Magnesium in PDB 5nlm: Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Protein crystallography data
The structure of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate, PDB code: 5nlm
was solved by
D.H.Welner,
T.Hsu,
J.Dueber,
P.D.Adams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.41 /
2.14
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.000,
172.820,
48.410,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.5 /
25.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
(pdb code 5nlm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate, PDB code: 5nlm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 5nlm
Go back to
Magnesium Binding Sites List in 5nlm
Magnesium binding site 1 out
of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1001
b:88.2
occ:1.00
|
HA
|
A:ALA393
|
2.8
|
54.2
|
1.0
|
O
|
A:HOH1123
|
2.9
|
45.6
|
1.0
|
H
|
A:ALA393
|
2.9
|
52.7
|
1.0
|
HB2
|
A:ASP189
|
3.0
|
56.1
|
1.0
|
HA
|
A:IOS1000
|
3.0
|
0.2
|
1.0
|
OE2
|
A:GLU88
|
3.2
|
51.3
|
1.0
|
H1
|
A:IOS1000
|
3.5
|
0.9
|
1.0
|
N
|
A:ALA393
|
3.5
|
43.8
|
1.0
|
C1
|
A:IOS1000
|
3.5
|
0.8
|
1.0
|
HB2
|
A:ALA393
|
3.5
|
52.2
|
1.0
|
CA
|
A:ALA393
|
3.5
|
45.1
|
1.0
|
HD3
|
A:PRO190
|
3.6
|
51.4
|
1.0
|
HG22
|
A:ILE87
|
3.6
|
60.7
|
1.0
|
HB3
|
A:ASP189
|
3.7
|
56.1
|
1.0
|
OD2
|
A:ASP189
|
3.7
|
51.6
|
1.0
|
CB
|
A:ASP189
|
3.7
|
46.7
|
1.0
|
N1
|
A:IOS1000
|
3.7
|
0.9
|
1.0
|
HB2
|
A:TYR392
|
3.7
|
55.0
|
1.0
|
HG21
|
A:ILE87
|
3.8
|
60.7
|
1.0
|
HD2
|
A:TYR392
|
3.9
|
56.6
|
1.0
|
CB
|
A:ALA393
|
4.0
|
43.4
|
1.0
|
CG2
|
A:ILE87
|
4.1
|
50.5
|
1.0
|
CG
|
A:ASP189
|
4.1
|
50.6
|
1.0
|
CD
|
A:GLU88
|
4.2
|
48.3
|
1.0
|
O4
|
A:IOS1000
|
4.3
|
0.5
|
1.0
|
HG23
|
A:ILE87
|
4.4
|
60.7
|
1.0
|
OE1
|
A:GLU88
|
4.4
|
51.5
|
1.0
|
HB1
|
A:ALA393
|
4.4
|
52.2
|
1.0
|
CD
|
A:PRO190
|
4.6
|
42.8
|
1.0
|
C2
|
A:IOS1000
|
4.6
|
1.0
|
1.0
|
CB
|
A:TYR392
|
4.7
|
45.8
|
1.0
|
CD2
|
A:TYR392
|
4.7
|
47.1
|
1.0
|
C
|
A:TYR392
|
4.7
|
40.9
|
1.0
|
O
|
A:HOH1166
|
4.7
|
60.3
|
1.0
|
C
|
A:ALA393
|
4.8
|
44.6
|
1.0
|
HB3
|
A:ALA393
|
4.8
|
52.2
|
1.0
|
H
|
A:ASP189
|
4.9
|
49.0
|
1.0
|
C8
|
A:IOS1000
|
4.9
|
0.1
|
1.0
|
HD2
|
A:PRO190
|
4.9
|
51.4
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 5nlm
Go back to
Magnesium Binding Sites List in 5nlm
Magnesium binding site 2 out
of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1002
b:29.6
occ:1.00
|
H
|
A:SER375
|
2.5
|
48.6
|
1.0
|
HB2
|
A:ASN374
|
2.7
|
42.5
|
1.0
|
HA3
|
A:GLY372
|
2.7
|
45.1
|
1.0
|
OG
|
A:SER375
|
3.1
|
41.1
|
1.0
|
HE1
|
A:HIS370
|
3.1
|
44.0
|
1.0
|
N
|
A:SER375
|
3.3
|
40.4
|
1.0
|
HG
|
A:SER375
|
3.3
|
49.4
|
1.0
|
H
|
A:ASN374
|
3.4
|
43.4
|
1.0
|
O
|
A:HOH1168
|
3.4
|
40.5
|
1.0
|
HB2
|
A:SER375
|
3.5
|
46.8
|
1.0
|
CA
|
A:GLY372
|
3.5
|
37.5
|
1.0
|
HE2
|
A:HIS370
|
3.6
|
47.9
|
1.0
|
CB
|
A:ASN374
|
3.6
|
35.4
|
1.0
|
C
|
A:GLY372
|
3.6
|
35.8
|
1.0
|
CE1
|
A:HIS370
|
3.7
|
36.6
|
1.0
|
CB
|
A:SER375
|
3.7
|
38.9
|
1.0
|
O
|
A:HOH1171
|
3.7
|
60.6
|
1.0
|
N
|
A:ASN374
|
3.8
|
36.1
|
1.0
|
O
|
A:GLY372
|
3.9
|
35.5
|
1.0
|
NE2
|
A:HIS370
|
3.9
|
39.9
|
1.0
|
CA
|
A:ASN374
|
4.0
|
36.9
|
1.0
|
HB3
|
A:ASN374
|
4.1
|
42.5
|
1.0
|
HD22
|
A:ASN374
|
4.1
|
47.5
|
1.0
|
C
|
A:ASN374
|
4.1
|
41.2
|
1.0
|
CA
|
A:SER375
|
4.1
|
39.5
|
1.0
|
HA2
|
A:GLY372
|
4.1
|
45.1
|
1.0
|
N
|
A:TRP373
|
4.1
|
33.9
|
1.0
|
H
|
A:TRP373
|
4.2
|
40.7
|
1.0
|
H
|
A:GLY372
|
4.4
|
42.2
|
1.0
|
N
|
A:GLY372
|
4.4
|
35.1
|
1.0
|
HA
|
A:SER375
|
4.5
|
47.4
|
1.0
|
CG
|
A:ASN374
|
4.6
|
41.3
|
1.0
|
ND2
|
A:ASN374
|
4.6
|
39.5
|
1.0
|
HB3
|
A:SER375
|
4.6
|
46.8
|
1.0
|
C
|
A:TRP373
|
4.7
|
35.2
|
1.0
|
ND1
|
A:HIS370
|
4.9
|
37.2
|
1.0
|
H
|
A:THR376
|
4.9
|
40.8
|
1.0
|
HA
|
A:ASN374
|
5.0
|
44.3
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 5nlm
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Magnesium Binding Sites List in 5nlm
Magnesium binding site 3 out
of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:70.4
occ:1.00
|
HH11
|
A:ARG442
|
2.0
|
97.3
|
1.0
|
HD2
|
A:ARG442
|
2.3
|
95.1
|
1.0
|
NH1
|
A:ARG442
|
2.7
|
81.0
|
1.0
|
O
|
A:GLY365
|
2.9
|
47.1
|
1.0
|
HG3
|
A:PRO385
|
2.9
|
56.9
|
1.0
|
HH12
|
A:ARG442
|
3.1
|
97.3
|
1.0
|
CD
|
A:ARG442
|
3.2
|
79.2
|
1.0
|
HB2
|
A:ARG442
|
3.3
|
84.3
|
1.0
|
HG2
|
A:PRO385
|
3.4
|
56.9
|
1.0
|
HG3
|
A:ARG442
|
3.4
|
90.0
|
1.0
|
CG
|
A:PRO385
|
3.5
|
47.4
|
1.0
|
CZ
|
A:ARG442
|
3.6
|
84.6
|
1.0
|
CG
|
A:ARG442
|
3.7
|
74.9
|
1.0
|
HD2
|
A:PRO385
|
3.8
|
57.2
|
1.0
|
NE
|
A:ARG442
|
3.8
|
84.4
|
1.0
|
HD3
|
A:ARG442
|
3.8
|
95.1
|
1.0
|
C
|
A:GLY365
|
3.8
|
45.3
|
1.0
|
HA2
|
A:GLY365
|
3.9
|
57.6
|
1.0
|
CB
|
A:ARG442
|
4.0
|
70.2
|
1.0
|
CD
|
A:PRO385
|
4.0
|
47.6
|
1.0
|
HA3
|
A:GLY365
|
4.0
|
57.6
|
1.0
|
HD3
|
A:PRO385
|
4.1
|
57.2
|
1.0
|
CA
|
A:GLY365
|
4.2
|
48.0
|
1.0
|
HE1
|
A:MET433
|
4.5
|
62.4
|
1.0
|
HB3
|
A:ARG442
|
4.6
|
84.3
|
1.0
|
HE
|
A:ARG442
|
4.6
|
0.4
|
1.0
|
HG2
|
A:ARG442
|
4.6
|
90.0
|
1.0
|
HA
|
A:MET433
|
4.6
|
68.7
|
1.0
|
HG
|
A:LEU432
|
4.7
|
59.5
|
1.0
|
O
|
A:LEU432
|
4.7
|
57.9
|
1.0
|
HA
|
A:ARG442
|
4.7
|
81.1
|
1.0
|
NH2
|
A:ARG442
|
4.8
|
88.7
|
1.0
|
O
|
A:GLY273
|
4.8
|
65.3
|
1.0
|
CB
|
A:PRO385
|
4.9
|
45.2
|
1.0
|
HD11
|
A:LEU432
|
4.9
|
61.6
|
1.0
|
HE3
|
A:MET433
|
5.0
|
62.4
|
1.0
|
CA
|
A:ARG442
|
5.0
|
67.5
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 5nlm
Go back to
Magnesium Binding Sites List in 5nlm
Magnesium binding site 4 out
of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:0.7
occ:1.00
|
HE
|
A:ARG58
|
2.2
|
72.0
|
1.0
|
HH21
|
A:ARG58
|
2.3
|
72.3
|
1.0
|
HD2
|
A:PRO53
|
2.8
|
80.5
|
1.0
|
O
|
A:PRO53
|
2.9
|
72.3
|
1.0
|
NE
|
A:ARG58
|
3.0
|
60.0
|
1.0
|
NH2
|
A:ARG58
|
3.1
|
60.2
|
1.0
|
CZ
|
A:ARG58
|
3.5
|
59.4
|
1.0
|
HB3
|
A:PRO52
|
3.5
|
93.2
|
1.0
|
CD
|
A:PRO53
|
3.6
|
67.0
|
1.0
|
N
|
A:PRO53
|
3.8
|
68.3
|
1.0
|
HB2
|
A:PRO53
|
3.8
|
76.6
|
1.0
|
HH22
|
A:ARG58
|
3.8
|
72.3
|
1.0
|
C
|
A:PRO53
|
3.9
|
67.5
|
1.0
|
HD2
|
A:ARG58
|
4.1
|
73.4
|
1.0
|
CD
|
A:ARG58
|
4.2
|
61.1
|
1.0
|
HB2
|
A:PRO52
|
4.2
|
93.2
|
1.0
|
CB
|
A:PRO52
|
4.2
|
77.6
|
1.0
|
C
|
A:PRO52
|
4.2
|
69.9
|
1.0
|
CA
|
A:PRO53
|
4.3
|
66.3
|
1.0
|
HA
|
A:PRO52
|
4.3
|
86.3
|
1.0
|
CB
|
A:PRO53
|
4.3
|
63.8
|
1.0
|
HD3
|
A:PRO53
|
4.3
|
80.5
|
1.0
|
HG2
|
A:PRO53
|
4.3
|
77.6
|
1.0
|
CG
|
A:PRO53
|
4.4
|
64.6
|
1.0
|
CA
|
A:PRO52
|
4.4
|
71.9
|
1.0
|
HG3
|
A:ARG58
|
4.5
|
70.1
|
1.0
|
NH1
|
A:ARG58
|
4.8
|
55.0
|
1.0
|
HD3
|
A:ARG58
|
4.9
|
73.4
|
1.0
|
CG
|
A:ARG58
|
4.9
|
58.3
|
1.0
|
O
|
A:PRO52
|
4.9
|
69.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 5nlm
Go back to
Magnesium Binding Sites List in 5nlm
Magnesium binding site 5 out
of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1001
b:52.3
occ:0.50
|
HH11
|
B:ARG36
|
1.9
|
100.0
|
1.0
|
HH12
|
B:ARG36
|
2.1
|
100.0
|
1.0
|
NH1
|
B:ARG36
|
2.2
|
83.3
|
1.0
|
HB3
|
B:GLU32
|
2.4
|
67.9
|
1.0
|
OE1
|
B:GLU32
|
2.6
|
60.8
|
1.0
|
HG3
|
B:ARG36
|
2.9
|
78.6
|
1.0
|
O
|
B:GLU32
|
3.1
|
52.4
|
1.0
|
HA
|
B:GLU32
|
3.1
|
65.3
|
1.0
|
CB
|
B:GLU32
|
3.2
|
56.5
|
1.0
|
CZ
|
B:ARG36
|
3.3
|
81.5
|
1.0
|
CA
|
B:GLU32
|
3.5
|
54.4
|
1.0
|
CD
|
B:GLU32
|
3.6
|
62.5
|
1.0
|
C
|
B:GLU32
|
3.6
|
51.7
|
1.0
|
CG
|
B:ARG36
|
3.6
|
65.5
|
1.0
|
HG2
|
B:ARG36
|
3.7
|
78.6
|
1.0
|
HB2
|
B:LYS35
|
3.8
|
64.5
|
1.0
|
HD2
|
B:ARG36
|
3.8
|
84.5
|
1.0
|
CG
|
B:GLU32
|
3.9
|
60.2
|
1.0
|
HD22
|
B:LEU247
|
3.9
|
77.0
|
1.0
|
HB2
|
B:GLU32
|
3.9
|
67.9
|
1.0
|
CD
|
B:ARG36
|
4.0
|
70.4
|
1.0
|
NE
|
B:ARG36
|
4.1
|
77.0
|
1.0
|
HH22
|
B:ARG36
|
4.1
|
0.3
|
1.0
|
HG3
|
B:GLU32
|
4.2
|
72.3
|
1.0
|
NH2
|
B:ARG36
|
4.2
|
85.2
|
1.0
|
HD3
|
B:LYS35
|
4.4
|
66.4
|
1.0
|
HE2
|
B:LYS35
|
4.4
|
69.6
|
1.0
|
O
|
B:ILE248
|
4.5
|
69.1
|
1.0
|
H
|
B:ARG36
|
4.5
|
64.9
|
1.0
|
CB
|
B:LYS35
|
4.7
|
53.7
|
1.0
|
OE2
|
B:GLU32
|
4.7
|
63.8
|
1.0
|
HB3
|
B:LYS35
|
4.7
|
64.5
|
1.0
|
HG2
|
B:GLU32
|
4.7
|
72.3
|
1.0
|
CD2
|
B:LEU247
|
4.8
|
64.2
|
1.0
|
N
|
B:PHE33
|
4.8
|
50.0
|
1.0
|
HD23
|
B:LEU247
|
4.8
|
77.0
|
1.0
|
HB3
|
B:LEU247
|
4.8
|
73.7
|
1.0
|
HZ3
|
B:LYS35
|
4.8
|
72.2
|
1.0
|
HE
|
B:ARG36
|
4.8
|
92.5
|
1.0
|
N
|
B:ARG36
|
4.9
|
54.0
|
1.0
|
CB
|
B:ARG36
|
4.9
|
58.7
|
1.0
|
N
|
B:GLU32
|
4.9
|
53.1
|
1.0
|
H
|
B:ILE248
|
4.9
|
77.6
|
1.0
|
HH21
|
B:ARG36
|
4.9
|
0.3
|
1.0
|
HA
|
B:LEU247
|
5.0
|
74.8
|
1.0
|
|
Reference:
T.M.Hsu,
D.H.Welner,
Z.N.Russ,
B.Cervantes,
R.L.Prathuri,
P.D.Adams,
J.E.Dueber.
Employing A Biochemical Protecting Group For A Sustainable Indigo Dyeing Strategy. Nat. Chem. Biol. V. 14 256 2018.
ISSN: ESSN 1552-4469
PubMed: 29309053
DOI: 10.1038/NCHEMBIO.2552
Page generated: Sun Sep 29 23:20:31 2024
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