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Sodium in PDB 5axr: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate, PDB code: 5axr was solved by J.Wachino, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.12 / 2.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 67.112, 67.112, 46.717, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 21.4

Other elements in 5axr:

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate (pdb code 5axr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate, PDB code: 5axr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5axr

Go back to Sodium Binding Sites List in 5axr
Sodium binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:26.7
occ:1.00
 O A:HOH559 2.6 17.5 1.0
OD1 A:ASN54 2.7 14.8 1.0
O A:HOH580 2.9 17.8 1.0
N A:GLN9 3.1 16.4 1.0
O A:GLN9 3.1 14.8 1.0
C A:GLN9 3.5 15.8 1.0
CG A:ASN54 3.6 14.4 1.0
O A:HOH503 3.6 15.3 1.0
CA A:PRO8 3.7 18.3 1.0
ND2 A:ASN54 3.8 14.6 1.0
CB A:PRO8 3.8 20.4 1.0
CG1 A:VAL50 3.8 16.9 1.0
C A:PRO8 3.8 20.0 1.0
CA A:GLN9 4.0 15.6 1.0
N A:GLN10 4.2 15.6 1.0
O A:VAL50 4.7 15.1 1.0
CA A:GLN10 4.7 17.4 1.0
CB A:VAL50 4.7 19.6 1.0
CG2 A:VAL50 4.9 22.5 1.0
CG A:PRO8 4.9 22.7 1.0
CA A:VAL50 4.9 17.5 1.0
O A:PRO8 5.0 20.4 1.0
CD A:PRO11 5.0 13.5 1.0

Sodium binding site 2 out of 6 in 5axr

Go back to Sodium Binding Sites List in 5axr
Sodium binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:26.7
occ:1.00
 O A:HOH482 2.7 19.3 1.0
O A:THR71 2.8 16.8 1.0
O A:SER70 2.8 21.6 1.0
O A:GLY153 2.9 20.0 1.0
N A:GLY95 3.0 18.8 1.0
C A:THR71 3.6 19.8 1.0
CG1 A:ILE155 3.6 14.3 1.0
C A:SER70 3.7 16.8 1.0
CA A:ALA94 3.7 18.9 1.0
N A:ILE155 3.7 17.7 1.0
CB A:ALA94 3.8 20.4 1.0
CB A:ILE155 3.8 16.2 1.0
C A:ALA94 3.9 20.3 1.0
CA A:GLY95 4.0 20.2 1.0
C A:GLY153 4.0 23.6 1.0
ND2 A:ASN98 4.2 19.6 1.0
CA A:THR71 4.3 16.3 1.0
OG A:SER70 4.3 16.8 1.0
C A:GLY154 4.3 19.2 1.0
N A:HIS72 4.3 18.7 1.0
CB A:SER70 4.3 16.9 1.0
N A:THR71 4.4 15.8 1.0
CA A:GLY154 4.4 21.3 1.0
CA A:ILE155 4.4 15.5 1.0
CA A:HIS72 4.4 18.0 1.0
CA A:SER70 4.6 16.2 1.0
N A:GLY154 4.6 22.6 1.0
CB A:ASN98 4.6 23.7 1.0
CG A:ASN98 4.8 22.9 1.0
O A:GLY95 4.8 20.3 1.0
C A:GLY95 4.9 22.2 1.0

Sodium binding site 3 out of 6 in 5axr

Go back to Sodium Binding Sites List in 5axr
Sodium binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:29.6
occ:1.00
 O A:THR13 2.7 13.8 1.0
O A:HOH548 2.7 22.3 1.0
O A:HOH530 2.8 26.9 1.0
OH A:TYR236 3.0 13.6 1.0
OD1 A:ASN233 3.2 16.6 1.0
O A:HOH524 3.3 34.5 1.0
CE2 A:TYR236 3.6 12.9 1.0
CZ A:TYR236 3.8 12.5 1.0
CB A:ALA228 3.8 21.8 1.0
C A:THR13 3.9 12.2 1.0
CD2 A:PHE12 4.0 12.8 1.0
CB A:PHE12 4.2 12.6 1.0
CG A:ASN233 4.3 17.3 1.0
O A:HOH541 4.4 26.5 1.0
NA A:NA308 4.4 7.8 1.0
N A:THR13 4.5 12.2 1.0
CG A:PHE12 4.5 12.3 1.0
CA A:THR13 4.7 12.6 1.0
ND2 A:ASN233 4.7 16.4 1.0
N A:ILE14 4.9 12.5 1.0
CD2 A:TYR236 4.9 12.7 1.0
CG A:GLN225 4.9 26.5 1.0
C A:PHE12 5.0 12.4 1.0

Sodium binding site 4 out of 6 in 5axr

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Sodium binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:26.4
occ:1.00
 O A:TYR236 2.8 17.1 1.0
O A:ASP238 3.1 14.6 1.0
N A:ALA211 3.2 13.8 1.0
ND2 A:ASN219 3.3 13.9 1.0
N A:ASP238 3.3 15.6 1.0
O A:ASP209 3.5 11.8 1.0
CB A:ALA241 3.5 13.7 1.0
CA A:ILE210 3.6 11.8 1.0
CB A:ASP238 3.6 16.8 1.0
O A:HOH488 3.7 13.0 1.0
CA A:ASP238 3.8 16.4 1.0
C A:ASP238 3.8 17.0 1.0
C A:ILE210 3.9 13.3 1.0
C A:TYR236 3.9 15.2 1.0
C A:VAL237 4.0 17.7 1.0
C A:ASP209 4.2 13.2 1.0
CZ A:ARG224 4.2 15.0 1.0
NH2 A:ARG224 4.2 14.5 1.0
CA A:ALA211 4.2 13.5 1.0
CB A:ALA211 4.3 14.3 1.0
O A:ALA211 4.3 13.6 1.0
NH1 A:ARG224 4.3 15.8 1.0
N A:ILE210 4.3 11.6 1.0
CA A:VAL237 4.3 15.1 1.0
CG A:ASN219 4.3 15.6 1.0
N A:VAL237 4.6 15.3 1.0
CG A:ASP238 4.6 20.2 1.0
OD1 A:ASN219 4.6 17.2 1.0
NE A:ARG224 4.6 14.2 1.0
CB A:ILE210 4.7 12.0 1.0
C A:ALA211 4.7 12.8 1.0
CG2 A:ILE210 4.8 13.0 1.0
CA A:ALA241 4.8 14.4 1.0
O A:VAL237 4.9 17.7 1.0
OD2 A:ASP238 5.0 18.2 1.0

Sodium binding site 5 out of 6 in 5axr

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Sodium binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:35.8
occ:1.00
 O A:HOH573 2.9 24.4 1.0
O A:GLU231 3.1 28.2 1.0
OG A:SER234 3.2 21.8 1.0
N A:SER234 3.3 16.1 1.0
N A:ASN233 3.4 18.3 1.0
CB A:SER234 3.6 19.9 1.0
C A:GLY232 3.7 19.6 1.0
CA A:GLY232 3.8 18.4 1.0
O A:HOH468 3.8 16.1 1.0
CA A:SER234 4.0 18.7 1.0
C A:GLU231 4.1 22.2 1.0
C A:ASN233 4.2 16.9 1.0
CA A:ASN233 4.3 17.7 1.0
O A:GLY232 4.3 14.4 1.0
N A:GLY232 4.4 20.3 1.0
OE1 A:GLU163 4.9 23.4 1.0
CB A:ASN233 5.0 17.4 1.0

Sodium binding site 6 out of 6 in 5axr

Go back to Sodium Binding Sites List in 5axr
Sodium binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate


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 Metallo-Beta-Lactamase Smb-1 Bound to 2- Mercaptoethanesulfonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:7.8
occ:1.00
 O A:HOH473 3.1 26.5 1.0
N A:THR13 3.3 12.2 1.0
O A:HOH530 3.3 26.9 1.0
CA A:PHE12 3.8 12.6 1.0
CB A:THR13 4.0 11.9 1.0
CB A:PHE12 4.0 12.6 1.0
OG1 A:THR13 4.1 11.7 1.0
C A:PHE12 4.1 12.4 1.0
CA A:THR13 4.2 12.6 1.0
O A:HOH548 4.4 22.3 1.0
NA A:NA305 4.4 29.6 1.0
O A:THR13 4.6 13.8 1.0
CE A:MET58 4.8 19.2 1.0
C A:THR13 4.9 12.2 1.0

Reference:

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to 2-Mercaptoethanesulfonate To Be Published.
Page generated: Tue Dec 15 10:23:50 2020

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