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Cobalt in PDB 1ya6: Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch

Enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch

All present enzymatic activity of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch:
2.4.1.26;

Protein crystallography data

The structure of Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch, PDB code: 1ya6 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 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.855, 119.318, 86.812, 90.00, 92.87, 90.00
R / Rfree (%) 23 / 28

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch (pdb code 1ya6). 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 Central A:G Mismatch, PDB code: 1ya6:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 1ya6

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Cobalt binding site 1 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1003

b:91.2
occ:1.00
 CO D:NCO1003 0.0 91.2 1.0
N6 D:NCO1003 2.0 89.5 1.0
N1 D:NCO1003 2.0 89.1 1.0
N4 D:NCO1003 2.0 89.4 1.0
N2 D:NCO1003 2.0 89.0 1.0
N5 D:NCO1003 2.0 88.8 1.0
N3 D:NCO1003 2.0 89.3 1.0
OP1 D:DT10 3.9 65.6 1.0

Cobalt binding site 2 out of 7 in 1ya6

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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 Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2002

b:63.9
occ:1.00
 CO A:NCO2002 0.0 63.9 1.0
N3 A:NCO2002 2.0 65.6 1.0
N4 A:NCO2002 2.0 63.7 1.0
N1 A:NCO2002 2.0 66.7 1.0
N2 A:NCO2002 2.0 65.8 1.0
N5 A:NCO2002 2.0 64.0 1.0
N6 A:NCO2002 2.0 64.7 1.0
O A:HOH132 3.5 59.0 1.0
NE2 A:HIS1116 3.6 64.1 1.0
CE1 A:HIS1116 3.7 68.2 1.0
O1B A:UDP2001 3.8 44.2 1.0
O3B A:UDP2001 3.9 38.3 1.0
O A:HOH62 4.0 48.6 1.0
OE2 A:GLU1306 4.1 50.0 1.0
O A:HOH89 4.3 51.0 1.0
O A:HIS1114 4.3 55.2 1.0
PB A:UDP2001 4.5 38.2 1.0
O1A A:UDP2001 4.5 42.0 1.0
O A:HOH119 4.5 44.2 1.0
ND1 A:HIS1116 4.5 68.9 1.0
CD2 A:HIS1116 4.6 65.7 1.0
O3A A:UDP2001 4.8 42.6 1.0

Cobalt binding site 3 out of 7 in 1ya6

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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 Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2003

b:84.4
occ:1.00
 CO A:NCO2003 0.0 84.4 1.0
N2 A:NCO2003 2.0 81.3 1.0
N5 A:NCO2003 2.0 82.9 1.0
N6 A:NCO2003 2.0 82.7 1.0
N1 A:NCO2003 2.0 84.5 1.0
N3 A:NCO2003 2.0 82.3 1.0
N4 A:NCO2003 2.0 84.4 1.0
O A:ARG1132 4.3 59.3 1.0
O A:ALA1134 4.6 52.7 1.0
O A:HOH61 4.8 45.5 1.0
OD2 A:ASP1135 4.8 58.7 1.0

Cobalt binding site 4 out of 7 in 1ya6

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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 Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2004

b:92.6
occ:0.50
 CO A:NCO2004 0.0 92.6 0.5
N2 A:NCO2004 2.0 93.2 0.5
N1 A:NCO2004 2.0 93.3 0.5
N3 A:NCO2004 2.0 93.1 0.5
N4 A:NCO2004 2.0 93.0 0.5
N6 A:NCO2004 2.0 93.6 0.5
N5 A:NCO2004 2.0 92.8 0.5
OE2 A:GLU1090 3.6 79.5 1.0
O A:VAL1088 3.8 62.6 1.0
O A:THR1086 4.2 59.9 1.0
O A:HOH122 4.4 68.0 1.0
CD A:GLU1090 4.8 78.2 1.0
C A:VAL1088 4.9 63.8 1.0

Cobalt binding site 5 out of 7 in 1ya6

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Cobalt binding site 5 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3002

b:79.1
occ:1.00
 CO B:NCO3002 0.0 79.1 1.0
N4 B:NCO3002 2.0 78.8 1.0
N3 B:NCO3002 2.0 79.4 1.0
N1 B:NCO3002 2.0 80.0 1.0
N5 B:NCO3002 2.0 79.8 1.0
N2 B:NCO3002 2.0 79.1 1.0
N6 B:NCO3002 2.0 78.3 1.0
NE2 B:HIS1116 3.4 71.9 1.0
CE1 B:HIS1116 3.8 72.8 1.0
O1B B:UDP3001 3.9 45.8 1.0
O3B B:UDP3001 4.0 43.6 1.0
O B:HOH63 4.2 49.2 1.0
O B:HIS1114 4.3 54.8 1.0
O1A B:UDP3001 4.4 47.9 1.0
OE2 B:GLU1306 4.4 57.5 1.0
O B:HOH64 4.4 54.9 1.0
CD2 B:HIS1116 4.4 72.3 1.0
PB B:UDP3001 4.4 42.4 1.0
O3A B:UDP3001 4.6 44.3 1.0
ND1 B:HIS1116 4.9 72.6 1.0

Cobalt binding site 6 out of 7 in 1ya6

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Cobalt binding site 6 out of 7 in the Alpha-Glucosyltransferase in Complex with Udp and A 13-Mer Dna Containing A Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3003

b:100.0
occ:1.00
 CO B:NCO3003 0.0 100.0 1.0
N2 B:NCO3003 2.0 100.0 1.0
N5 B:NCO3003 2.0 100.0 1.0
N3 B:NCO3003 2.0 99.6 1.0
N1 B:NCO3003 2.0 99.1 1.0
N6 B:NCO3003 2.0 99.8 1.0
N4 B:NCO3003 2.0 98.4 1.0
OD2 B:ASP1135 4.2 69.2 1.0
O B:ALA1134 4.3 67.2 1.0
O B:ARG1132 4.6 75.5 1.0

Cobalt binding site 7 out of 7 in 1ya6

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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 Central A:G Mismatch


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 Central A:G Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3004

b:73.2
occ:0.50
 CO B:NCO3004 0.0 73.2 0.5
N6 B:NCO3004 2.0 72.0 0.5
N5 B:NCO3004 2.0 71.1 0.5
N2 B:NCO3004 2.0 71.4 0.5
N4 B:NCO3004 2.0 71.8 0.5
N1 B:NCO3004 2.0 71.4 0.5
N3 B:NCO3004 2.0 71.9 0.5
O B:ASP1101 4.5 77.5 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 14:51:01 2024

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