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Sodium in PDB 4eqi: Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1

Enzymatic activity of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1

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

Protein crystallography data

The structure of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1, PDB code: 4eqi 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) 17.85 / 1.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.330, 85.430, 70.280, 90.00, 103.27, 90.00
R / Rfree (%) 14 / 18.8

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 (pdb code 4eqi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 22 binding sites of Sodium where determined in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1, PDB code: 4eqi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 22 in 4eqi

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Sodium binding site 1 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.3
occ:1.00
 O A:HOH751 2.5 30.4 1.0
O A:HOH556 2.8 17.4 1.0
O B:HOH536 3.1 18.8 1.0
CG A:GLU121 3.8 11.0 1.0
ND2 B:ASN228 3.9 35.6 1.0
CA A:GLU121 4.0 8.2 1.0
CB A:ALA124 4.0 7.9 1.0
O A:HOH661 4.2 26.3 1.0
CB A:GLU121 4.2 9.7 1.0
O A:HOH596 4.2 21.7 1.0
O A:HOH644 4.3 25.8 1.0
O A:HOH609 4.4 19.1 1.0
CB B:ASN228 4.4 27.3 1.0
CG B:ASN228 4.5 28.5 1.0
O A:HOH622 4.5 22.9 1.0
O A:GLU121 4.5 7.9 1.0
O A:HOH858 4.6 82.2 1.0
C A:GLU121 4.8 7.3 1.0
O B:HOH810 4.8 22.6 1.0
N A:GLU121 4.8 8.5 1.0
CD A:GLU121 5.0 11.8 1.0

Sodium binding site 2 out of 22 in 4eqi

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Sodium binding site 2 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:37.4
occ:1.00
 O B:HOH612 2.6 20.5 1.0
NE1 A:TRP251 3.1 16.8 1.0
ND1 B:HIS205 3.3 16.0 0.5
CD1 A:TRP251 3.6 16.0 1.0
CG A:PRO258 3.6 13.0 1.0
CB B:HIS205 3.6 11.0 0.5
CG B:HIS205 3.7 14.1 0.5
CB B:HIS205 3.7 11.5 0.5
O B:LEU201 3.9 11.8 1.0
CG B:HIS205 3.9 11.5 0.5
CE1 A:PHE195 4.0 14.7 1.0
CD A:PRO258 4.1 12.3 1.0
CA B:THR202 4.1 11.8 1.0
CE1 B:HIS205 4.2 16.9 0.5
CD2 B:HIS205 4.2 11.7 0.5
C B:LEU201 4.3 11.5 1.0
CE2 A:TRP251 4.4 16.7 1.0
N B:THR202 4.5 11.4 1.0
OG1 B:THR202 4.6 16.3 1.0
O A:HOH715 4.6 28.9 1.0
ND1 B:HIS205 4.6 11.8 0.5
CZ A:PHE195 4.7 13.6 1.0
CD2 B:HIS205 4.8 16.0 0.5
CB A:PRO258 4.8 12.4 1.0
O A:HOH692 4.8 26.6 1.0
CB B:THR202 4.9 13.4 1.0
CG A:TRP251 4.9 15.3 1.0
CD1 A:PHE195 5.0 14.6 1.0
CB B:LEU201 5.0 13.7 1.0
NE2 B:HIS205 5.0 17.0 0.5

Sodium binding site 3 out of 22 in 4eqi

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Sodium binding site 3 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:43.7
occ:1.00
 OE2 A:GLU203 2.6 15.6 1.0
OG A:SER84 2.8 11.7 1.0
O A:HOH761 3.2 28.9 1.0
CD A:GLU203 3.5 13.2 1.0
CG A:GLU203 3.5 12.5 1.0
O A:HOH697 3.6 26.1 1.0
CB A:SER84 3.7 10.8 1.0
O A:SER84 3.9 12.2 1.0
O A:HOH693 3.9 34.4 1.0
C A:SER84 4.0 10.8 1.0
O A:HOH572 4.2 19.3 1.0
N A:GLN85 4.3 11.9 1.0
CD1 A:LEU91 4.3 16.4 1.0
CG A:GLN85 4.5 13.6 1.0
CA A:SER84 4.5 9.5 1.0
CA A:GLN85 4.6 13.1 1.0
O A:LEU81 4.6 9.9 1.0
OE1 A:GLU203 4.7 13.9 1.0
O A:HOH763 4.9 34.8 1.0
CB A:GLU203 5.0 11.5 1.0
CG A:LEU91 5.0 12.5 1.0

Sodium binding site 4 out of 22 in 4eqi

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Sodium binding site 4 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:26.9
occ:0.50
 O A:HOH713 2.4 44.2 1.0
O A:HOH607 2.4 24.2 1.0
CB A:PRO268 3.7 11.3 1.0
CG A:PRO268 3.9 11.1 1.0
OD1 A:ASP269 4.3 21.2 1.0
OD2 A:ASP269 4.3 17.3 1.0
CG A:ASP269 4.6 15.3 1.0
O A:HOH582 4.8 23.1 1.0
O A:HOH699 4.8 48.4 1.0
C A:PRO268 4.9 11.1 1.0
CA A:PRO268 4.9 10.5 1.0

Sodium binding site 5 out of 22 in 4eqi

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Sodium binding site 5 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:41.5
occ:1.00
 OE1 A:GLN86 2.6 23.8 0.5
NE2 A:GLN86 2.8 22.9 0.5
OG A:SER82 3.0 11.2 1.0
CD A:GLN86 3.1 21.1 0.5
O A:SER82 3.2 11.2 1.0
NE2 A:GLN85 3.2 16.7 1.0
OE1 A:GLN86 3.8 22.3 0.5
C A:SER82 3.9 9.5 1.0
CB A:GLN85 3.9 13.0 1.0
CA A:SER82 4.1 9.2 1.0
CB A:SER82 4.1 9.3 1.0
CD A:GLN85 4.2 15.1 1.0
O A:HOH576 4.3 19.2 1.0
CG A:GLN86 4.4 20.0 0.5
CG A:GLN85 4.5 13.6 1.0
CD A:GLN86 4.6 20.9 0.5
CG A:GLN86 4.6 20.5 0.5
O A:VAL198 4.6 14.9 1.0
O A:HOH725 4.9 43.8 1.0
N A:LYS83 4.9 9.1 1.0
CA A:GLN85 5.0 13.1 1.0

Sodium binding site 6 out of 22 in 4eqi

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Sodium binding site 6 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:25.9
occ:0.50
 O A:HOH737 2.4 37.6 1.0
O A:HOH681 2.4 29.4 1.0
O A:HOH541 3.0 16.2 1.0
CG A:GLN191 3.6 11.8 1.0
CG A:LYS192 3.6 15.3 1.0
CA A:LYS192 3.7 10.5 1.0
CD A:GLN191 3.7 14.2 1.0
N A:LYS192 3.7 9.5 1.0
O A:HOH730 3.8 32.8 1.0
OE1 A:GLN191 3.9 16.9 1.0
C A:GLN191 3.9 9.5 1.0
O A:GLN191 4.0 10.2 1.0
CB A:GLN191 4.2 10.5 1.0
CB A:LYS192 4.3 12.3 1.0
NE2 A:GLN191 4.3 16.8 1.0
O A:HOH799 4.4 31.9 1.0
O A:HOH653 4.7 21.6 1.0
CA A:GLN191 4.7 9.2 1.0
O A:GLU188 4.8 8.8 1.0
C A:LYS192 4.9 10.5 1.0
CD A:LYS192 5.0 17.6 1.0

Sodium binding site 7 out of 22 in 4eqi

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Sodium binding site 7 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:41.8
occ:1.00
 OD1 A:ASP31 2.5 16.1 1.0
NZ A:LYS34 2.7 22.4 1.0
NE2 A:GLN27 3.1 15.3 0.5
CE A:LYS34 3.6 18.0 1.0
CD A:LYS34 3.6 15.7 1.0
CG A:ASP31 3.6 12.6 1.0
O A:HOH749 3.9 18.5 0.5
OD2 A:ASP31 4.0 13.7 1.0
O A:HOH728 4.2 27.3 1.0
CD A:GLN27 4.2 16.0 0.5
O A:HOH702 4.5 24.4 0.5
CB A:ASP31 4.8 11.4 1.0
CG1 A:VAL30 4.9 11.4 1.0
OE1 A:GLN27 5.0 19.9 0.5
CG A:GLN27 5.0 15.2 0.5

Sodium binding site 8 out of 22 in 4eqi

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Sodium binding site 8 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:16.6
occ:0.50
 O A:HOH815 1.5 27.8 1.0
OG A:SER266 2.3 13.3 1.0
O A:HOH569 2.6 14.3 1.0
NE A:ARG43 2.8 16.5 1.0
O A:HOH758 3.2 19.6 1.0
CB A:SER266 3.3 9.4 1.0
CD A:ARG43 3.4 17.2 1.0
CG A:ARG43 3.5 16.4 1.0
CZ A:ARG43 3.8 15.9 1.0
CB A:ARG43 3.9 12.6 1.0
NH2 A:ARG43 3.9 15.4 1.0
O A:HOH518 3.9 10.5 1.0
C A:SER266 3.9 8.4 1.0
O A:SER266 4.0 9.1 1.0
O A:HOH585 4.2 16.2 1.0
CA A:SER266 4.2 7.8 1.0
N A:LYS267 4.3 8.7 1.0
O A:HOH846 4.5 50.9 1.0
N A:ARG43 4.5 9.8 1.0
O A:HOH586 4.5 20.1 1.0
C A:LYS267 4.6 9.1 1.0
O A:HOH570 4.6 18.5 1.0
CA A:LYS267 4.6 8.9 1.0
O A:LYS267 4.8 9.5 1.0
CA A:ARG43 4.8 9.8 1.0
N A:PRO268 4.9 9.7 1.0

Sodium binding site 9 out of 22 in 4eqi

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Sodium binding site 9 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:55.0
occ:1.00
 O A:ALA255 2.9 16.6 1.0
O B:HOH704 3.4 17.9 0.5
CB A:ALA255 3.6 18.9 1.0
O B:HOH820 3.8 60.5 1.0
C A:ALA255 3.9 15.2 1.0
N B:GLY89 3.9 18.3 1.0
O B:HOH659 4.0 20.7 1.0
CA B:GLY89 4.1 17.0 1.0
O A:HOH773 4.1 33.9 1.0
CA A:ALA255 4.3 16.1 1.0
O B:HOH701 4.6 33.0 1.0
ND2 B:ASN92 4.8 24.1 1.0

Sodium binding site 10 out of 22 in 4eqi

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Sodium binding site 10 out of 22 in the Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:55.6
occ:1.00
 O A:HOH630 3.2 26.7 1.0
OD1 A:ASP163 3.3 16.2 1.0
O A:HOH590 3.8 20.4 1.0
NE A:ARG161 3.9 12.4 1.0
CB A:ARG161 3.9 10.4 1.0
NH2 A:ARG161 4.0 17.2 1.0
CG A:ASP163 4.1 11.7 1.0
CZ A:ARG161 4.1 13.7 1.0
OD2 A:ASP163 4.3 10.3 1.0
O A:HOH786 4.5 29.3 1.0
CG2 A:THR149 4.5 8.9 1.0
CD A:ARG161 4.6 11.2 1.0
O A:LEU162 4.6 10.0 1.0
OG1 A:THR149 4.8 8.7 1.0
CA A:ARG161 4.8 8.7 1.0
CG A:ARG161 4.8 10.1 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: Tue Dec 15 06:39:19 2020

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