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Cobalt in PDB 1y8z: Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution

Enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution

All present enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution:
2.4.1.26;

Protein crystallography data

The structure of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution, PDB code: 1y8z was solved by L.Lariviere, N.Sommer, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.263, 114.655, 86.143, 90.00, 89.49, 90.00
R / Rfree (%) 20.8 / 25

Other elements in 1y8z:

The structure of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution (pdb code 1y8z). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution, PDB code: 1y8z:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 1y8z

Go back to Cobalt Binding Sites List in 1y8z
Cobalt binding site 1 out of 5 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co3003

b:59.4
occ:1.00
 CO D:NCO3003 0.0 59.4 1.0
N4 D:NCO3003 2.0 58.6 1.0
N3 D:NCO3003 2.0 58.9 1.0
N1 D:NCO3003 2.0 59.6 1.0
N6 D:NCO3003 2.0 59.1 1.0
N5 D:NCO3003 2.0 58.8 1.0
N2 D:NCO3003 2.0 59.2 1.0
OP1 D:DG9 4.3 57.0 1.0

Cobalt binding site 2 out of 5 in 1y8z

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Cobalt binding site 2 out of 5 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co3001

b:44.1
occ:1.00
 CO A:NCO3001 0.0 44.1 1.0
N6 A:NCO3001 2.0 44.9 1.0
N2 A:NCO3001 2.0 43.6 1.0
N3 A:NCO3001 2.0 44.9 1.0
N5 A:NCO3001 2.0 45.0 1.0
N4 A:NCO3001 2.0 44.9 1.0
N1 A:NCO3001 2.0 43.9 1.0
O A:ARG1132 4.0 26.9 1.0
O A:ALA1134 4.3 23.7 1.0
O A:HOH336 4.4 41.1 1.0
OD2 A:ASP1135 4.5 26.7 1.0
O A:HOH420 4.7 36.2 1.0
O A:ARG1133 5.0 22.3 1.0

Cobalt binding site 3 out of 5 in 1y8z

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Cobalt binding site 3 out of 5 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co3005

b:46.5
occ:0.50
 CO A:NCO3005 0.0 46.5 0.5
N3 A:NCO3005 2.0 45.8 0.5
N6 A:NCO3005 2.0 45.3 0.5
N4 A:NCO3005 2.0 46.0 0.5
N1 A:NCO3005 2.0 45.5 0.5
N2 A:NCO3005 2.0 45.5 0.5
N5 A:NCO3005 2.0 45.6 0.5
O A:VAL1088 4.0 32.1 1.0
O A:THR1086 4.0 35.9 1.0
OE2 A:GLU1090 4.1 47.4 1.0

Cobalt binding site 4 out of 5 in 1y8z

Go back to Cobalt Binding Sites List in 1y8z
Cobalt binding site 4 out of 5 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3002

b:44.8
occ:1.00
 CO B:NCO3002 0.0 44.8 1.0
N1 B:NCO3002 2.0 43.4 1.0
N4 B:NCO3002 2.0 45.0 1.0
N2 B:NCO3002 2.0 44.4 1.0
N3 B:NCO3002 2.0 44.7 1.0
N6 B:NCO3002 2.0 44.7 1.0
N5 B:NCO3002 2.0 44.0 1.0
O B:ARG1132 4.0 33.8 1.0
O B:ALA1134 4.4 33.1 1.0
OD2 B:ASP1135 4.6 32.1 1.0

Cobalt binding site 5 out of 5 in 1y8z

Go back to Cobalt Binding Sites List in 1y8z
Cobalt binding site 5 out of 5 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Hmu Base at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3004

b:54.7
occ:0.50
 CO B:NCO3004 0.0 54.7 0.5
N2 B:NCO3004 2.0 53.6 0.5
N1 B:NCO3004 2.0 53.7 0.5
N6 B:NCO3004 2.0 53.9 0.5
N3 B:NCO3004 2.0 54.0 0.5
N4 B:NCO3004 2.0 53.3 0.5
N5 B:NCO3004 2.0 53.3 0.5
O B:HOH287 4.0 44.6 1.0
OD2 B:ASP1101 4.1 47.0 1.0
O B:ASP1101 4.1 38.8 1.0
O B:HOH445 4.6 41.5 1.0
CG B:ASP1101 4.7 44.9 1.0
OD1 B:ASP1101 4.7 46.6 1.0
ND2 B:ASN1102 4.8 33.3 1.0

Reference:

L.Lariviere, N.Sommer, S.Morera. Structural Evidence of A Passive Base-Flipping Mechanism For Agt, An Unusual Gt-B Glycosyltransferase. J.Mol.Biol. V. 352 139 2005.
ISSN: ISSN 0022-2836
PubMed: 16081100
DOI: 10.1016/J.JMB.2005.07.007
Page generated: Tue Jul 30 14:50:31 2024

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