Atomistry » Sodium » PDB 5xvd-5ysu » 5ypk
Atomistry »
  Sodium »
    PDB 5xvd-5ysu »
      5ypk »

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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Go back to Sodium Binding Sites List in 5ypk
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy