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

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

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem, PDB code: 5axo 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) 40.62 / 1.39
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.900, 41.170, 45.320, 107.95, 102.46, 106.85
R / Rfree (%) 13.7 / 16.3

Other elements in 5axo:

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

Sodium binding site 1 out of 10 in 5axo

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Sodium binding site 1 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:13.3
occ:1.00
 OD1 A:ASN54 2.8 5.9 1.0
N A:GLN9 3.1 6.7 1.0
O A:GLN9 3.1 6.8 1.0
C A:GLN9 3.5 7.3 1.0
CG1 A:VAL50 3.6 6.5 1.0
CG A:ASN54 3.6 5.5 1.0
CA A:PRO8 3.7 8.8 1.0
ND2 A:ASN54 3.7 5.8 1.0
CB A:PRO8 3.7 10.7 1.0
C A:PRO8 3.8 8.8 1.0
CA A:GLN9 3.9 6.8 1.0
N A:GLN10 4.3 6.1 1.0
O A:VAL50 4.5 6.1 1.0
CB A:VAL50 4.6 6.2 1.0
CA A:GLN10 4.7 5.9 1.0
CG A:PRO8 4.8 12.7 1.0
CA A:VAL50 4.9 6.5 1.0
CG2 A:VAL50 4.9 6.7 1.0
CB A:GLN9 5.0 7.6 1.0
CD A:PRO11 5.0 5.5 1.0

Sodium binding site 2 out of 10 in 5axo

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Sodium binding site 2 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:18.4
occ:1.00
 O A:HOH411 2.7 27.6 1.0
OE1 A:GLU217 2.8 9.8 1.0
O A:HOH698 3.0 17.5 1.0
NE1 A:TRP222 3.1 7.7 1.0
O A:GLY24 3.4 10.2 1.0
CD A:GLU217 3.6 11.3 1.0
CD1 A:TRP222 3.7 7.9 1.0
CG A:PRO216 3.9 7.2 1.0
CB A:GLU217 3.9 8.0 1.0
CD A:ARG3 4.0 21.8 1.0
CA A:GLY25 4.0 6.3 1.0
CG A:GLU217 4.1 9.9 1.0
O A:HOH430 4.1 9.1 1.0
CB A:ARG3 4.1 23.0 1.0
N A:GLU217 4.2 5.8 1.0
CE2 A:TRP222 4.2 7.3 1.0
O A:GLY25 4.3 7.2 1.0
C A:GLY24 4.4 7.7 1.0
CD A:PRO216 4.4 6.9 1.0
C A:GLY25 4.4 5.9 1.0
CA A:GLU217 4.6 6.6 1.0
OE2 A:GLU217 4.6 21.4 1.0
CG A:ARG3 4.7 23.6 1.0
N A:GLY25 4.7 7.5 1.0
O A:ARG3 4.7 21.3 1.0
CZ2 A:TRP222 4.8 7.9 1.0
CB A:PRO216 4.8 7.0 1.0
N A:PRO216 4.9 5.9 1.0
CG A:TRP222 5.0 6.8 1.0

Sodium binding site 3 out of 10 in 5axo

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Sodium binding site 3 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:20.4
occ:1.00
 O A:HOH620 2.8 7.8 1.0
O A:HOH474 2.8 16.1 1.0
O A:ILE245 2.9 6.9 1.0
O A:HOH534 3.1 18.7 1.0
N A:GLY249 3.4 6.0 1.0
CA A:GLY249 3.7 6.1 1.0
CG2 A:ILE245 3.8 7.9 1.0
C A:ILE245 3.8 6.2 1.0
CB A:ALA248 3.9 6.4 1.0
C A:ALA248 4.0 6.4 1.0
CA A:ILE245 4.3 6.6 1.0
CB A:LEU176 4.3 6.7 1.0
CG2 A:THR177 4.5 7.9 1.0
CA A:ALA248 4.5 6.1 1.0
CG1 A:VAL218 4.6 10.1 1.0
O A:ALA248 4.6 6.1 1.0
CB A:ILE245 4.6 7.2 1.0
O2 A:SO4313 4.7 14.9 1.0
N A:LEU176 4.8 5.0 1.0
CG A:LEU176 4.9 6.9 1.0
C A:LEU176 4.9 5.9 1.0
CD1 A:LEU176 4.9 7.7 1.0
CA A:LEU176 4.9 5.6 1.0
O A:HOH596 4.9 11.1 1.0
N A:ALA248 5.0 6.1 1.0
O A:LEU176 5.0 6.2 1.0
N A:ALA246 5.0 6.4 1.0

Sodium binding site 4 out of 10 in 5axo

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Sodium binding site 4 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:20.4
occ:1.00
 O A:HOH547 2.6 13.1 1.0
O A:VAL179 2.7 10.6 1.0
O A:HOH465 2.8 7.6 1.0
N A:VAL179 3.1 9.0 1.0
O A:THR177 3.2 6.9 1.0
CG2 A:VAL179 3.4 14.1 1.0
ND1 A:HIS150 3.5 5.5 1.0
C A:VAL179 3.6 9.5 1.0
CG A:PRO112 3.8 8.7 1.0
O A:HIS150 3.8 6.0 1.0
CA A:VAL179 3.8 9.7 1.0
CB A:PRO112 3.8 8.1 1.0
CA A:HIS150 3.9 5.4 1.0
C A:ALA178 4.1 8.8 1.0
CA A:ALA178 4.1 7.1 1.0
CG A:HIS150 4.2 4.9 1.0
CB A:VAL179 4.2 13.7 1.0
C A:THR177 4.2 6.3 1.0
CZ A:PHE186 4.3 7.7 1.0
CE1 A:HIS150 4.3 5.0 1.0
CD A:PRO112 4.3 8.3 1.0
C A:HIS150 4.3 5.2 1.0
NE2 A:GLN113 4.4 7.8 1.0
CB A:HIS150 4.4 5.1 1.0
O A:GLY149 4.5 7.3 1.0
CG A:GLN113 4.5 8.2 1.0
N A:ALA178 4.7 6.6 1.0
CE2 A:PHE186 4.8 7.1 1.0
N A:SER180 4.8 9.8 1.0
CD A:GLN113 4.9 7.9 1.0
N A:HIS150 4.9 5.8 1.0

Sodium binding site 5 out of 10 in 5axo

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Sodium binding site 5 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:14.9
occ:1.00
 O A:HOH673 2.7 16.7 1.0
OE1 A:GLN85 2.9 8.1 1.0
N A:ALA124 3.1 8.6 1.0
O A:SER82 3.1 6.8 1.0
OG A:SER82 3.2 8.3 1.0
CB A:GLN85 3.6 6.4 1.0
CB A:ALA124 3.7 9.1 1.0
CG A:LYS86 3.7 13.4 1.0
CA A:SER82 3.7 5.8 1.0
OG A:SER123 3.7 11.3 1.0
CD A:GLN85 3.7 7.9 1.0
CA A:SER123 3.7 8.3 1.0
C A:SER82 3.8 6.3 1.0
C A:SER123 3.9 8.5 1.0
CA A:ALA124 3.9 8.7 1.0
CG A:GLN85 3.9 6.4 1.0
CB A:SER82 4.0 6.6 1.0
O A:HOH493 4.1 15.9 1.0
N A:LYS86 4.2 7.5 1.0
O A:HOH735 4.2 19.2 1.0
CB A:SER123 4.3 9.4 1.0
CE A:LYS86 4.3 26.5 1.0
CD A:LYS86 4.4 20.2 1.0
O A:ALA124 4.4 7.2 1.0
O A:GLY122 4.5 8.4 1.0
C A:GLN85 4.6 6.6 1.0
C A:ALA124 4.6 7.9 1.0
CA A:GLN85 4.6 6.1 1.0
O A:HOH644 4.7 26.5 1.0
CB A:LYS86 4.7 11.6 1.0
O A:HOH678 4.8 20.4 1.0
CA A:LYS86 4.8 9.3 1.0
N A:SER123 4.9 7.7 1.0
NE2 A:GLN85 5.0 8.3 1.0

Sodium binding site 6 out of 10 in 5axo

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Sodium binding site 6 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:18.9
occ:1.00
 O A:HOH517 2.7 16.2 1.0
O1 A:SO4314 2.7 18.4 1.0
NE A:ARG103 2.8 13.1 1.0
N A:VAL126 3.0 6.5 1.0
N A:LYS125 3.3 7.4 1.0
CG A:ARG103 3.6 9.0 1.0
CD A:ARG103 3.6 10.6 1.0
CZ A:ARG103 3.6 13.7 1.0
NH2 A:ARG103 3.7 14.6 1.0
O3 A:SO4314 3.7 18.0 1.0
S A:SO4314 3.7 18.4 1.0
CB A:VAL126 3.8 6.4 1.0
O A:VAL126 3.8 6.5 1.0
CA A:VAL126 3.8 6.1 1.0
C A:ALA124 3.8 7.9 1.0
CA A:LYS125 3.9 8.6 1.0
NH2 A:ARG127 3.9 11.1 1.0
C A:LYS125 3.9 7.0 1.0
CG2 A:VAL126 3.9 7.1 1.0
O A:SER123 4.1 9.0 1.0
CA A:ALA124 4.2 8.7 1.0
O A:HOH523 4.2 24.3 1.0
C A:VAL126 4.3 6.2 1.0
O2 A:SO4314 4.6 20.3 1.0
O A:ALA124 4.6 7.2 1.0
O4 A:SO4314 4.7 21.6 1.0
CB A:ARG103 4.7 7.9 1.0
NH1 A:ARG103 4.8 15.2 1.0
C A:SER123 4.9 8.5 1.0

Sodium binding site 7 out of 10 in 5axo

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Sodium binding site 7 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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

b:30.1
occ:1.00
 O A:HOH705 2.5 18.9 1.0
O A:SER234 2.9 8.3 1.0
O A:HOH539 3.0 16.7 1.0
O A:HOH602 3.0 20.9 1.0
O A:HOH415 3.0 20.6 1.0
O A:VAL237 3.5 8.8 1.0
C A:SER234 3.8 8.9 1.0
CB A:SER234 3.8 10.5 1.0
O A:HOH723 4.1 24.2 1.0
CB A:VAL237 4.1 8.7 1.0
CA A:SER234 4.2 10.5 1.0
OE2 A:GLU231 4.3 18.3 1.0
C A:VAL237 4.4 8.2 1.0
CG1 A:VAL237 4.4 9.0 1.0
OG A:SER234 4.5 12.8 1.0
O A:HOH672 4.7 20.9 1.0
CA A:VAL237 4.7 7.3 1.0
N A:ALA235 4.7 8.1 1.0
O A:HOH684 4.8 25.3 1.0
N A:VAL237 5.0 7.7 1.0

Sodium binding site 8 out of 10 in 5axo

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Sodium binding site 8 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:11.5
occ:1.00
 O A:HOH546 2.8 6.0 1.0
O A:SER70 2.8 5.3 1.0
O A:GLY153 2.9 5.5 1.0
N A:GLY95 2.9 5.0 1.0
O A:THR71 3.0 5.2 1.0
CG1 A:ILE155 3.4 5.7 1.0
CA A:ALA94 3.5 5.8 1.0
CB A:ALA94 3.5 6.1 1.0
C A:ALA94 3.7 6.0 1.0
C A:THR71 3.7 4.8 1.0
C A:SER70 3.8 4.8 1.0
N A:ILE155 3.8 4.2 1.0
CB A:ILE155 3.8 5.2 1.0
CA A:GLY95 3.9 5.3 1.0
C A:GLY153 4.0 5.8 1.0
ND2 A:ASN98 4.2 5.3 1.0
OG A:SER70 4.2 5.3 1.0
CB A:SER70 4.2 5.2 1.0
C A:GLY154 4.3 4.5 1.0
CA A:THR71 4.4 4.7 1.0
CA A:GLY154 4.4 4.9 1.0
CA A:ILE155 4.4 5.1 1.0
N A:HIS72 4.5 4.3 1.0
N A:THR71 4.5 4.4 1.0
CA A:HIS72 4.5 4.8 1.0
CB A:ASN98 4.6 5.9 1.0
CA A:SER70 4.6 4.4 1.0
N A:GLY154 4.7 5.2 1.0
O A:GLY95 4.8 5.8 1.0
CD1 A:ILE155 4.8 6.2 1.0
C A:GLY95 4.9 6.1 1.0
N A:ALA94 4.9 5.8 1.0
CZ2 A:TRP157 4.9 6.5 1.0
O A:ALA94 4.9 6.7 1.0
CG A:ASN98 4.9 6.0 1.0
O A:LEU93 4.9 6.1 1.0

Sodium binding site 9 out of 10 in 5axo

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Sodium binding site 9 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:18.0
occ:1.00
 O A:HOH524 2.8 12.4 1.0
OD1 A:ASN98 2.8 5.5 1.0
OG1 A:THR101 2.8 9.8 1.0
OG A:SER73 3.3 7.4 1.0
O A:HOH618 3.3 13.6 1.0
CD A:PRO108 3.6 9.0 1.0
CG A:ASN98 3.6 6.0 1.0
O A:HOH404 3.7 19.8 1.0
O A:ALA97 3.7 9.6 1.0
CB A:THR101 3.7 7.5 1.0
CA A:ASN98 4.0 5.8 1.0
CG A:PRO108 4.0 10.6 1.0
CG2 A:THR101 4.2 8.8 1.0
CB A:ASN98 4.3 5.9 1.0
C A:ALA97 4.5 7.1 1.0
ND2 A:ASN98 4.6 5.3 1.0
CB A:THR151 4.6 5.2 1.0
CB A:SER73 4.6 5.7 1.0
N A:ASN98 4.7 6.1 1.0
O A:HOH402 4.8 25.0 1.0
CG2 A:THR151 4.9 5.1 1.0
N A:GLU152 5.0 5.7 1.0
C A:ASN98 5.0 5.3 1.0
N A:PRO108 5.0 8.0 1.0

Sodium binding site 10 out of 10 in 5axo

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Sodium binding site 10 out of 10 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:26.1
occ:1.00
 O A:HOH669 2.5 31.1 1.0
O A:HOH701 2.7 20.7 1.0
O A:HOH445 3.0 15.0 1.0
OG A:SER32 3.4 6.1 1.0
NE2 A:HIS19 3.4 7.0 1.0
CE1 A:HIS19 3.4 6.9 1.0
O A:GLY16 3.6 7.1 1.0
CA A:ASN17 3.6 6.2 1.0
CB A:ASN17 3.9 6.3 1.0
C A:GLY16 4.2 7.0 1.0
N A:ASN17 4.2 6.2 1.0
O A:HOH466 4.6 16.4 1.0
CZ A:PHE60 4.6 9.5 1.0
C A:ASN17 4.7 5.5 1.0
CB A:SER32 4.7 5.5 1.0
ND1 A:HIS19 4.8 6.7 1.0
CD2 A:HIS19 4.8 7.0 1.0

Reference:

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Meropenem To Be Published.
Page generated: Tue Dec 15 10:23:46 2020

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