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Cobalt in PDB 2bo7: Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase

Protein crystallography data

The structure of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase, PDB code: 2bo7 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) 223.61 / 2.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 406.699, 162.140, 108.431, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.4

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase (pdb code 2bo7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase, PDB code: 2bo7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 1 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1384

b:67.0
occ:1.00
O3B A:GDP1383 1.7 66.1 1.0
ND1 A:HIS217 2.0 66.1 1.0
OD2 A:ASP102 2.0 64.2 1.0
O1A A:GDP1383 2.0 63.9 1.0
CE1 A:HIS217 2.8 65.3 1.0
CG A:ASP102 2.8 63.4 1.0
OD1 A:ASP102 2.8 63.8 1.0
PB A:GDP1383 3.0 66.6 1.0
CG A:HIS217 3.2 64.3 1.0
PA A:GDP1383 3.3 63.4 1.0
O3A A:GDP1383 3.5 63.4 1.0
CB A:HIS217 3.7 63.5 1.0
O2B A:GDP1383 3.9 64.9 1.0
NE2 A:HIS217 4.0 66.0 1.0
O1B A:GDP1383 4.1 64.3 1.0
CB A:ASP102 4.2 62.7 1.0
CD2 A:HIS217 4.2 64.5 1.0
O A:ARG218 4.2 64.4 1.0
OD2 A:ASP100 4.3 65.6 1.0
O2A A:GDP1383 4.3 64.3 1.0
O5' A:GDP1383 4.4 63.9 1.0
O A:HOH2024 4.5 41.3 1.0
N A:ARG218 4.5 64.4 1.0
C5' A:GDP1383 4.5 63.8 1.0
O A:HOH2009 4.7 41.9 1.0
NH2 A:ARG218 4.7 63.7 1.0
CA A:HIS217 5.0 63.7 1.0

Cobalt binding site 2 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 2 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1384

b:67.5
occ:1.00
O3B B:GDP1383 1.8 66.0 1.0
OD2 B:ASP102 2.0 64.2 1.0
O1A B:GDP1383 2.0 64.1 1.0
ND1 B:HIS217 2.0 66.3 1.0
CG B:ASP102 2.7 63.5 1.0
OD1 B:ASP102 2.7 63.9 1.0
CE1 B:HIS217 2.8 65.4 1.0
PB B:GDP1383 3.1 66.4 1.0
CG B:HIS217 3.2 64.5 1.0
PA B:GDP1383 3.2 63.2 1.0
O3A B:GDP1383 3.5 63.5 1.0
CB B:HIS217 3.6 63.4 1.0
O2B B:GDP1383 3.8 64.9 1.0
NE2 B:HIS217 4.0 66.1 1.0
OD2 B:ASP100 4.2 65.9 1.0
CB B:ASP102 4.2 62.6 1.0
CD2 B:HIS217 4.2 64.7 1.0
O1B B:GDP1383 4.2 64.3 1.0
O2A B:GDP1383 4.2 64.6 1.0
O B:ARG218 4.3 64.6 1.0
O5' B:GDP1383 4.3 63.7 1.0
C5' B:GDP1383 4.5 63.9 1.0
N B:ARG218 4.5 64.2 1.0
NH2 B:ARG218 4.7 63.5 1.0
CA B:HIS217 5.0 63.7 1.0
CG B:ASP100 5.0 65.1 1.0
CE B:LYS215 5.0 64.5 1.0

Cobalt binding site 3 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 3 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1384

b:67.7
occ:1.00
OD2 C:ASP102 1.9 64.5 1.0
O3B C:GDP1383 1.9 66.0 1.0
O1A C:GDP1383 2.0 63.6 1.0
ND1 C:HIS217 2.0 66.2 1.0
CG C:ASP102 2.6 63.5 1.0
OD1 C:ASP102 2.7 63.7 1.0
CE1 C:HIS217 2.9 65.5 1.0
CG C:HIS217 3.1 64.5 1.0
PB C:GDP1383 3.2 66.3 1.0
PA C:GDP1383 3.2 63.3 1.0
CB C:HIS217 3.6 63.4 1.0
O3A C:GDP1383 3.6 63.6 1.0
O2B C:GDP1383 3.9 64.5 1.0
CB C:ASP102 4.1 62.5 1.0
NE2 C:HIS217 4.1 66.0 1.0
CD2 C:HIS217 4.2 64.7 1.0
O2A C:GDP1383 4.2 64.5 1.0
O C:ARG218 4.2 64.8 1.0
O1B C:GDP1383 4.3 64.5 1.0
OD2 C:ASP100 4.3 65.5 1.0
O5' C:GDP1383 4.4 63.7 1.0
N C:ARG218 4.5 64.3 1.0
C5' C:GDP1383 4.5 63.9 1.0
NH2 C:ARG218 4.7 63.8 1.0
CA C:HIS217 4.9 63.8 1.0
C C:HIS217 5.0 64.0 1.0

Cobalt binding site 4 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 4 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1384

b:68.6
occ:1.00
O3B D:GDP1383 1.9 65.9 1.0
O1A D:GDP1383 2.0 63.9 1.0
ND1 D:HIS217 2.0 66.3 1.0
OD2 D:ASP102 2.0 64.4 1.0
CE1 D:HIS217 2.8 65.6 1.0
CG D:ASP102 2.9 63.4 1.0
OD1 D:ASP102 2.9 63.5 1.0
PB D:GDP1383 3.1 66.4 1.0
CG D:HIS217 3.2 64.5 1.0
PA D:GDP1383 3.2 63.2 1.0
O3A D:GDP1383 3.5 63.7 1.0
O2B D:GDP1383 3.7 64.7 1.0
CB D:HIS217 3.8 63.5 1.0
NE2 D:HIS217 4.0 65.9 1.0
O D:ARG218 4.1 64.8 1.0
O2A D:GDP1383 4.1 64.3 1.0
CD2 D:HIS217 4.2 64.8 1.0
CB D:ASP102 4.2 62.6 1.0
O1B D:GDP1383 4.3 64.1 1.0
O5' D:GDP1383 4.4 63.6 1.0
OD2 D:ASP100 4.4 65.7 1.0
N D:ARG218 4.5 64.2 1.0
NH2 D:ARG218 4.6 63.8 1.0
C5' D:GDP1383 4.6 63.9 1.0
CA D:HIS217 5.0 63.7 1.0

Cobalt binding site 5 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 5 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1384

b:67.0
occ:1.00
O3B E:GDP1383 1.8 66.2 1.0
ND1 E:HIS217 2.0 66.2 1.0
OD2 E:ASP102 2.1 64.3 1.0
O1A E:GDP1383 2.1 63.8 1.0
OD1 E:ASP102 2.7 63.8 1.0
CG E:ASP102 2.7 63.6 1.0
CE1 E:HIS217 2.8 65.5 1.0
CG E:HIS217 3.1 64.4 1.0
PB E:GDP1383 3.2 66.0 1.0
PA E:GDP1383 3.3 63.0 1.0
CB E:HIS217 3.6 63.5 1.0
O3A E:GDP1383 3.6 63.5 1.0
O2B E:GDP1383 3.9 64.5 1.0
NE2 E:HIS217 4.0 66.0 1.0
CB E:ASP102 4.2 62.5 1.0
CD2 E:HIS217 4.2 64.7 1.0
OD2 E:ASP100 4.2 65.7 1.0
O1B E:GDP1383 4.3 64.1 1.0
O2A E:GDP1383 4.3 64.0 1.0
O E:ARG218 4.3 64.5 1.0
O5' E:GDP1383 4.4 63.5 1.0
N E:ARG218 4.5 64.2 1.0
C5' E:GDP1383 4.5 63.8 1.0
NH2 E:ARG218 4.7 63.7 1.0
CE E:LYS215 4.9 64.5 1.0
CA E:HIS217 4.9 63.8 1.0

Cobalt binding site 6 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 6 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co1384

b:67.0
occ:1.00
O3B F:GDP1383 1.8 65.7 1.0
OD2 F:ASP102 1.9 64.1 1.0
ND1 F:HIS217 2.1 66.1 1.0
O1A F:GDP1383 2.1 63.9 1.0
OD1 F:ASP102 2.6 63.7 1.0
CG F:ASP102 2.6 63.5 1.0
CE1 F:HIS217 2.9 65.3 1.0
PB F:GDP1383 3.1 65.8 1.0
CG F:HIS217 3.2 64.5 1.0
PA F:GDP1383 3.3 63.4 1.0
CB F:HIS217 3.6 63.5 1.0
O3A F:GDP1383 3.6 63.6 1.0
O2B F:GDP1383 3.9 64.4 1.0
CB F:ASP102 4.1 62.8 1.0
NE2 F:HIS217 4.1 65.8 1.0
OD2 F:ASP100 4.1 65.5 1.0
O1B F:GDP1383 4.2 64.1 1.0
CD2 F:HIS217 4.2 64.6 1.0
O2A F:GDP1383 4.3 64.1 1.0
O5' F:GDP1383 4.4 63.7 1.0
O F:ARG218 4.4 64.5 1.0
C5' F:GDP1383 4.5 63.8 1.0
N F:ARG218 4.6 64.2 1.0
NH2 F:ARG218 4.7 63.7 1.0
CE F:LYS215 4.8 64.3 1.0
CG F:ASP100 4.8 64.8 1.0
CB F:ASP100 4.8 63.4 1.0
NZ F:LYS215 4.9 64.9 1.0
CA F:HIS217 4.9 63.8 1.0

Cobalt binding site 7 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 7 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1384

b:66.9
occ:1.00
OD2 G:ASP102 1.9 64.2 1.0
ND1 G:HIS217 1.9 66.2 1.0
O3B G:GDP1383 1.9 65.8 1.0
O1A G:GDP1383 2.1 64.2 1.0
CE1 G:HIS217 2.7 65.5 1.0
CG G:ASP102 2.7 63.5 1.0
OD1 G:ASP102 2.8 63.7 1.0
CG G:HIS217 3.1 64.5 1.0
PB G:GDP1383 3.2 65.9 1.0
PA G:GDP1383 3.4 63.5 1.0
CB G:HIS217 3.6 63.6 1.0
O3A G:GDP1383 3.7 63.7 1.0
O2B G:GDP1383 3.8 64.4 1.0
NE2 G:HIS217 3.9 66.0 1.0
O G:ARG218 4.1 64.7 1.0
CD2 G:HIS217 4.1 64.6 1.0
CB G:ASP102 4.1 62.8 1.0
O2A G:GDP1383 4.2 64.2 1.0
O1B G:GDP1383 4.3 64.1 1.0
N G:ARG218 4.4 64.2 1.0
OD2 G:ASP100 4.4 65.4 1.0
O5' G:GDP1383 4.5 63.7 1.0
NH2 G:ARG218 4.6 63.9 1.0
C5' G:GDP1383 4.7 63.8 1.0
CA G:HIS217 4.9 63.8 1.0
C G:HIS217 4.9 64.0 1.0
C G:ARG218 5.0 64.6 1.0

Cobalt binding site 8 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 8 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co1384

b:67.7
occ:1.00
O3B H:GDP1383 1.9 65.8 1.0
ND1 H:HIS217 2.0 66.2 1.0
OD2 H:ASP102 2.0 64.2 1.0
O1A H:GDP1383 2.1 63.9 1.0
CE1 H:HIS217 2.7 65.4 1.0
CG H:ASP102 2.9 63.4 1.0
OD1 H:ASP102 3.0 63.5 1.0
PB H:GDP1383 3.1 65.9 1.0
CG H:HIS217 3.2 64.4 1.0
PA H:GDP1383 3.2 63.3 1.0
O3A H:GDP1383 3.5 63.6 1.0
O2B H:GDP1383 3.7 64.6 1.0
CB H:HIS217 3.7 63.6 1.0
NE2 H:HIS217 3.9 65.8 1.0
O H:ARG218 4.0 64.5 1.0
CD2 H:HIS217 4.1 64.6 1.0
O2A H:GDP1383 4.1 64.2 1.0
CB H:ASP102 4.2 62.7 1.0
O1B H:GDP1383 4.3 64.1 1.0
N H:ARG218 4.4 64.3 1.0
O5' H:GDP1383 4.5 63.9 1.0
NH2 H:ARG218 4.5 63.7 1.0
OD2 H:ASP100 4.6 65.3 1.0
C5' H:GDP1383 4.7 63.8 1.0
CA H:HIS217 5.0 63.8 1.0
C H:HIS217 5.0 64.1 1.0
C H:ARG218 5.0 64.5 1.0

Cobalt binding site 9 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 9 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co1384

b:67.4
occ:1.00
O3B I:GDP1383 1.7 66.1 1.0
ND1 I:HIS217 2.0 66.4 1.0
OD2 I:ASP102 2.1 64.2 1.0
O1A I:GDP1383 2.1 64.2 1.0
CE1 I:HIS217 2.7 65.4 1.0
CG I:ASP102 2.9 63.4 1.0
PB I:GDP1383 2.9 66.3 1.0
OD1 I:ASP102 3.0 63.6 1.0
PA I:GDP1383 3.3 63.5 1.0
CG I:HIS217 3.3 64.5 1.0
O3A I:GDP1383 3.5 63.7 1.0
O2B I:GDP1383 3.6 64.6 1.0
O I:HOH2008 3.6 56.2 1.0
CB I:HIS217 3.8 63.5 1.0
NE2 I:HIS217 4.0 65.8 1.0
O1B I:GDP1383 4.1 64.1 1.0
O2A I:GDP1383 4.2 64.1 1.0
CD2 I:HIS217 4.2 64.6 1.0
O I:ARG218 4.2 64.4 1.0
CB I:ASP102 4.3 62.7 1.0
OD2 I:ASP100 4.4 65.7 1.0
O5' I:GDP1383 4.4 63.7 1.0
C5' I:GDP1383 4.6 63.8 1.0
NH2 I:ARG218 4.7 63.7 1.0
N I:ARG218 4.7 64.3 1.0

Cobalt binding site 10 out of 10 in 2bo7

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Cobalt 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 Cobalt with other atoms in the Co binding site number 10 of Dissection of Mannosylglycerate Synthase: An Archetypal Mannosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Co1384

b:67.7
occ:1.00
OD2 J:ASP102 1.8 64.3 1.0
ND1 J:HIS217 1.9 66.2 1.0
O1A J:GDP1383 2.1 63.9 1.0
O3B J:GDP1383 2.1 66.0 1.0
CG J:ASP102 2.7 63.5 1.0
CE1 J:HIS217 2.7 65.5 1.0
OD1 J:ASP102 3.0 63.6 1.0
CG J:HIS217 3.1 64.5 1.0
PB J:GDP1383 3.3 66.2 1.0
PA J:GDP1383 3.3 63.3 1.0
CB J:HIS217 3.6 63.5 1.0
O3A J:GDP1383 3.6 63.6 1.0
O2B J:GDP1383 3.8 64.6 1.0
O J:ARG218 3.9 64.7 1.0
NE2 J:HIS217 3.9 65.9 1.0
CB J:ASP102 4.1 62.8 1.0
CD2 J:HIS217 4.1 64.7 1.0
O2A J:GDP1383 4.1 64.3 1.0
N J:ARG218 4.3 64.2 1.0
O1B J:GDP1383 4.5 64.2 1.0
NH2 J:ARG218 4.5 63.7 1.0
O5' J:GDP1383 4.5 63.8 1.0
OD2 J:ASP100 4.7 65.7 1.0
C5' J:GDP1383 4.8 63.9 1.0
C J:ARG218 4.8 64.6 1.0
CA J:HIS217 4.8 63.8 1.0
C J:HIS217 4.9 64.1 1.0
CA J:ARG218 4.9 64.2 1.0
CB J:ARG218 4.9 64.0 1.0
CZ J:ARG218 5.0 64.1 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: Tue Jul 30 14:58:18 2024

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