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Cobalt in PDB 1y6g: Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution

Enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution

All present enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution, PDB code: 1y6g 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.994, 120.520, 86.807, 90.00, 94.68, 90.00
R / Rfree (%) 21.9 / 28.7

Other elements in 1y6g:

The structure of Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution (pdb code 1y6g). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution, PDB code: 1y6g:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 1y6g

Go back to Cobalt Binding Sites List in 1y6g
Cobalt binding site 1 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1003

b:93.6
occ:1.00
 CO D:NCO1003 0.0 93.6 1.0
N2 D:NCO1003 2.0 92.5 1.0
N4 D:NCO1003 2.0 92.9 1.0
N3 D:NCO1003 2.0 92.1 1.0
N5 D:NCO1003 2.0 92.7 1.0
N1 D:NCO1003 2.0 93.0 1.0
N6 D:NCO1003 2.0 92.6 1.0
OP1 D:DT10 4.4 75.8 1.0

Cobalt binding site 2 out of 7 in 1y6g

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Cobalt binding site 2 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1401

b:95.2
occ:1.00
 CO A:NCO1401 0.0 95.2 1.0
N1 A:NCO1401 2.0 94.8 1.0
N4 A:NCO1401 2.0 94.5 1.0
N5 A:NCO1401 2.0 93.4 1.0
N2 A:NCO1401 2.0 94.4 1.0
N6 A:NCO1401 2.0 94.1 1.0
N3 A:NCO1401 2.0 94.1 1.0
O A:ARG1132 4.5 45.5 1.0
OD2 A:ASP1135 4.7 56.3 1.0
O A:ALA1134 4.8 46.8 1.0

Cobalt binding site 3 out of 7 in 1y6g

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Cobalt binding site 3 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1402

b:100.0
occ:0.50
 CO A:NCO1402 0.0 100.0 0.5
N3 A:NCO1402 2.0 99.5 0.5
N6 A:NCO1402 2.0 99.8 0.5
N4 A:NCO1402 2.0 99.7 0.5
N5 A:NCO1402 2.0 100.0 0.5
N2 A:NCO1402 2.0 99.6 0.5
N1 A:NCO1402 2.0 99.7 0.5
O A:VAL1088 3.8 60.3 1.0
O A:THR1086 3.9 60.5 1.0
OE2 A:GLU1090 4.7 74.6 1.0
C A:VAL1088 5.0 61.4 1.0

Cobalt binding site 4 out of 7 in 1y6g

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Cobalt binding site 4 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1403

b:100.0
occ:0.50
 CO A:NCO1403 0.0 100.0 0.5
N3 A:NCO1403 2.0 99.5 0.5
N6 A:NCO1403 2.0 100.0 0.5
N4 A:NCO1403 2.0 99.4 0.5
N5 A:NCO1403 2.0 99.6 0.5
N1 A:NCO1403 2.0 99.5 0.5
N2 A:NCO1403 2.0 100.0 0.5
O1B A:UDP1404 3.6 55.0 1.0
O A:HIS1114 3.6 56.4 1.0
O3B A:UDP1404 3.8 54.3 1.0
PB A:UDP1404 4.4 55.8 1.0
NE2 A:HIS1116 4.7 50.5 1.0
CD2 A:HIS1116 4.8 53.4 1.0
C A:HIS1114 4.8 54.3 1.0
O1A A:UDP1404 4.8 46.6 1.0
CB A:HIS1114 5.0 49.4 1.0

Cobalt binding site 5 out of 7 in 1y6g

Go back to Cobalt Binding Sites List in 1y6g
Cobalt binding site 5 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 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 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2018

b:85.8
occ:1.00
 CO B:NCO2018 0.0 85.8 1.0
N1 B:NCO2018 2.0 84.7 1.0
N2 B:NCO2018 2.0 84.7 1.0
N6 B:NCO2018 2.0 85.0 1.0
N5 B:NCO2018 2.0 84.5 1.0
N3 B:NCO2018 2.0 84.7 1.0
N4 B:NCO2018 2.0 84.2 1.0
O B:ARG1132 4.1 45.8 1.0
O B:ALA1134 4.4 43.0 1.0
OD2 B:ASP1135 4.8 50.9 1.0

Cobalt binding site 6 out of 7 in 1y6g

Go back to Cobalt Binding Sites List in 1y6g
Cobalt binding site 6 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2019

b:100.0
occ:0.50
 CO B:NCO2019 0.0 100.0 0.5
N1 B:NCO2019 2.0 100.0 0.5
N2 B:NCO2019 2.0 99.6 0.5
N5 B:NCO2019 2.0 98.8 0.5
N3 B:NCO2019 2.0 98.8 0.5
N4 B:NCO2019 2.0 99.7 0.5
N6 B:NCO2019 2.0 98.5 0.5
O1B B:UDP2021 3.4 43.3 1.0
O B:HIS1114 4.1 37.5 1.0
O3B B:UDP2021 4.1 41.8 1.0
CL B:CL2017 4.3 65.2 1.0
OD2 B:ASP1115 4.3 54.3 1.0
PB B:UDP2021 4.4 42.3 1.0
NE2 B:HIS1116 4.4 38.7 1.0
CD2 B:HIS1116 4.8 37.6 1.0
O1A B:UDP2021 4.8 40.6 1.0
C B:HIS1114 4.9 37.9 1.0

Cobalt binding site 7 out of 7 in 1y6g

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Cobalt binding site 7 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Alpha-Glucosyltransferase in Complex with Udp and A 13_MER Dna Containing A Hmu Base at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2020

b:100.0
occ:0.50
 CO B:NCO2020 0.0 100.0 0.5
N6 B:NCO2020 2.0 99.2 0.5
N5 B:NCO2020 2.0 99.4 0.5
N1 B:NCO2020 2.0 99.5 0.5
N4 B:NCO2020 2.0 99.7 0.5
N2 B:NCO2020 2.0 100.0 0.5
N3 B:NCO2020 2.0 99.4 0.5
O B:ASP1101 4.2 55.4 1.0
ND2 B:ASN1102 4.3 55.0 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 14:49:41 2024

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