Magnesium in PDB 6rd3: Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Protein crystallography data
The structure of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia, PDB code: 6rd3
was solved by
K.Beis,
M.Romano,
J.Kwong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
53.20 /
1.98
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.090,
316.090,
73.790,
90.00,
102.86,
90.00
|
R / Rfree (%)
|
19.4 /
23.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
(pdb code 6rd3). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia, PDB code: 6rd3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 1 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg508
b:23.5
occ:1.00
|
O
|
A:ARG212
|
2.3
|
24.8
|
1.0
|
O
|
A:HOH683
|
2.3
|
28.5
|
1.0
|
O
|
A:HOH690
|
2.3
|
25.6
|
1.0
|
OD1
|
A:ASN241
|
2.4
|
19.9
|
1.0
|
OD1
|
A:ASN252
|
2.4
|
22.4
|
1.0
|
O
|
A:HOH750
|
2.6
|
31.7
|
1.0
|
CG
|
A:ASN241
|
3.2
|
22.4
|
1.0
|
CG
|
A:ASN252
|
3.2
|
23.0
|
1.0
|
ND2
|
A:ASN241
|
3.3
|
19.6
|
1.0
|
C
|
A:ARG212
|
3.4
|
21.3
|
1.0
|
CB
|
A:ASN252
|
3.5
|
20.0
|
1.0
|
CA
|
A:ASN252
|
3.9
|
21.6
|
1.0
|
N
|
A:ARG212
|
4.0
|
20.3
|
1.0
|
O
|
A:ASN252
|
4.2
|
21.1
|
1.0
|
N
|
A:GLY213
|
4.3
|
24.6
|
1.0
|
CA
|
A:GLY213
|
4.3
|
26.6
|
1.0
|
CA
|
A:ARG212
|
4.3
|
19.5
|
1.0
|
ND2
|
A:ASN252
|
4.3
|
22.5
|
1.0
|
C
|
A:ASN252
|
4.5
|
21.5
|
1.0
|
CB
|
A:ASN241
|
4.6
|
18.4
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 2 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg809
b:33.2
occ:1.00
|
O
|
B:ARG212
|
2.3
|
24.0
|
1.0
|
OD1
|
B:ASN252
|
2.3
|
24.4
|
1.0
|
O
|
B:HOH1033
|
2.4
|
23.3
|
1.0
|
OD1
|
B:ASN241
|
2.5
|
23.7
|
1.0
|
O
|
B:HOH1046
|
2.5
|
34.7
|
1.0
|
O
|
B:HOH1035
|
2.6
|
24.7
|
1.0
|
CG
|
B:ASN252
|
3.1
|
22.1
|
1.0
|
CG
|
B:ASN241
|
3.4
|
26.1
|
1.0
|
C
|
B:ARG212
|
3.4
|
21.9
|
1.0
|
ND2
|
B:ASN241
|
3.6
|
22.7
|
1.0
|
CB
|
B:ASN252
|
3.6
|
26.0
|
1.0
|
CA
|
B:ASN252
|
4.0
|
21.9
|
1.0
|
N
|
B:ARG212
|
4.0
|
20.0
|
1.0
|
ND2
|
B:ASN252
|
4.2
|
23.7
|
1.0
|
N
|
B:GLY213
|
4.2
|
22.8
|
1.0
|
CA
|
B:GLY213
|
4.3
|
23.0
|
1.0
|
CA
|
B:ARG212
|
4.3
|
19.9
|
1.0
|
O
|
B:ASN252
|
4.3
|
24.2
|
1.0
|
C
|
B:ASN252
|
4.6
|
21.9
|
1.0
|
CB
|
B:ASN241
|
4.8
|
20.4
|
1.0
|
NZ
|
B:LYS253
|
5.0
|
41.9
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 3 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg403
b:24.7
occ:1.00
|
O
|
C:ARG212
|
2.3
|
20.6
|
1.0
|
O
|
C:HOH623
|
2.3
|
32.3
|
1.0
|
OD1
|
C:ASN241
|
2.4
|
24.2
|
1.0
|
O
|
C:HOH573
|
2.4
|
20.6
|
1.0
|
O
|
F:HOH540
|
2.4
|
25.7
|
1.0
|
OD1
|
C:ASN252
|
2.6
|
20.5
|
1.0
|
CG
|
C:ASN241
|
3.2
|
21.2
|
1.0
|
C
|
C:ARG212
|
3.4
|
22.1
|
1.0
|
ND2
|
C:ASN241
|
3.4
|
19.2
|
1.0
|
CG
|
C:ASN252
|
3.4
|
24.3
|
1.0
|
CB
|
C:ASN252
|
3.8
|
22.4
|
1.0
|
CA
|
C:ASN252
|
4.0
|
24.1
|
1.0
|
CA
|
C:GLY213
|
4.0
|
24.8
|
1.0
|
N
|
C:GLY213
|
4.1
|
24.5
|
1.0
|
N
|
C:ARG212
|
4.2
|
19.0
|
1.0
|
O
|
C:ASN252
|
4.3
|
22.7
|
1.0
|
CA
|
C:ARG212
|
4.4
|
24.8
|
1.0
|
ND2
|
C:ASN252
|
4.6
|
25.6
|
1.0
|
C
|
C:ASN252
|
4.6
|
20.8
|
1.0
|
CB
|
C:ASN241
|
4.7
|
18.1
|
1.0
|
OD2
|
F:ASP214
|
4.8
|
26.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 4 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:21.1
occ:1.00
|
O
|
D:HOH607
|
2.3
|
21.5
|
1.0
|
OD1
|
D:ASN241
|
2.3
|
18.1
|
1.0
|
O
|
D:HOH648
|
2.4
|
28.4
|
1.0
|
O
|
D:ARG212
|
2.4
|
22.3
|
1.0
|
O
|
D:HOH639
|
2.4
|
26.5
|
1.0
|
OD1
|
D:ASN252
|
2.4
|
19.0
|
1.0
|
CG
|
D:ASN252
|
3.2
|
23.1
|
1.0
|
CG
|
D:ASN241
|
3.2
|
21.1
|
1.0
|
ND2
|
D:ASN241
|
3.4
|
17.7
|
1.0
|
C
|
D:ARG212
|
3.5
|
22.6
|
1.0
|
CB
|
D:ASN252
|
3.6
|
21.7
|
1.0
|
CA
|
D:ASN252
|
3.9
|
22.1
|
1.0
|
ND2
|
D:ASN252
|
4.2
|
23.5
|
1.0
|
N
|
D:ARG212
|
4.2
|
22.3
|
1.0
|
O
|
D:ASN252
|
4.2
|
20.0
|
1.0
|
CA
|
D:GLY213
|
4.3
|
22.6
|
1.0
|
N
|
D:GLY213
|
4.3
|
22.6
|
1.0
|
CA
|
D:ARG212
|
4.4
|
19.9
|
1.0
|
C
|
D:ASN252
|
4.5
|
21.0
|
1.0
|
CB
|
D:ASN241
|
4.7
|
18.4
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 5 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg406
b:36.6
occ:1.00
|
O
|
E:HOH631
|
2.2
|
31.3
|
1.0
|
O
|
E:HOH627
|
2.3
|
37.7
|
1.0
|
O
|
E:ARG212
|
2.3
|
26.3
|
1.0
|
OD1
|
E:ASN241
|
2.5
|
26.5
|
1.0
|
O
|
E:HOH603
|
2.5
|
34.0
|
1.0
|
OD1
|
E:ASN252
|
2.6
|
26.1
|
1.0
|
CG
|
E:ASN241
|
3.2
|
25.4
|
1.0
|
ND2
|
E:ASN241
|
3.3
|
24.9
|
1.0
|
CG
|
E:ASN252
|
3.4
|
27.9
|
1.0
|
C
|
E:ARG212
|
3.5
|
23.5
|
1.0
|
CB
|
E:ASN252
|
3.8
|
25.7
|
1.0
|
CA
|
E:ASN252
|
4.2
|
25.4
|
1.0
|
CA
|
E:GLY213
|
4.3
|
23.1
|
1.0
|
N
|
E:ARG212
|
4.3
|
25.6
|
1.0
|
N
|
E:GLY213
|
4.3
|
22.4
|
1.0
|
O
|
E:ASN252
|
4.4
|
23.7
|
1.0
|
ND2
|
E:ASN252
|
4.4
|
25.5
|
1.0
|
CA
|
E:ARG212
|
4.5
|
26.4
|
1.0
|
CB
|
E:ASN241
|
4.7
|
27.3
|
1.0
|
C
|
E:ASN252
|
4.7
|
26.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6rd3
Go back to
Magnesium Binding Sites List in 6rd3
Magnesium binding site 6 out
of 6 in the Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the Wild Type OMPK36 From Klebsiella Pneumonia within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg404
b:29.6
occ:1.00
|
OD1
|
F:ASN241
|
2.3
|
25.2
|
1.0
|
O
|
F:ARG212
|
2.4
|
25.9
|
1.0
|
O
|
C:HOH607
|
2.4
|
24.9
|
1.0
|
O
|
F:HOH556
|
2.4
|
23.7
|
1.0
|
O
|
F:HOH622
|
2.6
|
33.9
|
1.0
|
OD1
|
F:ASN252
|
2.6
|
21.8
|
1.0
|
CG
|
F:ASN241
|
3.2
|
26.6
|
1.0
|
CG
|
F:ASN252
|
3.4
|
28.7
|
1.0
|
ND2
|
F:ASN241
|
3.4
|
24.2
|
1.0
|
C
|
F:ARG212
|
3.4
|
24.6
|
1.0
|
CB
|
F:ASN252
|
3.7
|
24.1
|
1.0
|
CA
|
F:ASN252
|
4.0
|
25.6
|
1.0
|
CA
|
F:GLY213
|
4.1
|
23.5
|
1.0
|
N
|
F:ARG212
|
4.2
|
22.5
|
1.0
|
O
|
F:ASN252
|
4.2
|
23.5
|
1.0
|
N
|
F:GLY213
|
4.2
|
22.7
|
1.0
|
CA
|
F:ARG212
|
4.4
|
24.5
|
1.0
|
ND2
|
F:ASN252
|
4.4
|
24.2
|
1.0
|
C
|
F:ASN252
|
4.5
|
22.2
|
1.0
|
CB
|
F:ASN241
|
4.6
|
22.9
|
1.0
|
O
|
C:HOH636
|
4.8
|
35.7
|
1.0
|
|
Reference:
J.L.C.Wong,
M.Romano,
L.E.Kerry,
H.S.Kwong,
W.W.Low,
S.J.Brett,
A.Clements,
K.Beis,
G.Frankel.
OMPK36-Mediated Carbapenem Resistance Attenuates ST258 Klebsiella Pneumoniae in Vivo. Nat Commun V. 10 3957 2019.
ISSN: ESSN 2041-1723
PubMed: 31477712
DOI: 10.1038/S41467-019-11756-Y
Page generated: Tue Oct 1 16:41:52 2024
|