
OD2 I:ASP102 2.4 62.2 1.0
O3B I:GDX400 2.6 66.2 1.0
CE1 I:HIS217 3.0 83.7 1.0
CG I:ASP102 3.2 61.0 1.0
OD1 I:ASP102 3.2 61.0 1.0
CG I:HIS217 3.2 82.8 1.0
PA I:GDX400 3.3 63.2 1.0
PB I:GDX400 3.3 63.0 1.0
O3A I:GDX400 3.4 61.3 1.0
CB I:HIS217 3.7 81.7 1.0
O2B I:GDX400 4.0 63.2 1.0
NE2 I:HIS217 4.0 83.6 1.0
CD2 I:HIS217 4.1 82.9 1.0
O1A I:GDX400 4.3 63.4 1.0
N I:ARG218 4.4 82.8 1.0
OD2 I:ASP100 4.4 62.7 1.0
O5D I:GDX400 4.4 63.2 1.0
O I:ARG218 4.5 83.2 1.0
C5D I:GDX400 4.6 62.4 1.0
NH2 I:ARG218 4.6 82.0 1.0
CB I:ASP102 4.6 60.8 1.0
CB I:ARG218 4.6 83.3 1.0
CE I:LYS215 4.8 77.3 1.0
O1B I:GDX400 4.8 62.9 1.0
OH I:TYR220 4.8 82.2 1.0
NH1 I:ARG218 4.8 82.4 1.0
NZ I:LYS215 4.9 79.0 1.0
CZ I:ARG218 4.9 82.4 1.0
C I:HIS217 4.9 82.3 1.0
CA I:HIS217 4.9 81.8 1.0
CA I:ARG218 5.0 83.2 1.0

Manganese binding site 10 out of 10 in 2bo8

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Manganese binding site 10 out of 10 in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn500

b:80.8
occ:1.00
 O2A J:GDX400 1.9 64.9 1.0
OD2 J:ASP102 2.4 62.5 1.0
ND1 J:HIS217 2.5 84.2 1.0
O3B J:GDX400 2.6 66.5 1.0
PA J:GDX400 3.0 63.6 1.0
CG J:ASP102 3.2 61.1 1.0
CE1 J:HIS217 3.2 83.7 1.0
OD1 J:ASP102 3.2 60.6 1.0
O3A J:GDX400 3.3 61.5 1.0
PB J:GDX400 3.3 62.6 1.0
CG J:HIS217 3.4 82.7 1.0
CB J:HIS217 3.8 81.8 1.0
O2B J:GDX400 3.9 63.4 1.0
O1A J:GDX400 4.0 63.5 1.0
O5D J:GDX400 4.1 63.2 1.0
NE2 J:HIS217 4.2 83.7 1.0
OD2 J:ASP100 4.3 62.5 1.0
CD2 J:HIS217 4.3 82.9 1.0
C5D J:GDX400 4.4 62.2 1.0
N J:ARG218 4.4 82.8 1.0
NH2 J:ARG218 4.5 82.1 1.0
O J:ARG218 4.6 83.3 1.0
CB J:ASP102 4.6 60.9 1.0
CB J:ARG218 4.7 83.1 1.0
NH1 J:ARG218 4.8 82.4 1.0
O1B J:GDX400 4.8 62.8 1.0
CZ J:ARG218 4.8 82.4 1.0
CE J:LYS215 4.8 77.4 1.0
NZ J:LYS215 4.9 79.1 1.0
OH J:TYR220 4.9 82.2 1.0

Reference:

J.Flint, E.Taylor, M.Yang, D.N.Bolam, L.E.Tailford, C.Martinez-Fleites, E.J.Dodson, B.G.Davis, H.J.Gilbert, G.J.Davies. Structural Dissection and High-Throughput Screening of Mannosylglycerate Synthase. Nat. Struct. Mol. Biol. V. 12 608 2005.
ISSN: ISSN 1545-9993
PubMed: 15951819
DOI: 10.1038/NSMB950
Page generated: Sat Oct 5 13:34:57 2024

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