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Zinc in PDB 4hl2: New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin

Enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin

All present enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin:
3.5.2.6;

Protein crystallography data

The structure of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin, PDB code: 4hl2 was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Known Mtbinhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.56 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.190, 79.171, 134.473, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.7

Zinc Binding Sites:

The binding sites of Zinc atom in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin (pdb code 4hl2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin, PDB code: 4hl2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4hl2

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Zinc binding site 1 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:6.0
occ:0.96
 O A:HOH701 1.9 8.0 1.0
ND1 A:HIS122 2.0 6.5 1.0
NE2 A:HIS189 2.0 5.6 1.0
NE2 A:HIS120 2.1 6.3 1.0
OXT A:ZZ7301 2.4 8.7 1.0
CE1 A:HIS122 2.9 7.0 1.0
CG A:HIS122 3.0 5.4 1.0
CD2 A:HIS189 3.0 5.0 1.0
CE1 A:HIS189 3.0 5.7 1.0
CE1 A:HIS120 3.1 6.7 1.0
CD2 A:HIS120 3.1 5.0 1.0
C15 A:ZZ7301 3.3 8.7 1.0
CB A:HIS122 3.4 5.6 1.0
C14 A:ZZ7301 3.9 8.4 1.0
N3 A:ZZ7301 4.1 7.2 1.0
NE2 A:HIS122 4.1 7.4 1.0
O4 A:ZZ7301 4.1 10.8 1.0
ND1 A:HIS189 4.1 5.8 1.0
CD2 A:HIS122 4.1 7.7 1.0
CG A:HIS189 4.2 4.9 1.0
OD1 A:ASP124 4.2 6.8 1.0
ND1 A:HIS120 4.2 5.9 1.0
CG2 A:THR190 4.3 5.9 1.0
CG A:HIS120 4.3 5.2 1.0
SG A:CYS208 4.4 4.6 0.8
CB A:CYS208 4.5 6.0 1.0
ZN A:ZN303 4.6 5.0 0.8
C13 A:ZZ7301 4.6 7.2 1.0
CA A:HIS122 4.8 5.0 1.0
C12 A:ZZ7301 4.9 7.9 1.0

Zinc binding site 2 out of 5 in 4hl2

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Zinc binding site 2 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:5.0
occ:0.82
 NE2 A:HIS250 2.0 6.9 1.0
OD2 A:ASP124 2.1 6.8 1.0
N3 A:ZZ7301 2.2 7.2 1.0
O1 A:ZZ7301 2.2 7.4 1.0
SG A:CYS208 2.4 4.6 0.8
C2 A:ZZ7301 3.0 7.5 1.0
CE1 A:HIS250 3.0 6.0 1.0
CD2 A:HIS250 3.0 6.4 1.0
O A:HOH701 3.0 8.0 1.0
C12 A:ZZ7301 3.1 7.9 1.0
CG A:ASP124 3.3 6.0 1.0
C13 A:ZZ7301 3.3 7.2 1.0
CB A:CYS208 3.4 6.0 1.0
C16 A:ZZ7301 3.6 10.1 1.0
OD1 A:ASP124 3.8 6.8 1.0
C6 A:ZZ7301 3.9 8.2 1.0
ND1 A:HIS250 4.1 6.8 1.0
CG A:HIS250 4.2 6.8 1.0
O2 A:ZZ7301 4.2 8.4 1.0
CB A:SER249 4.3 6.8 1.0
C14 A:ZZ7301 4.3 8.4 1.0
OXT A:ZZ7301 4.3 8.7 1.0
CB A:ASP124 4.5 6.1 1.0
CA A:CYS208 4.5 5.5 1.0
S1 A:ZZ7301 4.5 6.7 0.8
ZN A:ZN302 4.6 6.0 1.0
OG A:SER249 4.6 6.2 1.0
C15 A:ZZ7301 4.8 8.7 1.0
NE2 A:HIS189 4.9 5.6 1.0
CE1 A:HIS189 4.9 5.7 1.0
NZ A:LYS211 5.0 10.3 0.4

Zinc binding site 3 out of 5 in 4hl2

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Zinc binding site 3 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:5.8
occ:0.99
 O B:HOH687 2.0 7.1 1.0
ND1 B:HIS122 2.0 6.2 1.0
NE2 B:HIS189 2.0 5.4 1.0
NE2 B:HIS120 2.1 6.4 1.0
OXT B:ZZ7302 2.4 7.2 1.0
CE1 B:HIS122 2.9 6.1 1.0
CD2 B:HIS189 3.0 5.3 1.0
CE1 B:HIS189 3.0 5.1 1.0
CG B:HIS122 3.0 4.5 1.0
CE1 B:HIS120 3.1 6.7 1.0
CD2 B:HIS120 3.1 5.5 1.0
C15 B:ZZ7302 3.3 7.1 1.0
CB B:HIS122 3.4 5.6 1.0
C14 B:ZZ7302 4.0 8.0 1.0
NE2 B:HIS122 4.1 7.2 1.0
ND1 B:HIS189 4.1 5.9 1.0
CD2 B:HIS122 4.1 6.4 1.0
CG B:HIS189 4.1 4.7 1.0
OD1 B:ASP124 4.2 6.2 1.0
O4 B:ZZ7302 4.2 9.5 1.0
ND1 B:HIS120 4.2 6.0 1.0
N3 B:ZZ7302 4.2 9.1 1.0
CG2 B:THR190 4.3 5.9 1.0
CG B:HIS120 4.3 4.9 1.0
SG B:CYS208 4.4 5.6 1.0
CB B:CYS208 4.5 5.8 1.0
C13 B:ZZ7302 4.5 7.1 1.0
ZN B:ZN304 4.6 5.2 0.9
O B:HOH431 4.8 8.0 0.7
CA B:HIS122 4.8 5.1 1.0
C12 B:ZZ7302 4.8 7.0 1.0

Zinc binding site 4 out of 5 in 4hl2

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Zinc binding site 4 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:5.2
occ:0.89
 NE2 B:HIS250 2.0 6.0 1.0
N3 B:ZZ7302 2.1 9.1 1.0
OD2 B:ASP124 2.1 6.5 1.0
O1 B:ZZ7302 2.2 7.1 1.0
SG B:CYS208 2.4 5.6 1.0
CD2 B:HIS250 3.0 6.5 1.0
CE1 B:HIS250 3.0 6.7 1.0
C2 B:ZZ7302 3.0 6.5 1.0
C12 B:ZZ7302 3.0 7.0 1.0
O B:HOH687 3.0 7.1 1.0
C13 B:ZZ7302 3.2 7.1 1.0
CG B:ASP124 3.3 5.9 1.0
CB B:CYS208 3.5 5.8 1.0
C16 B:ZZ7302 3.6 8.3 1.0
C6 B:ZZ7302 3.8 6.9 1.0
OD1 B:ASP124 3.8 6.2 1.0
ND1 B:HIS250 4.1 6.8 1.0
CG B:HIS250 4.2 6.6 1.0
O2 B:ZZ7302 4.2 8.4 1.0
CB B:SER249 4.2 6.2 1.0
OXT B:ZZ7302 4.3 7.2 1.0
C14 B:ZZ7302 4.4 8.0 1.0
S1 B:ZZ7302 4.5 7.1 0.8
CA B:CYS208 4.5 5.7 1.0
CB B:ASP124 4.5 6.2 1.0
ZN B:ZN303 4.6 5.8 1.0
OG B:SER249 4.6 6.6 1.0
CE1 B:HIS189 4.8 5.1 1.0
C15 B:ZZ7302 4.8 7.1 1.0
NE2 B:HIS189 4.9 5.4 1.0

Zinc binding site 5 out of 5 in 4hl2

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Zinc binding site 5 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:6.9
occ:0.46
 OE1 A:GLU227 2.0 9.8 0.6
O B:HOH688 2.0 18.6 0.6
OD2 B:ASP223 2.1 10.3 1.0
OE2 B:GLU152 2.1 13.9 1.0
OE2 A:GLU227 2.7 13.5 0.6
CD A:GLU227 2.7 10.3 0.6
OE1 B:GLU152 2.7 11.0 1.0
CD B:GLU152 2.7 9.1 1.0
CG B:ASP223 2.8 10.2 1.0
OD1 B:ASP223 2.9 12.3 1.0
CG A:GLU227 3.9 11.5 0.4
NE2 A:HIS228 4.0 9.1 1.0
CE1 A:HIS228 4.0 7.8 1.0
O B:HOH408 4.1 8.7 1.0
NE2 B:HIS122 4.1 7.2 1.0
CG A:GLU227 4.2 7.9 0.6
O A:HOH601 4.2 14.8 1.0
CG B:GLU152 4.2 7.9 1.0
CB B:ASP223 4.3 8.3 1.0
O B:HOH621 4.3 27.1 0.7
O B:HOH555 4.6 19.1 0.7
CD A:GLU227 4.6 12.8 0.4
CB A:GLU227 4.7 9.7 0.4
OE2 A:GLU227 4.7 14.4 0.4
CB A:GLU227 4.7 8.0 0.6
CD2 B:HIS122 4.8 6.4 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak. New Delhi Metallo-Beta-Lactamase-1 1.05 A Structure Complexed with Hydrolyzed Ampicillin To Be Published.
Page generated: Wed Aug 20 18:34:35 2025

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