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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

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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

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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

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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

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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

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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

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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

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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

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