Magnesium in PDB 6ktz: The Complex Structure of Eanb/C412S with Hercynine
Protein crystallography data
The structure of The Complex Structure of Eanb/C412S with Hercynine, PDB code: 6ktz
was solved by
L.Wu,
P.H.Liu,
J.H.Zhou,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.10 /
2.00
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.240,
111.090,
60.360,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
21.6
|
Other elements in 6ktz:
The structure of The Complex Structure of Eanb/C412S with Hercynine also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The Complex Structure of Eanb/C412S with Hercynine
(pdb code 6ktz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
The Complex Structure of Eanb/C412S with Hercynine, PDB code: 6ktz:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 6ktz
Go back to
Magnesium Binding Sites List in 6ktz
Magnesium binding site 1 out
of 3 in the The Complex Structure of Eanb/C412S with Hercynine
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The Complex Structure of Eanb/C412S with Hercynine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:19.3
occ:1.00
|
O
|
A:THR414
|
2.3
|
17.9
|
1.0
|
O
|
A:ASP437
|
2.3
|
14.6
|
1.0
|
O
|
A:HOH756
|
2.4
|
21.3
|
1.0
|
O
|
A:TRP216
|
2.4
|
16.0
|
1.0
|
OD1
|
A:ASN217
|
2.4
|
21.1
|
1.0
|
OD1
|
A:ASP437
|
2.7
|
20.1
|
1.0
|
C
|
A:ASP437
|
3.1
|
21.3
|
1.0
|
C
|
A:TRP216
|
3.2
|
18.9
|
1.0
|
C
|
A:THR414
|
3.3
|
20.1
|
1.0
|
CG
|
A:ASP437
|
3.5
|
18.6
|
1.0
|
CG
|
A:ASN217
|
3.6
|
22.2
|
1.0
|
CA
|
A:ASN217
|
3.6
|
16.8
|
1.0
|
N
|
A:ASN217
|
3.7
|
16.1
|
1.0
|
NH2
|
A:ARG266
|
3.8
|
16.2
|
1.0
|
CA
|
A:THR414
|
3.8
|
17.1
|
1.0
|
N
|
A:GLY438
|
3.9
|
17.7
|
1.0
|
CA
|
A:ASP437
|
4.0
|
19.6
|
1.0
|
CA
|
A:GLY438
|
4.0
|
19.9
|
1.0
|
CB
|
A:THR414
|
4.1
|
20.0
|
1.0
|
O
|
A:GLY438
|
4.1
|
20.8
|
1.0
|
CB
|
A:ASP437
|
4.2
|
18.9
|
1.0
|
O
|
A:HOH735
|
4.2
|
21.2
|
1.0
|
CB
|
A:ASN217
|
4.2
|
18.4
|
1.0
|
C
|
A:GLY438
|
4.2
|
19.7
|
1.0
|
OD2
|
A:ASP437
|
4.2
|
19.1
|
1.0
|
N
|
A:GLY415
|
4.3
|
19.8
|
1.0
|
O
|
A:THR215
|
4.4
|
18.1
|
1.0
|
CA
|
A:TRP216
|
4.4
|
18.6
|
1.0
|
CB
|
A:TRP216
|
4.5
|
19.3
|
1.0
|
CZ
|
A:ARG266
|
4.6
|
17.6
|
1.0
|
CA
|
A:GLY415
|
4.6
|
21.5
|
1.0
|
O
|
A:HOH642
|
4.6
|
18.7
|
1.0
|
ND2
|
A:ASN217
|
4.7
|
25.8
|
1.0
|
NH1
|
A:ARG266
|
4.7
|
21.4
|
1.0
|
OG1
|
A:THR414
|
4.8
|
23.8
|
1.0
|
C
|
A:ASN217
|
4.9
|
19.5
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 6ktz
Go back to
Magnesium Binding Sites List in 6ktz
Magnesium binding site 2 out
of 3 in the The Complex Structure of Eanb/C412S with Hercynine
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The Complex Structure of Eanb/C412S with Hercynine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:33.9
occ:1.00
|
O
|
A:SER332
|
2.2
|
32.2
|
1.0
|
O
|
A:HOH931
|
2.4
|
32.7
|
1.0
|
O
|
A:SER335
|
2.4
|
24.1
|
1.0
|
O
|
A:HOH800
|
2.5
|
34.7
|
1.0
|
O
|
A:MET329
|
2.5
|
27.4
|
1.0
|
O
|
A:HOH761
|
2.5
|
35.5
|
1.0
|
C
|
A:SER332
|
3.4
|
31.5
|
1.0
|
C
|
A:SER335
|
3.5
|
21.8
|
1.0
|
C
|
A:MET329
|
3.7
|
22.7
|
1.0
|
N
|
A:SER332
|
3.7
|
29.7
|
1.0
|
O
|
A:LEU330
|
3.7
|
29.5
|
1.0
|
C
|
A:LEU330
|
3.8
|
23.8
|
1.0
|
OD1
|
A:ASP336
|
3.9
|
30.0
|
1.0
|
CA
|
A:LEU330
|
4.0
|
24.1
|
1.0
|
CA
|
A:SER332
|
4.1
|
29.4
|
1.0
|
N
|
A:SER335
|
4.2
|
24.3
|
1.0
|
N
|
A:GLN331
|
4.2
|
30.1
|
1.0
|
CA
|
A:SER335
|
4.3
|
25.3
|
1.0
|
N
|
A:LEU330
|
4.4
|
22.0
|
1.0
|
CG
|
A:ASP336
|
4.4
|
24.9
|
1.0
|
N
|
A:ASP336
|
4.4
|
17.9
|
1.0
|
N
|
A:GLU333
|
4.4
|
33.9
|
1.0
|
C
|
A:GLN331
|
4.4
|
31.9
|
1.0
|
CA
|
A:ASP336
|
4.5
|
18.2
|
1.0
|
CB
|
A:SER335
|
4.5
|
24.8
|
1.0
|
O
|
A:HOH717
|
4.5
|
18.5
|
1.0
|
CA
|
A:GLU333
|
4.6
|
37.9
|
1.0
|
C
|
A:GLU333
|
4.7
|
31.7
|
1.0
|
O
|
A:GLU333
|
4.7
|
36.4
|
1.0
|
CB
|
A:SER332
|
4.8
|
30.8
|
1.0
|
OD2
|
A:ASP336
|
4.8
|
30.3
|
1.0
|
CA
|
A:GLN331
|
4.8
|
28.5
|
1.0
|
O
|
A:HOH621
|
4.8
|
33.2
|
1.0
|
CA
|
A:MET329
|
4.9
|
23.1
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 6ktz
Go back to
Magnesium Binding Sites List in 6ktz
Magnesium binding site 3 out
of 3 in the The Complex Structure of Eanb/C412S with Hercynine
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The Complex Structure of Eanb/C412S with Hercynine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:34.1
occ:1.00
|
O
|
A:HOH854
|
2.3
|
26.6
|
1.0
|
O
|
A:HOH949
|
2.3
|
24.7
|
1.0
|
O
|
A:VAL50
|
2.4
|
22.3
|
1.0
|
O
|
A:SER47
|
2.4
|
25.8
|
1.0
|
O
|
A:HOH938
|
2.5
|
25.6
|
1.0
|
O
|
A:HOH873
|
2.6
|
31.1
|
1.0
|
C
|
A:VAL50
|
3.5
|
25.8
|
1.0
|
C
|
A:SER47
|
3.6
|
30.1
|
1.0
|
O
|
A:HOH990
|
4.0
|
30.2
|
1.0
|
CB
|
A:VAL50
|
4.1
|
24.4
|
1.0
|
O
|
A:HOH707
|
4.1
|
25.4
|
1.0
|
CA
|
A:VAL50
|
4.1
|
26.7
|
1.0
|
N
|
A:VAL50
|
4.1
|
26.8
|
1.0
|
O
|
A:HOH747
|
4.3
|
23.8
|
1.0
|
O
|
A:LEU45
|
4.3
|
28.9
|
1.0
|
N
|
A:SER47
|
4.4
|
26.6
|
1.0
|
N
|
A:GLU48
|
4.4
|
28.1
|
1.0
|
CA
|
A:GLU48
|
4.4
|
27.5
|
1.0
|
CA
|
A:SER47
|
4.5
|
29.0
|
1.0
|
O
|
A:HOH997
|
4.5
|
29.5
|
1.0
|
C
|
A:GLU48
|
4.5
|
31.0
|
1.0
|
N
|
A:LYS51
|
4.5
|
19.5
|
1.0
|
O
|
A:LEU44
|
4.6
|
24.1
|
1.0
|
O
|
A:GLU48
|
4.6
|
29.7
|
1.0
|
O
|
A:HOH709
|
4.7
|
30.2
|
1.0
|
CA
|
A:LYS51
|
4.8
|
18.7
|
1.0
|
CG1
|
A:VAL50
|
4.8
|
22.3
|
1.0
|
C
|
A:GLY46
|
4.9
|
30.6
|
1.0
|
C
|
A:LEU45
|
5.0
|
24.3
|
1.0
|
CB
|
A:SER47
|
5.0
|
26.8
|
1.0
|
|
Reference:
R.Cheng,
L.Wu,
R.Lai,
C.Peng,
N.Naowarojna,
W.Hu,
X.Li,
S.A.Whelan,
N.Lee,
J.Lopez,
C.Zhao,
Y.Yong,
J.Xue,
X.Jiang,
M.W.Grinstaff,
Z.Deng,
J.Chen,
Q.Cui,
J.H.Zhou,
P.Liu.
Single-Step Replacement of An Unreactive C-H Bond By A C-S Bond Using Polysulfide As the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis Acs Catalysis V. 10 8981 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C01809
Page generated: Tue Oct 1 09:53:59 2024
|