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Iodine in PDB 5mu1: Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6

Protein crystallography data

The structure of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6, PDB code: 5mu1 was solved by P.Roversi, A.T.Caputo, J.Hill, D.S.Alonzi, N.Zitzmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.28 / 3.48
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 116.950, 116.950, 301.491, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 25.2

Other elements in 5mu1:

The structure of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 also contains other interesting chemical elements:

Platinum (Pt) 6 atoms
Calcium (Ca) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 (pdb code 5mu1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6, PDB code: 5mu1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in 5mu1

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Iodine binding site 1 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1601

b:0.6
occ:0.37
PT A:PT1604 2.6 0.6 0.4
CE1 A:HIS582 3.1 0.8 1.0
NE2 A:HIS582 3.2 0.6 1.0
ND1 A:HIS582 3.4 0.5 1.0
CD2 A:HIS582 3.5 0.8 1.0
CG A:HIS582 3.6 0.3 1.0
I A:IOD1602 3.7 0.9 0.4
OE2 A:GLU578 4.2 0.1 1.0
CB A:HIS582 4.6 0.1 1.0

Iodine binding site 2 out of 14 in 5mu1

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Iodine binding site 2 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1602

b:0.9
occ:0.37
PT A:PT1604 2.6 0.6 0.4
I A:IOD1601 3.7 0.6 0.4
I A:IOD1603 3.7 0.2 0.4
CE1 A:HIS582 3.7 0.8 1.0
NE2 A:HIS582 4.3 0.6 1.0
ND1 A:HIS582 4.7 0.5 1.0

Iodine binding site 3 out of 14 in 5mu1

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Iodine binding site 3 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1603

b:0.2
occ:0.37
CE1 A:HIS582 2.6 0.8 1.0
PT A:PT1604 2.6 0.6 0.4
NE2 A:HIS582 3.2 0.6 1.0
ND1 A:HIS582 3.5 0.5 1.0
CD2 A:HIS586 3.5 0.6 1.0
I A:IOD1602 3.7 0.9 0.4
CB A:HIS586 4.0 0.6 1.0
CG A:HIS586 4.1 0.2 1.0
CD2 A:HIS582 4.3 0.8 1.0
CG A:HIS582 4.5 0.3 1.0
CA A:HIS586 4.6 1.0 1.0
NE2 A:HIS586 4.7 0.7 1.0
O A:HIS582 4.7 0.7 1.0

Iodine binding site 4 out of 14 in 5mu1

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Iodine binding site 4 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1606

b:0.3
occ:0.32
PT A:PT1605 2.6 0.2 0.3
OE2 A:GLU1042 2.9 0.1 1.0
CD A:GLU1042 3.0 0.8 1.0
NE2 A:HIS1267 3.1 0.8 1.0
CD2 A:HIS1267 3.1 0.9 1.0
NE2 A:HIS1044 3.2 0.1 1.0
CE1 A:HIS1044 3.4 0.5 1.0
OE1 A:GLU1042 3.5 1.0 1.0
CE1 A:PHE879 3.5 0.5 1.0
CZ A:PHE879 3.6 0.8 1.0
CG A:GLU1042 3.7 0.2 1.0
CE1 A:HIS1267 3.8 0.6 1.0
CG A:HIS1267 3.9 0.2 1.0
CE1 A:TYR1080 4.0 0.9 1.0
ND1 A:HIS1267 4.3 0.8 1.0
CD2 A:HIS1044 4.3 0.8 1.0
ND1 A:HIS1044 4.6 0.3 1.0
CD1 A:TYR1080 4.7 0.6 1.0
CB A:GLU1042 4.7 0.8 1.0
CD1 A:PHE879 4.7 0.7 1.0
CG2 A:THR1133 4.9 0.1 1.0
CE2 A:PHE879 4.9 0.5 1.0
CB A:HIS1267 4.9 0.2 1.0

Iodine binding site 5 out of 14 in 5mu1

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Iodine binding site 5 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1607

b:0.9
occ:0.34
PT A:PT1610 2.6 0.0 0.3
CG A:PHE634 3.3 0.0 1.0
CE A:MET636 3.3 0.0 1.0
CD2 A:PHE634 3.5 0.0 1.0
CB A:PHE634 3.6 0.3 1.0
CD1 A:PHE634 3.6 0.8 1.0
SD A:MET636 3.6 0.9 1.0
I A:IOD1608 3.7 0.2 0.3
CE2 A:PHE634 4.0 0.4 1.0
CE1 A:PHE634 4.1 0.4 1.0
CZ A:PHE634 4.3 0.7 1.0
O A:GLN630 4.3 0.3 1.0
CG A:MET636 4.5 0.9 1.0

Iodine binding site 6 out of 14 in 5mu1

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Iodine binding site 6 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1608

b:0.2
occ:0.34
PT A:PT1610 2.6 0.0 0.3
I A:IOD1607 3.7 0.9 0.3
I A:IOD1609 3.7 0.1 0.3
OE1 A:GLN630 4.0 0.4 1.0
CB A:GLN630 4.2 0.8 1.0
N A:ALA631 4.8 0.9 1.0
C A:GLN630 4.8 0.3 1.0
CD A:GLN630 4.9 0.5 1.0
CA A:ALA631 5.0 0.0 1.0

Iodine binding site 7 out of 14 in 5mu1

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Iodine binding site 7 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1609

b:0.1
occ:0.34
PT A:PT1610 2.6 0.0 0.3
SD A:MET636 3.6 0.9 1.0
I A:IOD1608 3.7 0.2 0.3
CB A:ALA631 3.8 0.9 1.0
CE2 A:PHE646 3.9 0.0 1.0
CZ A:PHE646 3.9 0.2 1.0
CG A:MET636 4.5 0.9 1.0
CA A:ALA631 4.5 0.0 1.0
CB A:MET636 4.7 0.6 1.0

Iodine binding site 8 out of 14 in 5mu1

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Iodine binding site 8 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1611

b:0.0
occ:0.29
PT A:PT1613 2.6 0.8 0.3
CD2 A:HIS619 3.2 0.7 1.0
NE2 A:HIS619 3.3 0.9 1.0
CB A:ASN618 3.6 0.6 1.0
O A:ARG615 3.9 0.8 1.0
CD A:ARG615 4.0 0.9 1.0
CG A:HIS619 4.0 0.4 1.0
CE1 A:HIS619 4.0 0.8 1.0
I A:IOD1614 4.1 0.3 0.4
N A:HIS619 4.3 0.1 1.0
C A:ASN618 4.4 0.2 1.0
ND1 A:HIS619 4.4 0.6 1.0
CG A:ARG615 4.5 0.4 1.0
CG A:ASN618 4.6 0.1 1.0
CA A:ASN618 4.6 0.5 1.0
NH1 A:ARG615 4.7 0.4 1.0
CA A:HIS619 4.7 0.8 1.0
C A:ARG615 4.8 0.8 1.0
PT A:PT1617 4.8 0.4 0.4
CA A:ARG615 4.8 0.4 1.0
O A:ASN618 4.9 0.1 1.0
CB A:HIS619 4.9 0.4 1.0

Iodine binding site 9 out of 14 in 5mu1

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Iodine binding site 9 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1612

b:0.9
occ:0.29
PT A:PT1613 2.6 0.8 0.3
CD2 A:HIS619 2.8 0.7 1.0
NE2 A:HIS619 3.3 0.9 1.0
CG A:HIS619 3.7 0.4 1.0
CE A:MET622 3.9 0.8 1.0
CA A:HIS619 4.2 0.8 1.0
CE1 A:HIS619 4.3 0.8 1.0
O A:HIS619 4.3 0.2 1.0
CB A:HIS619 4.4 0.4 1.0
CB A:MET622 4.5 0.5 1.0
ND1 A:HIS619 4.5 0.6 1.0
SD A:MET622 4.8 0.2 1.0
C A:HIS619 4.8 1.0 1.0

Iodine binding site 10 out of 14 in 5mu1

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Iodine binding site 10 out of 14 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1614

b:0.3
occ:0.36
PT A:PT1617 2.6 0.4 0.4
CE A:MET622 3.3 0.8 1.0
SD A:MET622 3.3 0.2 1.0
CB A:HIS456 3.4 0.0 1.0
ND1 A:HIS456 3.4 0.1 1.0
I A:IOD1615 3.7 0.5 0.4
CG A:HIS456 3.7 0.0 1.0
O A:HIS456 3.7 0.4 1.0
I A:IOD1611 4.1 0.0 0.3
PT A:PT1613 4.1 0.8 0.3
CA A:HIS456 4.3 0.0 1.0
C A:HIS456 4.4 0.3 1.0
CE1 A:HIS456 4.5 0.2 1.0
CD2 A:HIS456 4.9 0.7 1.0

Reference:

P.Roversi, L.Marti, A.T.Caputo, D.S.Alonzi, J.C.Hill, K.C.Dent, A.Kumar, M.D.Levasseur, A.Lia, T.Waksman, S.Basu, Y.Soto Albrecht, K.Qian, J.P.Mcivor, C.B.Lipp, D.Siliqi, S.Vasiljevic, S.Mohammed, P.Lukacik, M.A.Walsh, A.Santino, N.Zitzmann. Interdomain Conformational Flexibility Underpins the Activity of Uggt, the Eukaryotic Glycoprotein Secretion Checkpoint. Proc. Natl. Acad. Sci. V. 114 8544 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28739903
DOI: 10.1073/PNAS.1703682114
Page generated: Sun Dec 13 19:40:26 2020

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