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Sodium in PDB 5b15: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem

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

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem, PDB code: 5b15 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) 40.70 / 1.39
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.010, 40.920, 45.320, 107.57, 102.56, 107.01
R / Rfree (%) 13.6 / 15.8

Other elements in 5b15:

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem 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 Hydrolyzed Doripenem (pdb code 5b15). 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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem, PDB code: 5b15:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5b15

Go back to Sodium Binding Sites List in 5b15
Sodium binding site 1 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:15.2
occ:1.00
 O A:HOH670 2.8 16.4 1.0
OE1 A:GLN85 2.8 8.0 1.0
O A:SER82 3.0 6.5 1.0
N A:ALA124 3.1 7.7 1.0
OG A:SER82 3.2 8.4 1.0
CB A:GLN85 3.6 6.7 1.0
OG A:SER123 3.7 11.8 1.0
CG A:LYS86 3.7 13.1 1.0
CD A:GLN85 3.7 7.1 1.0
CA A:SER82 3.7 6.3 1.0
CB A:ALA124 3.7 9.2 1.0
C A:SER82 3.7 6.2 1.0
CA A:SER123 3.8 8.8 1.0
CG A:GLN85 3.9 6.8 1.0
C A:SER123 3.9 8.3 1.0
CA A:ALA124 4.0 8.7 1.0
CB A:SER82 4.0 6.8 1.0
O A:HOH474 4.1 15.8 1.0
N A:LYS86 4.1 7.7 1.0
O A:HOH733 4.2 17.0 1.0
CB A:SER123 4.3 10.1 1.0
CE A:LYS86 4.3 24.7 1.0
CD A:LYS86 4.3 19.1 1.0
O A:ALA124 4.4 8.1 1.0
C A:GLN85 4.6 7.4 1.0
O A:GLY122 4.6 8.9 1.0
CA A:GLN85 4.6 6.9 1.0
C A:ALA124 4.7 8.3 1.0
CB A:LYS86 4.7 10.8 1.0
O A:HOH659 4.8 26.4 1.0
CA A:LYS86 4.8 9.2 1.0
O A:HOH672 4.9 21.9 1.0
NE2 A:GLN85 4.9 8.5 1.0
N A:SER123 5.0 8.4 1.0

Sodium binding site 2 out of 7 in 5b15

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Sodium binding site 2 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:12.0
occ:1.00
 O A:SER70 2.8 5.0 1.0
O A:HOH499 2.8 6.3 1.0
O A:GLY153 2.9 5.7 1.0
N A:GLY95 2.9 5.5 1.0
O A:THR71 3.0 5.3 1.0
CG1 A:ILE155 3.4 5.3 1.0
CA A:ALA94 3.5 5.7 1.0
CB A:ALA94 3.6 6.1 1.0
C A:ALA94 3.7 6.2 1.0
C A:THR71 3.7 4.6 1.0
C A:SER70 3.8 4.7 1.0
N A:ILE155 3.8 4.4 1.0
CB A:ILE155 3.8 5.4 1.0
CA A:GLY95 3.9 5.8 1.0
C A:GLY153 4.0 4.8 1.0
OG A:SER70 4.2 5.4 1.0
ND2 A:ASN98 4.2 5.0 1.0
CB A:SER70 4.3 4.8 1.0
C A:GLY154 4.3 4.6 1.0
CA A:GLY154 4.4 4.5 1.0
CA A:THR71 4.4 4.6 1.0
CA A:ILE155 4.4 5.1 1.0
N A:THR71 4.5 4.8 1.0
N A:HIS72 4.5 4.2 1.0
CA A:SER70 4.6 4.4 1.0
CA A:HIS72 4.6 4.5 1.0
CB A:ASN98 4.7 5.9 1.0
N A:GLY154 4.7 5.0 1.0
O A:GLY95 4.8 5.8 1.0
CD1 A:ILE155 4.8 5.9 1.0
N A:ALA94 4.8 5.0 1.0
C A:GLY95 4.9 6.4 1.0
CZ2 A:TRP157 4.9 7.1 1.0
O A:ALA94 4.9 7.1 1.0
CG A:ASN98 4.9 5.5 1.0
O A:LEU93 4.9 6.3 1.0

Sodium binding site 3 out of 7 in 5b15

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Sodium binding site 3 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:15.1
occ:1.00
 OD1 A:ASN54 2.8 6.5 1.0
N A:GLN9 3.0 8.0 1.0
O A:GLN9 3.1 6.5 1.0
C A:GLN9 3.5 7.5 1.0
CG1 A:VAL50 3.6 6.5 1.0
CG A:ASN54 3.6 6.6 1.0
CA A:PRO8 3.7 9.7 1.0
CB A:PRO8 3.7 10.8 1.0
ND2 A:ASN54 3.7 6.4 1.0
C A:PRO8 3.8 9.9 1.0
CA A:GLN9 3.9 7.6 1.0
N A:GLN10 4.2 6.5 1.0
O A:VAL50 4.6 6.7 1.0
CB A:VAL50 4.6 6.8 1.0
CA A:GLN10 4.7 6.4 1.0
CG A:PRO8 4.9 12.0 1.0
CG2 A:VAL50 4.9 7.2 1.0
CB A:GLN9 4.9 8.9 1.0
CA A:VAL50 4.9 7.1 1.0
O A:PRO8 5.0 12.2 1.0

Sodium binding site 4 out of 7 in 5b15

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Sodium binding site 4 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:19.2
occ:1.00
 O A:HOH570 2.6 13.7 1.0
O A:VAL179 2.7 10.7 1.0
O A:HOH480 2.9 7.2 1.0
N A:VAL179 3.1 9.9 1.0
O A:THR177 3.2 7.3 1.0
CG2 A:VAL179 3.4 13.7 1.0
ND1 A:HIS150 3.6 5.4 1.0
C A:VAL179 3.6 11.3 1.0
CB A:PRO112 3.7 9.8 1.0
CG A:PRO112 3.8 10.3 1.0
CA A:VAL179 3.8 10.2 1.0
O A:HIS150 3.9 6.2 1.0
CA A:HIS150 4.0 5.0 1.0
C A:ALA178 4.1 8.4 1.0
CA A:ALA178 4.1 7.3 1.0
CB A:VAL179 4.2 14.0 1.0
CG A:HIS150 4.2 4.8 1.0
C A:THR177 4.3 5.8 1.0
CE1 A:HIS150 4.3 5.2 1.0
CZ A:PHE186 4.3 7.6 1.0
CD A:PRO112 4.3 10.1 1.0
C A:HIS150 4.4 5.2 1.0
NE2 A:GLN113 4.4 7.5 1.0
CG A:GLN113 4.4 8.3 1.0
CB A:HIS150 4.5 5.3 1.0
O A:GLY149 4.5 7.0 1.0
N A:ALA178 4.7 6.0 1.0
CE1 A:PHE186 4.8 7.5 1.0
N A:SER180 4.8 12.0 1.0
CD A:GLN113 4.9 8.2 1.0
CA A:PRO112 4.9 10.1 1.0
N A:HIS150 5.0 5.5 1.0

Sodium binding site 5 out of 7 in 5b15

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Sodium binding site 5 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:21.4
occ:1.00
 O A:HOH449 2.7 24.4 1.0
O A:HOH525 2.7 14.6 1.0
OD1 A:ASN219 2.8 7.8 1.0
O A:HOH565 3.0 21.4 1.0
CB A:ALA244 3.8 7.7 1.0
CG A:ASN219 3.9 6.1 1.0
NH2 A:ARG224 4.1 9.3 1.0
CA A:ALA241 4.3 7.5 1.0
CB A:ALA241 4.4 6.8 1.0
CA A:ASN219 4.4 5.5 1.0
OD2 A:ASP238 4.4 10.3 1.0
CB A:ASN219 4.6 5.8 1.0
OD2 A:ASP220 4.7 12.8 1.0
O A:ALA241 4.7 7.2 1.0
O A:VAL218 4.7 10.9 1.0
C A:ASN219 4.9 7.1 1.0
ND2 A:ASN219 4.9 6.1 1.0
O A:HOH678 5.0 22.1 1.0

Sodium binding site 6 out of 7 in 5b15

Go back to Sodium Binding Sites List in 5b15
Sodium binding site 6 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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

b:18.6
occ:1.00
 O1 A:SO4311 2.7 19.9 1.0
O A:HOH524 2.7 15.6 1.0
NE A:ARG103 2.9 14.1 1.0
N A:VAL126 3.0 7.4 1.0
N A:LYS125 3.3 8.0 1.0
O3 A:SO4311 3.5 17.0 1.0
NH2 A:ARG103 3.6 14.0 1.0
S A:SO4311 3.6 17.2 1.0
CZ A:ARG103 3.6 15.7 1.0
CG A:ARG103 3.7 9.4 1.0
CD A:ARG103 3.7 10.4 1.0
CB A:VAL126 3.8 7.2 1.0
O A:VAL126 3.8 7.3 1.0
NH1 A:ARG127 3.8 11.9 1.0
C A:ALA124 3.8 8.3 1.0
CA A:VAL126 3.8 7.4 1.0
CA A:LYS125 3.9 8.7 1.0
C A:LYS125 3.9 7.6 1.0
CG2 A:VAL126 3.9 7.9 1.0
O A:SER123 4.1 9.8 1.0
CA A:ALA124 4.2 8.7 1.0
O A:HOH465 4.2 27.5 1.0
C A:VAL126 4.3 6.6 1.0
O4 A:SO4311 4.5 16.9 1.0
O A:ALA124 4.6 8.1 1.0
O2 A:SO4311 4.6 19.0 1.0
NH1 A:ARG103 4.8 16.0 1.0
CB A:ARG103 4.9 7.7 1.0
C A:SER123 5.0 8.3 1.0

Sodium binding site 7 out of 7 in 5b15

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Sodium binding site 7 out of 7 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem


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 Doripenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:25.1
occ:1.00
 O A:HOH533 2.4 16.0 1.0
O A:HOH421 2.9 19.7 1.0
OD1 A:ASN98 2.9 5.6 1.0
OG1 A:THR101 2.9 11.6 1.0
OG A:SER73 3.4 6.5 1.0
O A:HOH416 3.4 12.4 1.0
CD A:PRO108 3.5 9.7 1.0
O A:HOH579 3.6 16.2 1.0
O A:ALA97 3.7 9.2 1.0
CG A:ASN98 3.7 5.5 1.0
CB A:THR101 3.8 8.4 1.0
CG A:PRO108 4.0 12.8 1.0
CA A:ASN98 4.0 5.4 1.0
CB A:ASN98 4.3 5.9 1.0
CG2 A:THR101 4.4 8.2 1.0
C A:ALA97 4.5 6.6 1.0
ND2 A:ASN98 4.6 5.0 1.0
N A:ASN98 4.6 5.3 1.0
CB A:SER73 4.7 5.5 1.0
CB A:THR151 4.7 5.7 1.0
O A:HOH658 4.9 22.6 1.0
C A:ASN98 4.9 5.2 1.0
N A:PRO108 5.0 9.5 1.0
O A:ASN98 5.0 5.8 1.0

Reference:

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem To Be Published.
Page generated: Mon Oct 7 20:01:17 2024

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