Atomistry » Zinc » PDB 4r6t-4rlr » 4rbs
Atomistry »
  Zinc »
    PDB 4r6t-4rlr »
      4rbs »

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

Go back to Zinc Binding Sites List in 4rbs
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy