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Sodium in PDB 5ypk: Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk was solved by H.Feng, D.Wang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.21 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.240, 73.610, 154.520, 90.00, 90.08, 90.00
R / Rfree (%) 18.6 / 22.9

Other elements in 5ypk:

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex (pdb code 5ypk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5ypk

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Sodium binding site 1 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na306

b:52.2
occ:0.96
 O C:HOH636 2.3 37.8 1.0
O C:HOH559 2.4 52.0 1.0
O C:HOH545 2.5 45.7 1.0
ND2 C:ASN166 3.0 25.8 1.0
O C:HOH590 3.0 31.4 1.0
O C:HOH611 3.7 39.9 1.0
CG C:ASN166 4.1 24.2 1.0
OD1 C:ASN166 4.4 22.8 1.0
CD1 C:TRP168 4.4 23.0 1.0
O C:HOH597 4.7 36.8 1.0
CB C:TRP168 5.0 15.7 1.0
CG C:TRP168 5.0 16.3 1.0

Sodium binding site 2 out of 7 in 5ypk

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Sodium binding site 2 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na307

b:32.9
occ:0.81
 O C:GLY47 2.3 31.4 1.0
NE C:ARG45 2.4 47.5 1.0
OD1 E:ASP48 2.6 34.6 1.0
CZ C:ARG45 2.9 48.3 1.0
NH2 C:ARG45 3.0 42.8 1.0
OD2 E:ASP48 3.0 47.7 1.0
N C:GLY47 3.1 32.8 1.0
CG E:ASP48 3.1 36.5 1.0
C C:GLY47 3.1 34.5 1.0
CA C:GLY47 3.3 34.7 1.0
CD C:ARG45 3.3 41.8 1.0
O E:HOH494 3.3 38.1 1.0
CG C:ARG45 3.4 34.5 1.0
C C:PHE46 4.0 30.2 1.0
NH1 C:ARG45 4.1 56.7 1.0
CB C:ARG45 4.3 31.6 1.0
N C:PHE46 4.3 24.7 1.0
CA C:PHE46 4.4 22.8 1.0
C C:ARG45 4.4 31.0 1.0
N C:ASP48 4.4 32.1 1.0
O C:ARG45 4.5 35.6 1.0
CB E:ASP48 4.6 25.6 1.0
O C:PHE46 4.9 28.1 1.0
O E:HOH495 4.9 35.0 1.0
CA C:ARG45 4.9 34.4 1.0

Sodium binding site 3 out of 7 in 5ypk

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Sodium binding site 3 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na306

b:46.3
occ:1.00
 O D:HOH567 3.1 47.6 1.0
O D:HOH521 3.3 43.4 1.0
O D:HOH569 4.7 47.5 1.0
O D:HOH409 4.8 50.3 1.0

Sodium binding site 4 out of 7 in 5ypk

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Sodium binding site 4 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na307

b:24.7
occ:0.71
 O D:HOH444 2.3 21.9 1.0
NE2 D:GLN151 2.6 30.0 1.0
O D:HOH480 2.6 35.2 1.0
O F:PRO185 2.7 17.1 1.0
CD D:GLN151 3.8 26.8 1.0
O D:HOH492 3.8 36.6 1.0
C F:PRO185 3.8 18.6 1.0
O F:ALA231 4.0 14.1 1.0
CB F:ALA235 4.1 14.7 1.0
OG F:SER232 4.1 21.5 1.0
CA F:SER232 4.1 14.5 1.0
NE2 D:GLN147 4.1 14.1 1.0
CA F:GLY186 4.2 15.8 1.0
C F:ALA231 4.2 13.5 1.0
N F:SER232 4.3 14.5 1.0
OE1 D:GLN151 4.3 22.5 1.0
CG D:GLN147 4.4 19.1 1.0
N F:GLY186 4.4 17.9 1.0
CD D:GLN147 4.6 21.8 1.0
CB F:SER232 4.7 15.8 1.0
CB F:ALA231 4.7 12.3 1.0
O F:HOH436 4.7 18.7 1.0
O D:GLN147 4.8 18.1 1.0
O D:HOH435 4.9 23.5 1.0
CA F:PRO185 5.0 15.8 1.0
CG D:GLN151 5.0 30.4 1.0

Sodium binding site 5 out of 7 in 5ypk

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Sodium binding site 5 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na305

b:28.0
occ:0.48
 O E:HOH599 2.5 37.4 1.0
O E:HOH482 2.6 28.9 1.0
O E:HOH600 2.8 37.7 1.0
O E:ASN166 3.0 19.4 1.0
CZ E:PHE183 3.7 19.6 1.0
C E:ASN166 3.8 20.8 1.0
CE1 E:PHE183 4.1 15.9 1.0
CA E:ASN166 4.3 22.4 1.0
O E:HOH560 4.4 46.9 1.0
CB E:ALA235 4.5 25.8 1.0
CB E:ASN166 4.6 21.4 1.0
N E:GLY167 4.9 16.9 1.0
O E:HOH421 4.9 30.9 1.0
CE2 E:PHE183 4.9 23.5 1.0

Sodium binding site 6 out of 7 in 5ypk

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Sodium binding site 6 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na305

b:46.5
occ:1.00
 O F:HOH587 1.8 37.0 1.0
O F:HOH618 2.2 34.4 1.0
O F:HOH626 2.4 39.4 1.0
O F:HOH595 2.5 41.2 1.0
O F:HOH636 3.7 47.2 1.0
OD2 F:ASP43 3.8 35.7 1.0
O F:HOH646 3.8 45.2 1.0
CG F:ASP43 3.9 44.2 1.0
O F:HOH560 4.1 40.0 1.0
OD1 F:ASP43 4.2 37.0 1.0
CB F:ASP43 4.4 33.8 1.0
NH2 F:ARG52 4.5 38.1 1.0
N F:ASP43 4.7 36.5 1.0
O F:HOH564 4.8 41.3 1.0
O F:HOH604 4.8 28.1 1.0

Sodium binding site 7 out of 7 in 5ypk

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Sodium binding site 7 out of 7 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:30.4
occ:0.58
 OD2 G:ASP223 2.3 42.0 1.0
OE2 G:GLU152 2.3 35.9 1.0
CD G:GLU152 2.7 32.1 1.0
OE1 G:GLU152 2.8 30.6 1.0
O G:HOH525 2.8 23.0 1.0
NE2 G:HIS122 3.0 25.1 1.0
CG G:ASP223 3.1 40.2 1.0
CE1 B:HIS228 3.4 20.7 1.0
NE2 B:HIS228 3.4 26.1 1.0
CD2 G:HIS122 3.5 24.8 1.0
OD1 G:ASP223 3.6 40.3 1.0
CG G:GLU152 3.9 24.2 1.0
CB G:ASP223 4.2 26.8 1.0
CE1 G:HIS122 4.2 26.5 1.0
O G:HOH521 4.4 26.9 1.0
CG B:GLU227 4.4 30.2 1.0
ND1 B:HIS228 4.6 26.0 1.0
O G:ALA121 4.7 21.0 1.0
CD2 B:HIS228 4.7 21.3 1.0
CG G:HIS122 4.8 21.1 1.0
O B:HOH536 4.9 36.8 1.0
CB G:GLU152 5.0 25.2 1.0

Reference:

H.Feng, X.Liu, S.Wang, J.Fleming, D.C.Wang, W.Liu. The Mechanism of Ndm-1-Catalyzed Carbapenem Hydrolysis Is Distinct From That of Penicillin or Cephalosporin Hydrolysis. Nat Commun V. 8 2242 2017.
ISSN: ESSN 2041-1723
PubMed: 29269938
DOI: 10.1038/S41467-017-02339-W
Page generated: Tue Oct 8 01:25:07 2024

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