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Platinum 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:

Iodine (I) 14 atoms
Calcium (Ca) 1 atom

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 6 binding sites of Platinum where determined in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6, PDB code: 5mu1:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 5mu1

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Platinum binding site 1 out of 6 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1604

b:0.6
occ:0.37
CE1 A:HIS582 1.2 0.8 1.0
NE2 A:HIS582 1.8 0.6 1.0
ND1 A:HIS582 2.3 0.5 1.0
I A:IOD1601 2.6 0.6 0.4
I A:IOD1602 2.6 0.9 0.4
I A:IOD1603 2.6 0.2 0.4
CD2 A:HIS582 2.9 0.8 1.0
CG A:HIS582 3.1 0.3 1.0
CB A:HIS582 4.5 0.1 1.0

Platinum binding site 2 out of 6 in 5mu1

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Platinum binding site 2 out of 6 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1605

b:0.2
occ:0.31
NE2 A:HIS1267 1.8 0.8 1.0
NE2 A:HIS1044 2.1 0.1 1.0
CE1 A:HIS1267 2.1 0.6 1.0
CE1 A:HIS1044 2.2 0.5 1.0
I A:IOD1606 2.6 0.3 0.3
CD2 A:HIS1267 2.9 0.9 1.0
CG2 A:ILE878 3.0 0.5 1.0
ND1 A:HIS1267 3.2 0.8 1.0
CE1 A:PHE879 3.3 0.5 1.0
CD2 A:HIS1044 3.4 0.8 1.0
CZ A:PHE879 3.4 0.8 1.0
ND1 A:HIS1044 3.5 0.3 1.0
CG A:HIS1267 3.6 0.2 1.0
CD1 A:PHE879 4.0 0.7 1.0
CG A:HIS1044 4.0 0.8 1.0
CE2 A:PHE879 4.2 0.5 1.0
CD1 A:LEU1078 4.4 0.0 1.0
CB A:ILE878 4.5 0.5 1.0
O A:ILE878 4.6 0.9 1.0
CG A:PHE879 4.7 0.9 1.0
CD2 A:PHE879 4.7 0.3 1.0
CD1 A:TYR1080 4.8 0.6 1.0
CE1 A:TYR1080 4.8 0.9 1.0
C A:ILE878 4.8 0.8 1.0

Platinum binding site 3 out of 6 in 5mu1

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Platinum binding site 3 out of 6 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1610

b:0.0
occ:0.34
SD A:MET636 2.5 0.9 1.0
I A:IOD1607 2.6 0.9 0.3
I A:IOD1608 2.6 0.2 0.3
I A:IOD1609 2.6 0.1 0.3
CE A:MET636 3.5 0.0 1.0
CG A:MET636 3.7 0.9 1.0
CA A:ALA631 4.1 0.0 1.0
CB A:ALA631 4.3 0.9 1.0
N A:ALA631 4.6 0.9 1.0
CB A:MET636 4.7 0.6 1.0
O A:GLN630 4.8 0.3 1.0
C A:GLN630 4.9 0.3 1.0
CB A:PHE634 5.0 0.3 1.0

Platinum binding site 4 out of 6 in 5mu1

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Platinum binding site 4 out of 6 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1613

b:0.8
occ:0.29
CD2 A:HIS619 1.5 0.7 1.0
NE2 A:HIS619 2.0 0.9 1.0
I A:IOD1611 2.6 0.0 0.3
I A:IOD1612 2.6 0.9 0.3
CG A:HIS619 2.8 0.4 1.0
CE1 A:HIS619 3.2 0.8 1.0
ND1 A:HIS619 3.6 0.6 1.0
CA A:HIS619 3.6 0.8 1.0
CB A:HIS619 3.8 0.4 1.0
N A:HIS619 4.0 0.1 1.0
I A:IOD1614 4.1 0.3 0.4
CE A:MET622 4.2 0.8 1.0
C A:ASN618 4.3 0.2 1.0
SD A:MET622 4.3 0.2 1.0
O A:ASN618 4.4 0.1 1.0
C A:HIS619 4.9 1.0 1.0
PT A:PT1617 4.9 0.4 0.4
CB A:ASN618 4.9 0.6 1.0
O A:HIS619 5.0 0.2 1.0

Platinum binding site 5 out of 6 in 5mu1

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Platinum binding site 5 out of 6 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum Soaked with K2PTI6


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1617

b:0.4
occ:0.36
SD A:MET622 2.1 0.2 1.0
O A:HIS456 2.2 0.4 1.0
I A:IOD1616 2.6 0.9 0.4
I A:IOD1614 2.6 0.3 0.4
I A:IOD1615 2.6 0.5 0.4
CE A:MET622 3.4 0.8 1.0
C A:HIS456 3.4 0.3 1.0
CG A:MET622 3.6 0.4 1.0
ND1 A:HIS456 3.8 0.1 1.0
ND2 A:ASN618 4.0 0.9 1.0
CB A:HIS456 4.1 0.0 1.0
CA A:HIS456 4.1 0.0 1.0
CG A:HIS456 4.4 0.0 1.0
N A:GLY457 4.5 0.5 1.0
O A:ASN618 4.7 0.1 1.0
CB A:MET622 4.7 0.5 1.0
O A:GLY457 4.7 0.4 1.0
CA A:GLY457 4.8 0.4 1.0
CB A:ASN618 4.8 0.6 1.0
I A:IOD1611 4.8 0.0 0.3
PT A:PT1613 4.9 0.8 0.3
CG A:ASN618 4.9 0.1 1.0
CE1 A:HIS456 4.9 0.2 1.0

Platinum binding site 6 out of 6 in 5mu1

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


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt1620

b:0.5
occ:0.34
SD A:MET1441 1.6 0.0 1.0
SD A:MET1336 2.1 0.7 1.0
CE A:MET1441 2.4 0.1 1.0
I A:IOD1618 2.6 0.9 0.3
I A:IOD1619 2.6 0.3 0.3
CE A:MET1336 2.6 0.6 1.0
CG A:MET1441 3.3 0.6 1.0
CG A:MET1336 3.8 0.5 1.0
CB A:MET1441 4.0 0.5 1.0
CA A:MET1336 4.4 0.2 1.0
OD1 A:ASN1439 4.4 0.9 1.0
CB A:MET1336 4.5 0.7 1.0
O A:GLU1335 4.8 0.3 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: Wed Dec 16 02:05:23 2020

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