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

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy