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Zinc in PDB 4wbg: Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam

Enzymatic activity of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam

All present enzymatic activity of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam, PDB code: 4wbg was solved by T.Oguri, A.Shimizu-Ibuka, Y.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.540, 59.250, 62.480, 90.00, 102.72, 90.00
R / Rfree (%) 17.5 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam (pdb code 4wbg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam, PDB code: 4wbg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4wbg

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Zinc binding site 1 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:18.4
occ:1.00
 O A:HOH1139 2.1 2.2 1.0
ND1 A:HIS24 2.2 16.8 1.0
O A:ACT1011 2.3 23.1 1.0
C A:ACT1011 3.0 23.6 1.0
OXT A:ACT1011 3.1 27.7 1.0
CG A:HIS24 3.1 16.9 1.0
CE1 A:HIS24 3.2 17.1 1.0
CB A:HIS24 3.4 17.1 1.0
CA A:HIS24 3.8 17.5 1.0
CD A:PRO342 4.1 14.4 1.0
NE2 A:HIS24 4.3 17.0 1.0
CD2 A:HIS24 4.3 16.9 1.0
CH3 A:ACT1011 4.4 25.1 1.0
O A:GLU23 4.6 19.1 1.0
CG A:PRO342 4.7 14.3 1.0
O A:HIS24 4.7 14.8 1.0
C A:HIS24 4.7 17.2 1.0
NZ A:LYS206 4.7 29.8 1.0
N A:HIS24 4.8 18.2 1.0
CB A:TYR341 4.9 12.3 1.0

Zinc binding site 2 out of 7 in 4wbg

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Zinc binding site 2 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:15.3
occ:1.00
 OE1 A:GLU130 2.0 13.7 1.0
OXT A:ACT1009 2.0 16.5 1.0
CD A:GLU130 2.8 14.0 1.0
C A:ACT1009 2.8 16.1 1.0
O A:ACT1009 2.9 17.4 1.0
OE2 A:GLU130 3.0 13.8 1.0
O A:HOH1111 3.7 28.6 1.0
O A:HOH1114 4.2 14.0 1.0
CG A:GLU130 4.2 14.0 1.0
CH3 A:ACT1009 4.2 17.2 1.0
CD A:ARG133 4.4 16.2 1.0
CA A:GLU130 4.6 14.5 1.0
NH1 A:ARG133 4.6 15.6 1.0
CB A:GLU130 4.6 14.2 1.0

Zinc binding site 3 out of 7 in 4wbg

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Zinc binding site 3 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:10.3
occ:0.50
 OE2 A:GLU207 2.0 20.9 1.0
O A:HOH1132 2.1 36.5 1.0
CD A:GLU207 3.0 24.3 1.0
OE1 A:GLU207 3.4 25.7 1.0
CG A:GLU207 4.3 24.8 1.0
CB A:LYS206 5.0 24.9 1.0

Zinc binding site 4 out of 7 in 4wbg

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Zinc binding site 4 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:33.7
occ:1.00
 ND1 A:HIS259 2.1 20.2 1.0
O A:HOH1238 2.2 24.3 1.0
O A:HOH1213 2.4 22.7 1.0
O A:HOH1272 2.6 26.2 1.0
CE1 A:HIS259 3.1 21.0 1.0
CG A:HIS259 3.1 18.3 1.0
CB A:HIS259 3.5 17.4 1.0
NE2 A:HIS259 4.2 20.5 1.0
CD2 A:HIS259 4.3 19.9 1.0
CA A:HIS259 4.5 17.0 1.0
OG1 A:THR112 4.9 14.3 1.0
CG2 A:THR112 4.9 13.5 1.0
O A:GLY108 5.0 14.2 1.0
C A:GLY108 5.0 14.9 1.0
CA A:GLY108 5.0 14.9 1.0

Zinc binding site 5 out of 7 in 4wbg

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Zinc binding site 5 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:24.0
occ:1.00
 OXT A:ACT1010 2.0 20.1 1.0
NE2 A:HIS161 2.1 16.7 1.0
O A:HOH1136 2.3 17.0 1.0
O A:HOH1263 2.3 30.3 1.0
C A:ACT1010 2.7 23.2 1.0
O A:ACT1010 2.8 24.0 1.0
CD2 A:HIS161 3.0 16.2 1.0
CE1 A:HIS161 3.1 16.9 1.0
NH2 A:ARG133 3.9 15.1 1.0
CG A:HIS161 4.2 16.2 1.0
CH3 A:ACT1010 4.2 24.0 1.0
ND1 A:HIS161 4.2 16.9 1.0
O A:HOH1219 4.4 19.6 1.0
NE1 A:TRP96 4.7 19.8 1.0
CZ A:ARG133 4.9 15.4 1.0

Zinc binding site 6 out of 7 in 4wbg

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Zinc binding site 6 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1007

b:15.6
occ:0.50
 NE2 A:HIS148 2.1 20.2 1.0
CD2 A:HIS148 2.9 19.7 1.0
CE1 A:HIS148 3.1 20.0 1.0
CG A:HIS148 4.1 18.3 1.0
ND1 A:HIS148 4.2 18.9 1.0
CE1 A:TYR143 4.5 24.9 1.0
CD A:PRO297 4.6 20.9 1.0
CB A:PRO297 4.8 20.5 1.0
CD1 A:TYR143 4.9 25.2 1.0
CG A:PRO297 4.9 20.9 1.0

Zinc binding site 7 out of 7 in 4wbg

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Zinc binding site 7 out of 7 in the Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Class C Beta-Lactamase Mox-1 Covalently Complexed with Aztorenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1008

b:41.3
occ:1.00
 O A:HOH1113 2.6 34.1 1.0
OD1 A:ASP244 3.7 43.8 1.0
OD2 A:ASP244 4.0 45.6 1.0
CG A:ASP244 4.1 42.0 1.0
O A:ASP244 4.6 35.6 1.0

Reference:

T.Oguri, Y.Ishii, A.Shimizu-Ibuka. Conformational Change Observed in the Active Site of Class C Beta-Lactamase Mox-1 Upon Binding to Aztreonam Antimicrob.Agents Chemother. V. 59 5069 2015.
ISSN: ESSN 1098-6596
PubMed: 26055361
DOI: 10.1128/AAC.04428-14
Page generated: Sun Oct 27 09:46:08 2024

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