Atomistry » Cobalt » PDB 1vz0-1zft » 1y8z
Atomistry »
  Cobalt »
    PDB 1vz0-1zft »
      1y8z »

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

Go back to Cobalt Binding Sites List in 1y8z
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

Go back to Cobalt Binding Sites List in 1y8z
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: Sun Dec 13 10:36:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy