Atomistry » Sodium » PDB 4ehu-4f5q » 4euz
Atomistry »
  Sodium »
    PDB 4ehu-4f5q »
      4euz »

Sodium in PDB 4euz: Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex

Enzymatic activity of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex

All present enzymatic activity of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex, PDB code: 4euz was solved by F.Fonseca, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.42 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.060, 61.910, 79.010, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 13.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex (pdb code 4euz). 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex, PDB code: 4euz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 1 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:29.4
occ:1.00
 O A:HOH844 2.6 35.5 1.0
OE2 A:GLU203 2.7 13.0 1.0
OG A:SER84 2.8 15.3 1.0
O A:HOH836 3.1 29.1 1.0
CD A:GLU203 3.5 11.3 1.0
CG A:GLU203 3.5 10.7 1.0
CB A:SER84 3.9 11.0 1.0
CD1 A:LEU91 3.9 14.1 1.0
O A:HOH775 3.9 29.1 1.0
O A:HOH759 4.3 22.9 1.0
C A:SER84 4.3 11.6 1.0
O A:SER84 4.5 13.0 1.0
N A:GLN85 4.5 13.2 1.0
O A:LEU81 4.5 8.3 1.0
CD2 A:LEU81 4.5 9.7 1.0
CG A:LEU91 4.5 11.5 1.0
CG2 A:THR202 4.6 17.3 1.0
O A:HOH668 4.6 16.7 1.0
OE1 A:GLU203 4.7 11.3 1.0
CA A:GLN85 4.7 15.7 1.0
O A:HOH750 4.7 30.8 1.0
CA A:SER84 4.8 10.5 1.0
CB A:GLU203 4.8 8.9 1.0

Sodium binding site 2 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 2 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:75.0
occ:1.00
 O A:HOH816 2.2 32.7 1.0
O A:HOH694 2.9 15.9 1.0
NH2 A:ARG43 3.2 10.6 0.5
NH2 A:ARG43 3.3 8.4 0.5
O A:HOH654 3.6 11.7 1.0
NE A:ARG43 3.7 9.9 0.5
CB A:PRO174 3.7 10.3 1.0
CZ A:ARG43 3.7 8.4 0.5
CA A:PRO174 3.7 9.2 1.0
CZ A:ARG43 3.8 9.0 0.5
O A:HOH957 3.9 47.8 1.0
O A:HOH1050 3.9 43.0 1.0
NE A:ARG43 4.1 10.8 0.5
OG A:SER266 4.1 13.7 1.0
CG A:PRO174 4.2 10.8 1.0
N A:GLY175 4.3 10.7 1.0
O A:HOH644 4.4 21.6 1.0
O A:HOH877 4.4 16.4 1.0
NH1 A:ARG43 4.5 7.3 0.5
C A:PRO174 4.6 8.9 1.0
O A:HOH1073 4.6 51.1 1.0
NH1 A:ARG43 4.6 9.2 0.5
CD A:ARG43 4.7 11.1 0.5
O A:HOH1024 4.8 47.7 1.0
O A:HOH622 4.8 7.3 1.0
N A:PRO174 4.9 8.1 1.0

Sodium binding site 3 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 3 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:21.6
occ:1.00
 O A:HOH938 2.4 39.7 1.0
O A:HOH985 2.6 38.5 1.0
O A:GLU121 2.8 6.9 1.0
O A:HOH714 2.8 21.4 1.0
O A:HOH689 3.0 13.7 1.0
C A:GLU121 3.6 6.3 1.0
N A:ALA125 3.6 6.7 1.0
CA A:GLU121 3.6 7.1 1.0
CB A:ALA124 3.7 8.4 1.0
CB A:ALA125 3.9 7.0 1.0
CB A:GLU121 4.0 7.5 1.0
CA A:ALA125 4.0 6.4 1.0
C A:ALA124 4.2 7.3 1.0
CE A:MET117 4.4 10.2 1.0
O A:HOH1053 4.4 41.7 1.0
CA A:ALA124 4.5 7.9 1.0
CG A:GLU121 4.5 8.4 1.0
CG1 A:VAL108 4.5 10.6 1.0
O A:HOH1019 4.6 42.6 1.0
O A:HOH702 4.6 24.7 1.0
O A:HOH1003 4.6 40.3 1.0
O A:HOH857 4.7 17.6 1.0
N A:LEU122 4.8 6.1 1.0
N A:ALA124 4.9 6.7 1.0
O A:ALA124 5.0 8.2 1.0

Sodium binding site 4 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 4 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:29.9
occ:1.00
 O A:HOH664 1.6 13.5 1.0
O A:ARG178 2.7 7.0 1.0
O A:HOH643 2.7 17.1 1.0
O A:HOH637 2.9 11.3 1.0
CG2 A:THR180 3.2 6.7 1.0
O A:ASP179 3.3 5.8 1.0
CB A:PRO67 3.4 6.0 1.0
CA A:PRO67 3.5 5.4 1.0
CG A:PRO67 3.5 6.7 1.0
C A:ASP179 3.8 5.2 1.0
O A:ASP176 3.9 12.0 1.0
O A:HOH610 3.9 9.1 1.0
C A:ARG178 3.9 6.4 1.0
N A:PRO67 4.2 5.6 1.0
O A:HOH639 4.2 9.1 1.0
CA A:ALA172 4.2 6.5 1.0
CB A:ASP179 4.3 5.6 1.0
N A:THR180 4.4 5.4 1.0
CA A:ASP179 4.5 5.5 1.0
N A:ALA172 4.5 6.5 1.0
CD A:PRO67 4.5 6.4 1.0
CB A:THR180 4.5 6.2 1.0
CA A:THR180 4.7 5.2 1.0
N A:ASP179 4.7 6.0 1.0
C A:PRO67 4.7 5.1 1.0
O A:LEU169 4.8 7.1 1.0
N A:LEU68 4.8 5.2 1.0
C A:ALA172 4.9 6.7 1.0
C A:ASP176 5.0 9.7 1.0
C A:PHE66 5.0 5.6 1.0
N A:ARG178 5.0 7.7 1.0
NH2 A:ARG164 5.0 8.4 1.0

Sodium binding site 5 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 5 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:68.2
occ:1.00
 O A:HOH977 2.2 44.8 1.0
O A:HOH1012 3.0 36.6 1.0
O A:HOH948 3.1 33.0 1.0
O A:HOH1084 3.2 29.5 1.0
O A:LEU167 3.2 6.8 1.0
O A:HOH986 3.2 35.0 1.0
O A:HOH1059 3.8 53.5 1.0
O A:HOH768 4.0 31.3 1.0
C A:LEU167 4.1 6.2 1.0
CB A:ASN170 4.3 7.0 1.0
N A:SER171 4.4 6.8 1.0
C A:ASN170 4.4 7.1 1.0
O A:HOH726 4.4 16.6 1.0
CA A:GLU168 4.4 7.4 1.0
CB A:LEU167 4.6 6.9 1.0
O A:HOH1077 4.6 63.0 1.0
CA A:SER171 4.6 7.3 1.0
O A:GLU168 4.6 7.6 1.0
N A:GLU168 4.7 6.4 1.0
CA A:ASN170 4.7 6.6 1.0
N A:ASN170 4.7 6.3 1.0
O A:ASN170 4.7 8.5 1.0
C A:GLU168 4.8 6.7 1.0
O A:HOH1037 4.9 44.6 1.0
O A:HOH1048 4.9 41.2 1.0
CB A:SER171 5.0 8.4 1.0

Sodium binding site 6 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 6 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:0.1
occ:1.00
 O A:HOH853 3.1 39.0 1.0
NZ A:LYS32 3.7 16.9 0.5
NZ A:LYS32 3.7 16.0 0.5
CE A:LYS32 3.9 13.2 0.5
CE A:LYS32 4.1 12.4 0.5
CG1 A:VAL28 4.6 11.8 1.0
NE2 A:GLN24 4.8 20.0 1.0

Sodium binding site 7 out of 7 in 4euz

Go back to Sodium Binding Sites List in 4euz
Sodium binding site 7 out of 7 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem 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 Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:51.0
occ:1.00
 O A:HOH1080 1.7 81.3 1.0
OG A:SER275 2.6 9.8 1.0
CB A:SER275 3.4 8.8 1.0
O A:HOH983 3.7 43.5 1.0
O A:HOH960 3.9 46.2 1.0
CG2 A:VAL278 4.1 12.4 1.0
O A:HOH918 4.2 32.3 1.0
CB A:ALA277 4.3 10.3 1.0
O A:HOH666 4.4 16.0 1.0
CA A:SER275 4.5 7.7 1.0
O A:HOH785 4.6 34.8 1.0
N A:VAL278 4.7 7.5 1.0

Reference:

F.Fonseca, E.I.Chudyk, M.W.Van Der Kamp, A.Correia, A.J.Mulholland, J.Spencer. The Basis For Carbapenem Hydrolysis By Class A Beta-Lactamases: A Combined Investigation Using Crystallography and Simulations. J.Am.Chem.Soc. V. 134 18275 2012.
ISSN: ISSN 0002-7863
PubMed: 23030300
DOI: 10.1021/JA304460J
Page generated: Mon Oct 7 15:13:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy