Magnesium in PDB 6peu: Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Protein crystallography data
The structure of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide, PDB code: 6peu
was solved by
S.-H.Dong,
S.K.Nair,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.324,
149.755,
105.671,
90.00,
103.57,
90.00
|
R / Rfree (%)
|
19.5 /
23.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
(pdb code 6peu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide, PDB code: 6peu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 6peu
Go back to
Magnesium Binding Sites List in 6peu
Magnesium binding site 1 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:33.8
occ:1.00
|
O
|
A:HOH690
|
2.2
|
29.2
|
1.0
|
OE2
|
A:GLU173
|
2.2
|
27.0
|
1.0
|
O
|
M:HOH501
|
2.2
|
25.9
|
1.0
|
O1B
|
A:ATP500
|
2.3
|
34.8
|
1.0
|
O
|
A:HOH620
|
2.3
|
26.7
|
1.0
|
O
|
A:HOH645
|
2.4
|
23.6
|
1.0
|
CD
|
A:GLU173
|
3.3
|
25.7
|
1.0
|
PB
|
A:ATP500
|
3.5
|
37.0
|
1.0
|
OE1
|
A:GLU173
|
3.6
|
24.4
|
1.0
|
O
|
A:HOH601
|
3.8
|
32.4
|
1.0
|
O2B
|
A:ATP500
|
3.8
|
36.1
|
1.0
|
O1G
|
A:ATP500
|
3.8
|
34.1
|
1.0
|
O2G
|
A:ATP500
|
3.9
|
34.1
|
1.0
|
OE1
|
A:GLU85
|
3.9
|
27.6
|
1.0
|
O
|
A:LEU157
|
4.1
|
23.5
|
1.0
|
NE2
|
A:HIS169
|
4.2
|
31.8
|
1.0
|
OE2
|
A:GLU85
|
4.2
|
27.4
|
1.0
|
O3B
|
A:ATP500
|
4.2
|
36.1
|
1.0
|
NH2
|
A:ARG86
|
4.2
|
23.1
|
1.0
|
PG
|
A:ATP500
|
4.3
|
35.5
|
1.0
|
O
|
M:HOH502
|
4.3
|
24.8
|
1.0
|
O
|
M:GLY448
|
4.3
|
30.8
|
1.0
|
CD
|
A:GLU85
|
4.5
|
27.5
|
1.0
|
C3'
|
A:ATP500
|
4.6
|
24.4
|
1.0
|
CG
|
A:GLU173
|
4.6
|
24.2
|
1.0
|
C5'
|
A:ATP500
|
4.6
|
27.1
|
1.0
|
CD2
|
A:HIS169
|
4.6
|
30.5
|
1.0
|
O3A
|
A:ATP500
|
4.8
|
35.2
|
1.0
|
C4'
|
A:ATP500
|
4.9
|
26.2
|
1.0
|
O3'
|
A:ATP500
|
4.9
|
23.3
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 6peu
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Magnesium Binding Sites List in 6peu
Magnesium binding site 2 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:29.1
occ:1.00
|
O
|
A:HOH657
|
2.1
|
34.8
|
1.0
|
O3G
|
A:ATP500
|
2.3
|
32.3
|
1.0
|
O
|
A:VAL249
|
2.4
|
25.6
|
1.0
|
OE2
|
A:GLU176
|
2.4
|
25.2
|
1.0
|
OE2
|
A:GLU265
|
2.5
|
25.5
|
1.0
|
OE1
|
A:GLU265
|
2.7
|
24.1
|
1.0
|
CD
|
A:GLU265
|
2.9
|
24.6
|
1.0
|
CD
|
A:GLU176
|
3.1
|
26.3
|
1.0
|
PG
|
A:ATP500
|
3.2
|
35.5
|
1.0
|
O1G
|
A:ATP500
|
3.3
|
34.1
|
1.0
|
OE1
|
A:GLU176
|
3.3
|
26.8
|
1.0
|
C
|
A:VAL249
|
3.5
|
24.6
|
1.0
|
O
|
A:HOH746
|
4.0
|
48.8
|
1.0
|
CA
|
A:VAL249
|
4.1
|
25.1
|
1.0
|
N
|
A:VAL249
|
4.1
|
25.0
|
1.0
|
CB
|
A:VAL249
|
4.1
|
25.4
|
1.0
|
O2G
|
A:ATP500
|
4.2
|
34.1
|
1.0
|
CZ3
|
A:TRP180
|
4.3
|
28.5
|
1.0
|
CG
|
A:GLU265
|
4.4
|
23.6
|
1.0
|
O
|
M:HOH506
|
4.4
|
0.2
|
1.0
|
O3B
|
A:ATP500
|
4.4
|
36.1
|
1.0
|
NH2
|
A:ARG177
|
4.4
|
24.2
|
1.0
|
O
|
M:TYR447
|
4.4
|
29.5
|
1.0
|
NE
|
A:ARG177
|
4.5
|
24.7
|
1.0
|
CG
|
A:GLU176
|
4.5
|
24.8
|
1.0
|
O
|
A:HOH738
|
4.6
|
35.7
|
1.0
|
N
|
A:GLY250
|
4.7
|
23.5
|
1.0
|
O
|
A:HOH653
|
4.9
|
30.3
|
1.0
|
CZ
|
A:ARG177
|
4.9
|
24.5
|
1.0
|
CG1
|
A:VAL249
|
4.9
|
26.0
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 6peu
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Magnesium Binding Sites List in 6peu
Magnesium binding site 3 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:29.9
occ:1.00
|
O
|
B:HOH740
|
2.1
|
25.4
|
1.0
|
O
|
B:HOH688
|
2.2
|
29.3
|
1.0
|
O
|
B:HOH634
|
2.3
|
23.8
|
1.0
|
O1B
|
B:ATP500
|
2.3
|
33.2
|
1.0
|
OE2
|
B:GLU173
|
2.3
|
21.4
|
1.0
|
O
|
B:HOH670
|
2.5
|
24.2
|
1.0
|
CD
|
B:GLU173
|
3.3
|
20.4
|
1.0
|
PB
|
B:ATP500
|
3.5
|
39.6
|
1.0
|
OE1
|
B:GLU173
|
3.7
|
21.2
|
1.0
|
O
|
B:HOH615
|
3.8
|
32.9
|
1.0
|
O2G
|
B:ATP500
|
3.8
|
39.4
|
1.0
|
O2B
|
B:ATP500
|
3.8
|
36.9
|
1.0
|
O1G
|
B:ATP500
|
3.9
|
38.8
|
1.0
|
OE1
|
B:GLU85
|
4.0
|
21.4
|
1.0
|
O
|
B:LEU157
|
4.1
|
21.0
|
1.0
|
CE1
|
B:HIS169
|
4.2
|
25.1
|
1.0
|
OE2
|
B:GLU85
|
4.2
|
22.0
|
1.0
|
PG
|
B:ATP500
|
4.3
|
42.4
|
1.0
|
O3B
|
B:ATP500
|
4.3
|
39.8
|
1.0
|
O
|
N:GLY448
|
4.3
|
23.1
|
1.0
|
O
|
N:HOH501
|
4.4
|
19.9
|
1.0
|
CD
|
B:GLU85
|
4.5
|
21.0
|
1.0
|
C3'
|
B:ATP500
|
4.6
|
23.1
|
1.0
|
C5'
|
B:ATP500
|
4.6
|
24.6
|
1.0
|
CG
|
B:GLU173
|
4.6
|
19.6
|
1.0
|
NH2
|
B:ARG86
|
4.7
|
33.5
|
1.0
|
ND1
|
B:HIS169
|
4.8
|
25.4
|
1.0
|
O3A
|
B:ATP500
|
4.8
|
33.7
|
1.0
|
C4'
|
B:ATP500
|
4.9
|
23.8
|
1.0
|
O3'
|
B:ATP500
|
4.9
|
22.0
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 6peu
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Magnesium Binding Sites List in 6peu
Magnesium binding site 4 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:34.3
occ:1.00
|
O
|
B:HOH642
|
2.3
|
32.9
|
1.0
|
O3G
|
B:ATP500
|
2.3
|
39.2
|
1.0
|
O
|
B:VAL249
|
2.4
|
25.6
|
1.0
|
OE2
|
B:GLU176
|
2.4
|
22.8
|
1.0
|
OE2
|
B:GLU265
|
2.5
|
23.9
|
1.0
|
OE1
|
B:GLU265
|
2.6
|
23.3
|
1.0
|
CD
|
B:GLU265
|
2.9
|
24.2
|
1.0
|
CD
|
B:GLU176
|
3.1
|
23.3
|
1.0
|
OE1
|
B:GLU176
|
3.2
|
25.5
|
1.0
|
O1G
|
B:ATP500
|
3.2
|
38.8
|
1.0
|
PG
|
B:ATP500
|
3.2
|
42.4
|
1.0
|
C
|
B:VAL249
|
3.5
|
23.9
|
1.0
|
N
|
B:VAL249
|
4.0
|
25.5
|
1.0
|
CA
|
B:VAL249
|
4.0
|
24.2
|
1.0
|
CB
|
B:VAL249
|
4.1
|
24.5
|
1.0
|
CZ3
|
B:TRP180
|
4.2
|
23.8
|
1.0
|
O2G
|
B:ATP500
|
4.3
|
39.4
|
1.0
|
CG
|
B:GLU265
|
4.4
|
22.1
|
1.0
|
O3B
|
B:ATP500
|
4.4
|
39.8
|
1.0
|
O
|
N:TYR447
|
4.5
|
26.3
|
1.0
|
CG
|
B:GLU176
|
4.5
|
23.1
|
1.0
|
O
|
N:HOH503
|
4.5
|
0.2
|
1.0
|
NE
|
B:ARG177
|
4.5
|
21.0
|
1.0
|
NH2
|
B:ARG177
|
4.5
|
21.7
|
1.0
|
N
|
B:GLY250
|
4.6
|
22.3
|
1.0
|
O
|
B:HOH757
|
4.7
|
53.2
|
1.0
|
O
|
B:HOH672
|
4.9
|
27.2
|
1.0
|
CE3
|
B:TRP180
|
4.9
|
23.6
|
1.0
|
CH2
|
B:TRP180
|
5.0
|
23.8
|
1.0
|
CG1
|
B:VAL249
|
5.0
|
23.9
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 6peu
Go back to
Magnesium Binding Sites List in 6peu
Magnesium binding site 5 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:31.2
occ:1.00
|
O
|
C:HOH642
|
2.1
|
29.5
|
1.0
|
OE2
|
C:GLU173
|
2.2
|
25.6
|
1.0
|
O
|
C:HOH672
|
2.3
|
24.4
|
1.0
|
O1B
|
C:ATP500
|
2.4
|
30.9
|
1.0
|
O
|
C:HOH624
|
2.4
|
24.0
|
1.0
|
O
|
P:HOH501
|
2.5
|
29.0
|
1.0
|
CD
|
C:GLU173
|
3.2
|
24.9
|
1.0
|
PB
|
C:ATP500
|
3.5
|
39.6
|
1.0
|
OE1
|
C:GLU173
|
3.6
|
24.2
|
1.0
|
O2B
|
C:ATP500
|
3.8
|
38.4
|
1.0
|
O
|
C:HOH616
|
3.8
|
42.4
|
1.0
|
O2G
|
C:ATP500
|
3.9
|
36.9
|
1.0
|
OE1
|
C:GLU85
|
4.0
|
27.5
|
1.0
|
O1G
|
C:ATP500
|
4.0
|
38.7
|
1.0
|
O
|
C:LEU157
|
4.0
|
21.7
|
1.0
|
O
|
P:HOH503
|
4.1
|
21.5
|
1.0
|
OE2
|
C:GLU85
|
4.2
|
27.6
|
1.0
|
NE2
|
C:HIS169
|
4.2
|
28.0
|
1.0
|
NH2
|
C:ARG86
|
4.3
|
22.7
|
1.0
|
O
|
P:GLY448
|
4.3
|
26.5
|
1.0
|
O3B
|
C:ATP500
|
4.3
|
39.7
|
1.0
|
PG
|
C:ATP500
|
4.3
|
40.6
|
1.0
|
CD
|
C:GLU85
|
4.5
|
27.7
|
1.0
|
CG
|
C:GLU173
|
4.5
|
24.8
|
1.0
|
C3'
|
C:ATP500
|
4.6
|
23.1
|
1.0
|
CD2
|
C:HIS169
|
4.7
|
26.6
|
1.0
|
C5'
|
C:ATP500
|
4.7
|
24.5
|
1.0
|
O3'
|
C:ATP500
|
4.8
|
24.0
|
1.0
|
O3A
|
C:ATP500
|
4.8
|
33.7
|
1.0
|
NH2
|
C:ARG177
|
4.9
|
26.9
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 6peu
Go back to
Magnesium Binding Sites List in 6peu
Magnesium binding site 6 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:36.2
occ:1.00
|
O
|
D:HOH638
|
2.1
|
26.3
|
1.0
|
O
|
D:HOH657
|
2.3
|
32.4
|
1.0
|
OE2
|
D:GLU173
|
2.3
|
25.5
|
1.0
|
O1B
|
D:ATP500
|
2.3
|
37.4
|
1.0
|
O
|
D:HOH609
|
2.5
|
35.7
|
1.0
|
O
|
D:HOH634
|
2.6
|
25.9
|
1.0
|
CD
|
D:GLU173
|
3.3
|
24.5
|
1.0
|
PB
|
D:ATP500
|
3.4
|
43.0
|
1.0
|
OE1
|
D:GLU173
|
3.7
|
25.3
|
1.0
|
O2B
|
D:ATP500
|
3.7
|
43.1
|
1.0
|
O2G
|
D:ATP500
|
3.8
|
36.4
|
1.0
|
O
|
D:HOH618
|
3.9
|
32.6
|
1.0
|
OE1
|
D:GLU85
|
3.9
|
29.1
|
1.0
|
O1G
|
D:ATP500
|
3.9
|
39.3
|
1.0
|
O
|
D:LEU157
|
4.1
|
27.4
|
1.0
|
O3B
|
D:ATP500
|
4.2
|
40.0
|
1.0
|
PG
|
D:ATP500
|
4.2
|
37.3
|
1.0
|
OE2
|
D:GLU85
|
4.3
|
31.4
|
1.0
|
NE2
|
D:HIS169
|
4.3
|
33.6
|
1.0
|
NH2
|
D:ARG86
|
4.4
|
25.6
|
1.0
|
C3'
|
D:ATP500
|
4.4
|
27.4
|
1.0
|
O
|
Q:GLY448
|
4.4
|
29.3
|
1.0
|
O
|
Q:HOH501
|
4.5
|
21.6
|
1.0
|
CD
|
D:GLU85
|
4.5
|
30.0
|
1.0
|
C5'
|
D:ATP500
|
4.6
|
28.3
|
1.0
|
CD2
|
D:HIS169
|
4.6
|
31.4
|
1.0
|
CG
|
D:GLU173
|
4.6
|
24.8
|
1.0
|
O3'
|
D:ATP500
|
4.7
|
28.1
|
1.0
|
C4'
|
D:ATP500
|
4.8
|
29.1
|
1.0
|
O3A
|
D:ATP500
|
4.8
|
40.4
|
1.0
|
O5'
|
D:ATP500
|
5.0
|
29.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 6peu
Go back to
Magnesium Binding Sites List in 6peu
Magnesium binding site 7 out
of 7 in the Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Ycao Enzyme From Methanocaldococcus Jannaschii in Complex with Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:34.4
occ:1.00
|
O
|
D:HOH631
|
2.2
|
32.9
|
1.0
|
O
|
D:VAL249
|
2.3
|
25.6
|
1.0
|
O3G
|
D:ATP500
|
2.4
|
35.6
|
1.0
|
OE2
|
D:GLU176
|
2.4
|
28.0
|
1.0
|
OE1
|
D:GLU265
|
2.5
|
26.1
|
1.0
|
OE2
|
D:GLU265
|
2.6
|
25.6
|
1.0
|
CD
|
D:GLU265
|
2.9
|
24.2
|
1.0
|
CD
|
D:GLU176
|
3.1
|
27.8
|
1.0
|
O1G
|
D:ATP500
|
3.3
|
39.3
|
1.0
|
OE1
|
D:GLU176
|
3.3
|
29.1
|
1.0
|
PG
|
D:ATP500
|
3.3
|
37.3
|
1.0
|
C
|
D:VAL249
|
3.4
|
25.5
|
1.0
|
N
|
D:VAL249
|
4.0
|
24.4
|
1.0
|
CA
|
D:VAL249
|
4.0
|
25.8
|
1.0
|
CB
|
D:VAL249
|
4.1
|
25.4
|
1.0
|
O2G
|
D:ATP500
|
4.3
|
36.4
|
1.0
|
CG
|
D:GLU265
|
4.4
|
23.8
|
1.0
|
CZ3
|
D:TRP180
|
4.4
|
26.0
|
1.0
|
CG
|
D:GLU176
|
4.5
|
26.9
|
1.0
|
O3B
|
D:ATP500
|
4.5
|
40.0
|
1.0
|
N
|
D:GLY250
|
4.5
|
26.8
|
1.0
|
O
|
Q:TYR447
|
4.5
|
29.4
|
1.0
|
NE
|
D:ARG177
|
4.6
|
23.6
|
1.0
|
NH2
|
D:ARG177
|
4.6
|
21.9
|
1.0
|
O
|
D:HOH735
|
4.7
|
35.8
|
1.0
|
CG1
|
D:VAL249
|
4.8
|
26.1
|
1.0
|
O
|
D:HOH616
|
4.8
|
48.4
|
1.0
|
CA
|
D:GLY250
|
4.9
|
26.4
|
1.0
|
O
|
D:HOH711
|
5.0
|
32.7
|
1.0
|
|
Reference:
S.H.Dong,
A.Liu,
N.Mahanta,
D.A.Mitchell,
S.K.Nair.
Mechanistic Basis For Ribosomal Peptide Backbone Modifications. Acs Cent.Sci. V. 5 842 2019.
ISSN: ESSN 2374-7951
PubMed: 31139720
DOI: 10.1021/ACSCENTSCI.9B00124
Page generated: Tue Oct 1 14:07:21 2024
|