Atomistry » Sodium » PDB 5b05-5bom » 5b1u
Atomistry »
  Sodium »
    PDB 5b05-5bom »
      5b1u »

Sodium in PDB 5b1u: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem, PDB code: 5b1u 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) 40.58 / 1.57
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.030, 41.460, 45.440, 108.32, 102.78, 106.28
R / Rfree (%) 12.2 / 15.5

Other elements in 5b1u:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem (pdb code 5b1u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem, PDB code: 5b1u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 1 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:18.5
occ:1.00
O A:HOH536 2.5 24.6 1.0
NA A:NA311 2.7 20.9 1.0
OD1 A:ASN98 2.8 3.9 1.0
OG1 A:THR101 2.9 8.2 1.0
OG A:SER73 3.3 3.4 1.0
O A:HOH627 3.5 13.6 1.0
CD A:PRO108 3.6 6.3 1.0
CG A:ASN98 3.7 3.4 1.0
O A:ALA97 3.7 5.5 1.0
O A:HOH418 3.7 18.4 1.0
CB A:THR101 3.8 5.7 1.0
CG A:PRO108 4.0 7.3 1.0
CA A:ASN98 4.1 3.4 1.0
CG2 A:THR101 4.3 6.0 1.0
CB A:ASN98 4.3 3.6 1.0
CB A:THR151 4.5 3.0 1.0
C A:ALA97 4.6 3.9 1.0
ND2 A:ASN98 4.6 3.3 1.0
CB A:SER73 4.6 3.0 1.0
N A:ASN98 4.8 3.6 1.0
O A:HOH406 4.8 27.3 1.0
CG2 A:THR151 4.9 3.0 1.0
OG A:SER107 5.0 6.0 1.0
N A:PRO108 5.0 5.9 1.0
N A:GLU152 5.0 4.4 1.0

Sodium binding site 2 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 2 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:10.7
occ:1.00
O A:HOH535 2.8 4.7 1.0
O A:SER70 2.8 2.8 1.0
N A:GLY95 2.9 2.9 1.0
O A:GLY153 2.9 3.1 1.0
O A:THR71 3.0 2.6 1.0
CG1 A:ILE155 3.4 3.1 1.0
CA A:ALA94 3.5 3.0 1.0
CB A:ALA94 3.6 2.9 1.0
C A:ALA94 3.7 3.0 1.0
C A:THR71 3.7 2.7 1.0
C A:SER70 3.7 3.0 1.0
N A:ILE155 3.8 2.5 1.0
CB A:ILE155 3.8 2.9 1.0
CA A:GLY95 3.9 2.9 1.0
C A:GLY153 4.0 3.2 1.0
ND2 A:ASN98 4.2 3.3 1.0
OG A:SER70 4.2 3.6 1.0
CB A:SER70 4.3 3.3 1.0
C A:GLY154 4.3 2.8 1.0
CA A:THR71 4.4 3.0 1.0
CA A:GLY154 4.4 3.0 1.0
CA A:ILE155 4.4 2.7 1.0
N A:HIS72 4.5 2.6 1.0
N A:THR71 4.5 2.8 1.0
CA A:HIS72 4.5 2.8 1.0
CA A:SER70 4.6 3.0 1.0
CB A:ASN98 4.6 3.6 1.0
N A:GLY154 4.7 3.0 1.0
CD1 A:ILE155 4.8 3.7 1.0
O A:GLY95 4.8 3.3 1.0
CG A:ASN98 4.8 3.4 1.0
N A:ALA94 4.9 3.2 1.0
CZ2 A:TRP157 4.9 5.0 1.0
O A:ALA94 4.9 3.3 1.0
C A:GLY95 4.9 3.3 1.0
O A:LEU93 4.9 3.6 1.0

Sodium binding site 3 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 3 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:13.1
occ:1.00
O A:HOH691 2.7 14.3 1.0
OE1 A:GLN85 2.8 5.4 1.0
O A:SER82 3.0 4.3 1.0
N A:ALA124 3.1 5.4 1.0
OG A:SER82 3.3 4.8 1.0
CB A:GLN85 3.6 5.0 1.0
CD A:GLN85 3.6 5.2 1.0
CG A:LYS86 3.7 12.3 1.0
OG A:SER123 3.7 4.4 0.5
CB A:ALA124 3.7 6.1 1.0
CA A:SER82 3.7 4.1 1.0
C A:SER82 3.8 4.2 1.0
CA A:SER123 3.8 4.7 0.5
CA A:SER123 3.8 5.0 0.5
CG A:GLN85 3.9 4.6 1.0
C A:SER123 3.9 5.1 1.0
CA A:ALA124 4.0 6.2 1.0
CE A:LYS86 4.0 24.6 1.0
CB A:SER82 4.1 4.5 1.0
N A:LYS86 4.1 5.3 1.0
O A:HOH474 4.1 13.4 1.0
CB A:SER123 4.3 4.5 0.5
O A:HOH771 4.3 15.8 1.0
CB A:SER123 4.3 5.2 0.5
O A:ALA124 4.4 4.9 1.0
CD A:LYS86 4.4 18.4 1.0
C A:GLN85 4.6 4.5 1.0
O A:GLY122 4.6 5.6 1.0
OG A:SER123 4.6 6.0 0.5
CA A:GLN85 4.6 4.5 1.0
C A:ALA124 4.6 5.8 1.0
CB A:LYS86 4.7 9.1 1.0
O A:HOH404 4.7 22.8 1.0
CA A:LYS86 4.8 7.0 1.0
NE2 A:GLN85 4.9 6.2 1.0
O A:HOH703 4.9 19.1 1.0
N A:SER123 5.0 4.8 1.0

Sodium binding site 4 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 4 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:16.7
occ:1.00
O A:HOH537 2.7 11.2 1.0
O1 A:SO4319 2.7 14.5 1.0
NE A:ARG103 2.8 10.4 1.0
N A:VAL126 3.0 4.7 1.0
N A:LYS125 3.3 6.0 1.0
CG A:ARG103 3.5 7.1 1.0
CD A:ARG103 3.5 8.3 1.0
CZ A:ARG103 3.6 12.2 1.0
NH2 A:ARG103 3.7 13.9 1.0
CB A:VAL126 3.7 4.6 1.0
O A:VAL126 3.8 4.6 1.0
CA A:VAL126 3.8 4.3 1.0
S A:SO4319 3.8 14.2 1.0
C A:ALA124 3.8 5.8 1.0
CG2 A:VAL126 3.8 4.6 1.0
O3 A:SO4319 3.8 13.0 1.0
CA A:LYS125 3.9 6.3 1.0
C A:LYS125 4.0 5.2 1.0
NH2 A:ARG127 4.0 8.3 1.0
O A:SER123 4.0 5.6 1.0
CA A:ALA124 4.2 6.2 1.0
C A:VAL126 4.3 4.2 1.0
O A:HOH553 4.3 18.9 1.0
O A:ALA124 4.6 4.9 1.0
O2 A:SO4319 4.7 16.2 1.0
CB A:ARG103 4.7 6.0 1.0
O4 A:SO4319 4.8 13.4 1.0
NH1 A:ARG103 4.8 12.5 1.0
C A:SER123 4.9 5.1 1.0
O A:HOH739 5.0 29.9 1.0

Sodium binding site 5 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 5 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:12.2
occ:1.00
OD1 A:ASN54 2.8 3.5 1.0
N A:GLN9 3.0 4.8 1.0
O A:GLN9 3.1 4.4 1.0
C A:GLN9 3.6 4.4 1.0
CA A:PRO8 3.6 6.3 1.0
CG1 A:VAL50 3.6 4.3 1.0
CG A:ASN54 3.7 3.5 1.0
CB A:PRO8 3.7 7.9 1.0
ND2 A:ASN54 3.8 3.2 1.0
C A:PRO8 3.8 6.2 1.0
CA A:GLN9 3.9 5.0 1.0
N A:GLN10 4.3 4.2 1.0
O A:VAL50 4.6 3.8 1.0
CB A:VAL50 4.7 4.1 1.0
CA A:GLN10 4.7 4.2 1.0
CG A:PRO8 4.7 9.1 1.0
CA A:VAL50 4.9 4.1 1.0
CG2 A:VAL50 4.9 4.4 1.0
CB A:GLN9 5.0 6.0 1.0
O A:PRO8 5.0 7.5 1.0
N A:PRO8 5.0 7.0 1.0

Sodium binding site 6 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 6 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:13.4
occ:1.00
O A:HOH637 2.8 5.8 1.0
O31 A:HIW321 2.9 8.3 1.0
N26 A:HIW321 3.0 23.9 1.0
O A:HOH638 3.0 5.1 1.0
N24 A:HIW321 3.1 24.0 1.0
C25 A:HIW321 3.4 23.5 1.0
CG2 A:THR177 3.4 5.3 1.0
OG A:SER175 3.6 2.1 0.5
OG A:SER175 3.6 6.7 0.5
CG2 A:VAL218 3.7 5.9 1.0
C31 A:HIW321 3.8 7.8 1.0
CB A:SER175 3.8 2.8 0.5
CD2 A:HIS215 4.0 3.0 1.0
CB A:SER175 4.0 4.5 0.5
CA A:SER175 4.2 3.1 0.5
CA A:SER175 4.2 3.9 0.5
O A:HOH634 4.2 4.0 1.0
O32 A:HIW321 4.2 5.3 1.0
C23 A:HIW321 4.4 22.9 1.0
OG1 A:THR177 4.4 6.1 1.0
CG A:HIS215 4.4 3.1 1.0
CB A:HIS215 4.4 2.9 1.0
S21 A:HIW321 4.5 16.9 1.0
CB A:THR177 4.5 5.2 1.0
C22 A:HIW321 4.7 19.9 1.0
N A:LEU176 4.7 3.4 1.0
CB A:VAL218 4.8 6.0 1.0
C3 A:HIW321 4.8 8.7 1.0
O A:HOH603 4.9 10.3 1.0
CG1 A:VAL218 4.9 6.9 1.0
C A:SER175 5.0 3.5 1.0

Sodium binding site 7 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 7 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:19.8
occ:1.00
O A:GLY89 2.7 6.0 1.0
OG1 A:THR91 2.8 6.2 1.0
NZ A:LYS125 3.1 22.5 1.0
O A:HOH529 3.2 16.5 1.0
N A:THR91 3.3 4.2 1.0
C A:ALA90 3.5 4.5 1.0
CD A:LYS125 3.9 16.0 1.0
C A:GLY89 3.9 5.3 1.0
O A:HOH542 3.9 17.1 1.0
CB A:THR91 3.9 4.6 1.0
CA A:ALA90 3.9 4.5 1.0
O A:HOH704 3.9 16.3 1.0
CE A:LYS125 3.9 24.4 1.0
CA A:THR91 4.0 4.1 1.0
O A:ALA90 4.0 3.6 1.0
O A:LYS66 4.3 4.3 1.0
N A:ALA90 4.4 5.0 1.0
O A:HOH472 4.9 9.2 1.0

Sodium binding site 8 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 8 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:19.4
occ:1.00
O A:HOH424 2.8 16.7 1.0
NA A:NA317 2.8 18.0 1.0
N A:ARG185 3.0 4.5 1.0
O A:HOH636 3.0 14.8 1.0
O A:SER183 3.4 8.6 1.0
CA A:TYR184 3.5 5.0 1.0
NE2 A:HIS189 3.5 7.5 1.0
C A:TYR184 3.7 4.7 1.0
CB A:ARG185 3.8 5.0 1.0
CA A:ARG185 3.9 4.7 1.0
OD2 A:ASP188 4.1 10.2 1.0
O A:HOH734 4.2 25.8 1.0
O A:ARG185 4.2 4.2 1.0
CD2 A:HIS189 4.2 5.3 1.0
C A:SER183 4.3 7.0 1.0
O A:HOH483 4.3 28.9 1.0
N A:TYR184 4.4 6.1 1.0
O A:HOH451 4.4 14.7 1.0
C A:ARG185 4.5 4.7 1.0
CD1 A:TYR184 4.6 4.7 1.0
CB A:TYR184 4.6 5.1 1.0
CG A:TYR184 4.6 4.4 1.0
CE1 A:HIS189 4.6 5.3 1.0
CB A:ASP188 4.7 5.8 1.0
O A:HOH701 4.8 20.6 1.0
CG A:ASP188 4.8 7.4 1.0
O A:TYR184 4.9 5.8 1.0
O A:HOH441 4.9 10.5 1.0
O A:HOH697 5.0 26.0 1.0

Sodium binding site 9 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 9 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:20.9
occ:1.00
O A:HOH536 2.2 24.6 1.0
NA A:NA303 2.7 18.5 1.0
OG A:SER107 2.7 6.0 1.0
OD2 A:ASP111 3.1 5.2 1.0
OG A:SER73 3.1 3.4 1.0
O A:SER73 3.3 3.2 1.0
CB A:SER107 3.4 6.0 1.0
CG2 A:THR101 3.8 6.0 1.0
CG2 A:THR151 3.8 3.0 1.0
CD2 A:HIS74 3.9 3.5 1.0
NE2 A:HIS74 3.9 3.3 1.0
CD A:PRO108 3.9 6.3 1.0
OG1 A:THR101 4.0 8.2 1.0
CA A:SER107 4.0 6.0 1.0
CG A:ASP111 4.2 4.7 1.0
CB A:SER73 4.2 3.0 1.0
C A:SER73 4.2 3.1 1.0
CB A:THR101 4.3 5.7 1.0
CB A:THR151 4.4 3.0 1.0
O A:HOH627 4.4 13.6 1.0
CB A:ASP111 4.5 5.2 1.0
OD1 A:ASN98 4.6 3.9 1.0
CA A:SER73 4.7 3.0 1.0
N A:PRO108 4.8 5.9 1.0
C A:SER107 4.9 5.7 1.0
N A:SER73 5.0 2.8 1.0

Sodium binding site 10 out of 15 in 5b1u

Go back to Sodium Binding Sites List in 5b1u
Sodium binding site 10 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:19.8
occ:1.00
O A:HOH557 2.5 14.6 1.0
O A:VAL179 2.7 6.0 1.0
O A:HOH479 3.0 4.7 1.0
O A:THR177 3.1 5.4 1.0
N A:VAL179 3.2 5.7 1.0
CG1 A:VAL179 3.6 8.6 1.0
ND1 A:HIS150 3.6 3.3 1.0
C A:VAL179 3.7 5.4 1.0
CB A:PRO112 3.8 5.1 1.0
CG A:PRO112 3.8 5.2 1.0
CA A:HIS150 3.8 3.7 1.0
O A:HIS150 3.8 3.9 1.0
CA A:VAL179 3.9 5.8 1.0
CA A:ALA178 4.0 5.3 1.0
C A:ALA178 4.1 6.1 1.0
CZ A:PHE186 4.2 4.0 1.0
C A:THR177 4.2 4.5 1.0
CG A:HIS150 4.2 3.4 1.0
C A:HIS150 4.3 3.7 1.0
CD A:PRO112 4.3 5.3 1.0
O A:GLY149 4.3 5.6 1.0
CE1 A:HIS150 4.4 3.1 1.0
CB A:VAL179 4.4 8.5 1.0
CB A:HIS150 4.4 3.5 1.0
NE2 A:GLN113 4.5 4.6 1.0
N A:ALA178 4.6 4.8 1.0
CG A:GLN113 4.6 4.5 1.0
CE1 A:PHE186 4.7 4.5 1.0
N A:HIS150 4.8 3.8 1.0
N A:SER180 4.9 5.2 1.0
C A:GLY149 5.0 4.5 1.0
CD A:GLN113 5.0 4.5 1.0

Reference:

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem To Be Published.
Page generated: Tue Dec 15 10:25:28 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy