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Zinc in PDB 4rbs: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem

Enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem

All present enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem, PDB code: 4rbs 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) 41.83 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.428, 74.428, 219.960, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 4rbs

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Zinc binding site 1 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem


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 in the Complex with Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:43.0
occ:0.68
 OAF A:0RV302 2.0 76.0 1.0
ND1 A:HIS122 2.0 41.2 1.0
NE2 A:HIS189 2.0 55.4 1.0
NE2 A:HIS120 2.1 48.0 1.0
CD2 A:HIS189 2.9 51.4 1.0
CG A:HIS122 3.0 59.6 1.0
CE1 A:HIS122 3.0 54.3 1.0
CAQ A:0RV302 3.0 74.1 1.0
CE1 A:HIS120 3.0 52.9 1.0
CD2 A:HIS120 3.1 48.0 1.0
CE1 A:HIS189 3.1 60.2 1.0
CB A:HIS122 3.3 59.2 1.0
OAI A:0RV302 3.4 71.3 1.0
SG A:CYS208 4.0 42.1 0.7
ZN A:ZN301 4.0 57.0 0.9
NAN A:0RV302 4.0 82.7 1.0
CG A:HIS189 4.0 53.3 1.0
OAJ A:0RV302 4.1 79.0 1.0
CB A:CYS208 4.1 47.0 1.0
NE2 A:HIS122 4.1 50.1 1.0
CD2 A:HIS122 4.1 50.5 1.0
ND1 A:HIS120 4.1 51.0 1.0
ND1 A:HIS189 4.1 59.7 1.0
CG A:HIS120 4.2 51.2 1.0
OD1 A:ASP124 4.3 69.7 1.0
OAH A:0RV302 4.3 90.4 1.0
CBA A:0RV302 4.3 75.6 1.0
CG2 A:THR190 4.5 45.5 1.0
CAU A:0RV302 4.6 75.6 1.0
CAZ A:0RV302 4.7 79.1 1.0
OD2 A:ASP124 4.7 70.2 1.0
CA A:HIS122 4.8 60.7 1.0
CG A:ASP124 4.9 62.7 1.0
CAS A:0RV302 5.0 84.7 1.0

Zinc binding site 2 out of 4 in 4rbs

Go back to Zinc Binding Sites List in 4rbs
Zinc binding site 2 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem


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 in the Complex with Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:57.0
occ:0.90
 NE2 A:HIS250 2.0 62.4 1.0
NAN A:0RV302 2.1 82.7 1.0
OD2 A:ASP124 2.2 70.2 1.0
SG A:CYS208 2.3 42.1 0.7
CAS A:0RV302 2.9 84.7 1.0
CE1 A:HIS250 3.0 58.1 1.0
OAH A:0RV302 3.0 90.4 1.0
CD2 A:HIS250 3.0 57.2 1.0
CAZ A:0RV302 3.1 79.1 1.0
OAF A:0RV302 3.3 76.0 1.0
CB A:CYS208 3.3 47.0 1.0
CAP A:0RV302 3.3 83.2 1.0
CG A:ASP124 3.4 62.7 1.0
CAT A:0RV302 3.8 86.7 1.0
OD1 A:ASP124 3.9 69.7 1.0
CAQ A:0RV302 3.9 74.1 1.0
CAV A:0RV302 3.9 78.4 1.0
ZN A:ZN300 4.0 43.0 0.7
ND1 A:HIS250 4.1 48.8 1.0
CBA A:0RV302 4.1 75.6 1.0
CG A:HIS250 4.2 52.3 1.0
CB A:SER249 4.3 43.3 1.0
OAJ A:0RV302 4.3 79.0 1.0
CA A:CYS208 4.4 47.4 1.0
OAE A:0RV302 4.4 84.6 1.0
CB A:ASP124 4.5 55.9 1.0
NE2 A:HIS189 4.6 55.4 1.0
OG A:SER249 4.6 51.8 1.0
CE1 A:HIS189 4.9 60.2 1.0
CE1 A:HIS120 4.9 52.9 1.0
CAU A:0RV302 4.9 75.6 1.0
OAI A:0RV302 4.9 71.3 1.0
NE2 A:HIS120 5.0 48.0 1.0

Zinc binding site 3 out of 4 in 4rbs

Go back to Zinc Binding Sites List in 4rbs
Zinc binding site 3 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem


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 in the Complex with Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:48.8
occ:0.75
 ND1 B:HIS122 2.0 46.2 1.0
NE2 B:HIS189 2.0 66.6 1.0
NE2 B:HIS120 2.1 56.2 1.0
OAF B:0RV302 2.2 82.5 1.0
CG B:HIS122 2.9 66.6 1.0
CD2 B:HIS189 2.9 61.8 1.0
CE1 B:HIS122 3.0 58.7 1.0
CE1 B:HIS189 3.0 60.1 1.0
CD2 B:HIS120 3.1 53.7 1.0
CE1 B:HIS120 3.1 62.4 1.0
CAQ B:0RV302 3.1 86.4 1.0
CB B:HIS122 3.2 57.7 1.0
OAI B:0RV302 3.5 89.3 1.0
SG B:CYS208 3.7 68.3 1.0
CB B:CYS208 4.0 57.3 1.0
ZN B:ZN301 4.0 56.6 0.7
NE2 B:HIS122 4.1 59.7 1.0
CD2 B:HIS122 4.1 59.7 1.0
CG B:HIS189 4.1 59.7 1.0
ND1 B:HIS189 4.1 62.1 1.0
OD1 B:ASP124 4.2 69.8 1.0
ND1 B:HIS120 4.2 61.6 1.0
NAN B:0RV302 4.2 85.6 1.0
CG B:HIS120 4.2 56.7 1.0
CAA B:0RV302 4.4 71.0 1.0
OD2 B:ASP124 4.4 75.0 1.0
CG2 B:THR190 4.5 51.5 1.0
CBA B:0RV302 4.5 84.9 1.0
OAE B:0RV302 4.5 90.6 1.0
CG B:ASP124 4.7 65.6 1.0
CA B:HIS122 4.7 56.0 1.0
CAZ B:0RV302 4.8 82.2 1.0

Zinc binding site 4 out of 4 in 4rbs

Go back to Zinc Binding Sites List in 4rbs
Zinc binding site 4 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem


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 in the Complex with Hydrolyzed Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:56.6
occ:0.72
 NE2 B:HIS250 2.0 73.5 1.0
OD2 B:ASP124 2.1 75.0 1.0
NAN B:0RV302 2.1 85.6 1.0
SG B:CYS208 2.3 68.3 1.0
CE1 B:HIS250 2.9 69.0 1.0
CAZ B:0RV302 2.9 82.2 1.0
CAS B:0RV302 3.0 91.2 1.0
OAF B:0RV302 3.0 82.5 1.0
CD2 B:HIS250 3.0 73.3 1.0
OAE B:0RV302 3.1 90.6 1.0
CG B:ASP124 3.3 65.6 1.0
CB B:CYS208 3.4 57.3 1.0
CAP B:0RV302 3.4 93.0 1.0
CAQ B:0RV302 3.8 86.4 1.0
CAT B:0RV302 3.9 91.9 1.0
OD1 B:ASP124 3.9 69.8 1.0
CAV B:0RV302 3.9 83.3 1.0
CBA B:0RV302 4.0 84.9 1.0
ZN B:ZN300 4.0 48.8 0.8
ND1 B:HIS250 4.1 62.9 1.0
CG B:HIS250 4.1 65.9 1.0
CB B:SER249 4.2 50.2 1.0
CA B:CYS208 4.4 58.4 1.0
CB B:ASP124 4.5 59.0 1.0
OAH B:0RV302 4.5 0.1 1.0
NE2 B:HIS189 4.6 66.6 1.0
OG B:SER249 4.7 54.6 1.0
CE1 B:HIS189 4.8 60.1 1.0
CAA B:0RV302 4.8 71.0 1.0
CAU B:0RV302 4.8 79.9 1.0
CE1 B:HIS120 4.9 62.4 1.0
OAI B:0RV302 5.0 89.3 1.0
NE2 B:HIS120 5.0 56.2 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, J.Sacchettini, A.Joachimiak. Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem To Be Published.
Page generated: Sun Oct 27 06:59:26 2024

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