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Zinc in PDB 4ram: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G

Enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G

All present enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G, PDB code: 4ram was solved by Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtbproteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.97 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.065, 79.212, 133.307, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 18

Other elements in 4ram:

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G (pdb code 4ram). 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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G, PDB code: 4ram:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4ram

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Zinc binding site 1 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:15.0
occ:1.00
 NE2 A:HIS250 2.1 14.4 1.0
O12 A:PNM304 2.2 25.7 1.0
OD1 A:ASP124 2.3 14.1 1.0
N4 A:PNM304 2.3 28.0 1.0
SG A:CYS208 2.4 12.8 0.9
O A:HOH559 2.7 25.3 1.0
C11 A:PNM304 3.0 26.1 1.0
CD2 A:HIS250 3.0 14.9 1.0
CE1 A:HIS250 3.1 14.4 1.0
C3 A:PNM304 3.1 27.2 1.0
C5 A:PNM304 3.3 29.2 1.0
CG A:ASP124 3.4 13.8 1.0
CB A:CYS208 3.5 12.6 1.0
C10 A:PNM304 3.7 29.5 1.0
OD2 A:ASP124 3.8 14.9 1.0
C2 A:PNM304 3.9 28.6 1.0
ND1 A:HIS250 4.2 14.7 1.0
CG A:HIS250 4.2 14.8 1.0
O13 A:PNM304 4.2 25.5 1.0
C6 A:PNM304 4.2 30.3 1.0
ZN A:ZN302 4.3 15.3 1.0
CB A:SER249 4.3 13.1 1.0
S1 A:PNM304 4.5 29.5 1.0
O8 A:PNM304 4.5 30.2 1.0
CA A:CYS208 4.5 12.0 1.0
NE2 A:HIS189 4.6 11.1 1.0
CB A:ASP124 4.6 13.6 1.0
CE1 A:HIS189 4.7 10.5 1.0
OG A:SER249 4.7 13.9 1.0
C7 A:PNM304 4.8 30.1 1.0

Zinc binding site 2 out of 7 in 4ram

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Zinc binding site 2 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.3
occ:1.00
 O A:HOH559 1.9 25.3 1.0
ND1 A:HIS122 2.0 11.5 1.0
NE2 A:HIS189 2.1 11.1 1.0
NE2 A:HIS120 2.1 13.1 1.0
O8 A:PNM304 2.7 30.2 1.0
CE1 A:HIS122 3.0 12.7 1.0
CD2 A:HIS189 3.0 11.3 1.0
CG A:HIS122 3.0 11.5 1.0
CE1 A:HIS120 3.0 13.6 1.0
CE1 A:HIS189 3.1 10.5 1.0
CD2 A:HIS120 3.1 12.2 1.0
CB A:HIS122 3.4 10.4 1.0
C7 A:PNM304 3.5 30.1 1.0
C6 A:PNM304 3.8 30.3 1.0
N4 A:PNM304 3.9 28.0 1.0
NE2 A:HIS122 4.1 12.9 1.0
OD2 A:ASP124 4.1 14.9 1.0
CD2 A:HIS122 4.1 12.0 1.0
CG A:HIS189 4.2 10.0 1.0
ND1 A:HIS120 4.2 13.1 1.0
SG A:CYS208 4.2 12.8 0.9
ND1 A:HIS189 4.2 10.2 1.0
CG A:HIS120 4.2 11.7 1.0
ZN A:ZN301 4.3 15.0 1.0
CB A:CYS208 4.4 12.6 1.0
CG2 A:THR190 4.4 11.3 1.0
C5 A:PNM304 4.4 29.2 1.0
O A:HOH557 4.8 31.1 1.0
C3 A:PNM304 4.8 27.2 1.0
CA A:HIS122 4.8 9.9 1.0
OD1 A:ASP124 4.9 14.1 1.0
O12 A:PNM304 4.9 25.7 1.0
CG A:ASP124 5.0 13.8 1.0

Zinc binding site 3 out of 7 in 4ram

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Zinc binding site 3 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:12.5
occ:1.00
 OD2 A:ASP223 2.2 14.9 1.0
OE1 A:GLU152 2.3 17.7 1.0
OE1 B:GLU227 2.4 19.0 0.9
CL A:CL305 2.4 31.8 1.0
OE2 B:GLU227 2.4 20.2 0.9
OE2 A:GLU152 2.5 17.6 1.0
CD B:GLU227 2.7 18.6 0.9
CD A:GLU152 2.8 16.5 1.0
CG A:ASP223 3.0 14.7 1.0
OD1 A:ASP223 3.0 14.8 0.8
NE2 A:HIS122 4.1 12.9 1.0
O A:HOH516 4.2 46.2 1.0
O A:HOH439 4.2 16.3 1.0
CG B:GLU227 4.2 16.5 0.9
NE2 B:HIS228 4.3 14.5 1.0
CG A:GLU152 4.3 14.7 1.0
CB A:ASP223 4.4 13.9 1.0
O A:HOH533 4.5 31.9 1.0
CE1 B:HIS228 4.5 14.7 1.0
CD2 A:HIS122 4.7 12.0 1.0
O B:HOH459 4.7 28.1 1.0
O A:HOH402 4.7 25.6 1.0

Zinc binding site 4 out of 7 in 4ram

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Zinc binding site 4 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:15.9
occ:1.00
 NE2 B:HIS250 2.1 15.4 1.0
O12 B:PNM304 2.1 51.4 1.0
OD1 B:ASP124 2.2 13.7 1.0
SG B:CYS208 2.4 14.6 0.9
N4 B:PNM304 2.4 55.0 1.0
O B:HOH521 2.6 28.1 1.0
C11 B:PNM304 3.0 52.2 1.0
CE1 B:HIS250 3.0 14.9 1.0
CD2 B:HIS250 3.1 15.7 1.0
C3 B:PNM304 3.2 54.0 1.0
C5 B:PNM304 3.2 55.6 1.0
CG B:ASP124 3.3 12.6 1.0
CB B:CYS208 3.5 12.9 1.0
OD2 B:ASP124 3.7 13.5 1.0
C10 B:PNM304 3.8 55.6 1.0
C2 B:PNM304 4.0 55.2 1.0
ZN B:ZN302 4.1 15.4 1.0
ND1 B:HIS250 4.2 14.9 1.0
O13 B:PNM304 4.2 51.2 1.0
CG B:HIS250 4.2 15.6 1.0
C6 B:PNM304 4.2 57.0 1.0
CB B:SER249 4.3 14.0 1.0
S1 B:PNM304 4.4 56.1 1.0
NE2 B:HIS189 4.5 11.2 1.0
O8 B:PNM304 4.6 57.0 1.0
CB B:ASP124 4.6 12.1 1.0
CA B:CYS208 4.6 12.5 1.0
CE1 B:HIS189 4.6 10.8 1.0
OG B:SER249 4.7 14.7 1.0
C7 B:PNM304 4.9 57.3 1.0
CE1 B:HIS120 4.9 13.6 1.0

Zinc binding site 5 out of 7 in 4ram

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Zinc binding site 5 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:15.4
occ:1.00
 O B:HOH521 1.8 28.1 1.0
NE2 B:HIS189 2.0 11.2 1.0
ND1 B:HIS122 2.0 11.1 1.0
NE2 B:HIS120 2.1 13.2 1.0
O8 B:PNM304 2.8 57.0 1.0
CD2 B:HIS189 2.9 10.6 1.0
CE1 B:HIS122 3.0 13.0 1.0
CG B:HIS122 3.0 11.1 1.0
CE1 B:HIS120 3.0 13.6 1.0
CE1 B:HIS189 3.1 10.8 1.0
CD2 B:HIS120 3.1 13.3 1.0
CB B:HIS122 3.4 10.2 1.0
C7 B:PNM304 3.7 57.3 1.0
N4 B:PNM304 3.7 55.0 1.0
C6 B:PNM304 3.9 57.0 1.0
OD2 B:ASP124 4.1 13.5 1.0
NE2 B:HIS122 4.1 12.5 1.0
CG B:HIS189 4.1 10.2 1.0
ZN B:ZN301 4.1 15.9 1.0
ND1 B:HIS120 4.1 14.2 1.0
ND1 B:HIS189 4.1 11.5 1.0
CD2 B:HIS122 4.1 11.9 1.0
SG B:CYS208 4.2 14.6 0.9
CG B:HIS120 4.2 12.9 1.0
CB B:CYS208 4.3 12.9 1.0
C5 B:PNM304 4.4 55.6 1.0
CG2 B:THR190 4.4 10.4 1.0
O12 B:PNM304 4.8 51.4 1.0
C3 B:PNM304 4.8 54.0 1.0
OD1 B:ASP124 4.8 13.7 1.0
CA B:HIS122 4.8 9.7 1.0
O B:HOH501 4.9 32.8 1.0
CG B:ASP124 4.9 12.6 1.0

Zinc binding site 6 out of 7 in 4ram

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Zinc binding site 6 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:11.2
occ:1.00
 OD2 B:ASP223 2.3 14.2 1.0
CL B:CL306 2.3 35.0 1.0
OE1 B:GLU152 2.3 16.4 1.0
OE1 A:GLU227 2.4 17.3 1.0
OE2 A:GLU227 2.5 18.0 1.0
OE2 B:GLU152 2.5 14.6 1.0
CD B:GLU152 2.8 14.6 1.0
CD A:GLU227 2.8 16.7 1.0
CG B:ASP223 3.0 13.9 1.0
OD1 B:ASP223 3.0 13.8 0.7
NE2 B:HIS122 4.2 12.5 1.0
O B:HOH503 4.2 30.9 1.0
O B:HOH410 4.3 15.8 1.0
CG B:GLU152 4.3 12.9 1.0
CG A:GLU227 4.3 14.9 1.0
NE2 A:HIS228 4.3 13.6 1.0
O B:HOH545 4.4 35.1 1.0
CB B:ASP223 4.4 14.0 1.0
CE1 A:HIS228 4.5 13.6 1.0
O B:HOH402 4.7 26.1 1.0
O A:HOH436 4.7 26.7 1.0
CD2 B:HIS122 4.8 11.9 1.0

Zinc binding site 7 out of 7 in 4ram

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Zinc binding site 7 out of 7 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:74.5
occ:1.00
 O B:HOH569 2.3 39.9 1.0
ND1 B:HIS159 2.3 15.5 1.0
O B:HOH411 2.6 23.6 1.0
O B:HOH450 2.9 35.2 1.0
CE1 B:HIS159 3.2 16.8 1.0
CG B:HIS159 3.4 13.9 1.0
CB B:HIS159 3.7 12.1 1.0
CA B:HIS159 4.1 10.5 1.0
O B:HOH439 4.3 17.7 1.0
NE2 B:HIS159 4.4 16.5 1.0
O B:GLN158 4.4 14.2 1.0
CD2 B:HIS159 4.5 14.9 1.0
O B:HOH428 4.5 23.9 1.0
N B:SER160 4.9 10.1 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility Toknown Mtb Inhibitors (Mtbi). Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G To Be Published.
Page generated: Wed Dec 16 05:45:33 2020

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