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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

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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

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Sodium binding site 2 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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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

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Sodium binding site 3 out of 15 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 20:01:17 2024

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