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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

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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

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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

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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

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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

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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

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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

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