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Calcium in PDB 3vu1: Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii

Enzymatic activity of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii

All present enzymatic activity of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii:
2.4.1.119;

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii, PDB code: 3vu1 was solved by J.Nyirenda, S.Matsumoto, T.Saitoh, N.Maita, N.N.Noda, F.Inagaki, D.Kohda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.467, 94.844, 186.345, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.5

Other elements in 3vu1:

The structure of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii (pdb code 3vu1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii, PDB code: 3vu1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vu1

Go back to Calcium Binding Sites List in 3vu1
Calcium binding site 1 out of 2 in the Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:49.8
occ:1.00
 O A:ALA765 2.3 28.1 1.0
O A:HIS799 2.4 33.4 1.0
OE2 A:GLU556 2.5 45.9 1.0
OE1 A:GLU556 2.6 45.5 1.0
CD A:GLU556 2.9 45.4 1.0
OE1 A:GLU802 2.9 37.9 1.0
OE2 A:GLU802 3.2 42.4 1.0
C A:ALA765 3.4 28.4 1.0
CD A:GLU802 3.4 42.0 1.0
C A:HIS799 3.6 33.2 1.0
N A:ALA765 4.0 28.2 1.0
CA A:ALA765 4.3 27.6 1.0
N A:PHE766 4.3 27.4 1.0
CA A:PHE766 4.3 30.0 1.0
CG A:GLU556 4.3 41.5 1.0
CA A:HIS799 4.4 35.4 1.0
CB A:HIS799 4.5 37.1 1.0
ND1 A:HIS799 4.5 37.8 1.0
CE A:LYS711 4.6 42.9 1.0
N A:LEU800 4.6 38.0 1.0
OG A:SER764 4.6 34.7 1.0
CA A:LEU800 4.8 42.4 1.0
CB A:ALA765 4.9 26.1 1.0
C A:SER764 4.9 30.0 1.0
CG A:GLU802 4.9 44.8 1.0
N A:GLY767 5.0 34.5 1.0
CG A:HIS799 5.0 39.3 1.0

Calcium binding site 2 out of 2 in 3vu1

Go back to Calcium Binding Sites List in 3vu1
Calcium binding site 2 out of 2 in the Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase (Phaglb-L, O74088_PYRHO) From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:65.9
occ:1.00
 O B:HIS799 2.5 35.3 1.0
O B:ALA765 2.5 34.4 1.0
OE2 B:GLU802 2.6 37.5 1.0
OE2 B:GLU556 2.6 49.3 1.0
OE1 B:GLU556 2.7 40.4 1.0
CD B:GLU556 3.0 43.9 1.0
CD B:GLU802 3.4 41.4 1.0
OE1 B:GLU802 3.4 45.0 1.0
C B:ALA765 3.5 34.7 1.0
C B:HIS799 3.7 34.9 1.0
N B:ALA765 3.9 30.3 1.0
NZ B:LYS711 4.2 52.7 1.0
OG B:SER764 4.3 41.3 1.0
CA B:ALA765 4.3 33.0 1.0
N B:PHE766 4.3 34.1 1.0
CA B:HIS799 4.3 35.4 1.0
CA B:PHE766 4.4 34.2 1.0
CB B:HIS799 4.4 36.2 1.0
CG B:GLU556 4.5 41.7 1.0
N B:LEU800 4.7 33.1 1.0
CG B:GLU802 4.7 41.0 1.0
C B:SER764 4.8 31.9 1.0
CB B:ALA765 4.8 31.3 1.0
CD2 B:HIS799 4.9 35.6 1.0
CA B:LEU800 4.9 37.7 1.0
CE B:LYS711 4.9 46.3 1.0
CD2 B:LEU800 4.9 35.0 1.0
CA B:SER764 4.9 33.6 1.0
N B:GLY767 5.0 32.1 1.0

Reference:

J.Nyirenda, S.Matsumoto, T.Saitoh, N.Maita, N.N.Noda, F.Inagaki, D.Kohda. Crystallographic and uc(Nmr) Evidence For Flexibility in Oligosaccharyltransferases and Its Catalytic Significance Structure V. 21 32 2013.
ISSN: ISSN 0969-2126
PubMed: 23177926
DOI: 10.1016/J.STR.2012.10.011
Page generated: Sat Jul 13 20:52:27 2024

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