Atomistry » Manganese » PDB 4gwc-4ilk » 4h0d
Atomistry »
  Manganese »
    PDB 4gwc-4ilk »
      4h0d »

Manganese in PDB 4h0d: New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae

Enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae

All present enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae:
3.5.2.6;

Protein crystallography data

The structure of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae, PDB code: 4h0d was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, T.A.Binkowski, J.Mire, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Knownmtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.77 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.101, 78.606, 133.711, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 15.8

Other elements in 4h0d:

The structure of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae (pdb code 4h0d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae, PDB code: 4h0d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4h0d

Go back to Manganese Binding Sites List in 4h0d
Manganese binding site 1 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:16.3
occ:1.00
 O A:HOH402 2.1 14.9 1.0
OXT A:ZZ7301 2.1 16.7 1.0
ND1 A:HIS122 2.2 14.0 1.0
NE2 A:HIS189 2.2 12.8 1.0
NE2 A:HIS120 2.3 13.1 1.0
CE1 A:HIS122 3.1 15.7 1.0
C15 A:ZZ7301 3.1 16.9 1.0
CD2 A:HIS189 3.1 14.2 1.0
CG A:HIS122 3.2 13.2 1.0
CE1 A:HIS189 3.2 13.5 1.0
CE1 A:HIS120 3.2 14.1 1.0
CD2 A:HIS120 3.3 13.4 1.0
CB A:HIS122 3.5 13.1 1.0
C14 A:ZZ7301 3.7 16.0 1.0
N3 A:ZZ7301 4.0 15.1 1.0
O4 A:ZZ7301 4.1 20.3 1.0
NE2 A:HIS122 4.2 17.0 1.0
CG2 A:THR190 4.3 13.5 1.0
CD2 A:HIS122 4.3 16.3 1.0
ND1 A:HIS189 4.3 12.6 1.0
CG A:HIS189 4.3 12.2 1.0
ND1 A:HIS120 4.3 13.3 1.0
OD1 A:ASP124 4.4 14.2 1.0
CG A:HIS120 4.4 12.3 1.0
O A:HOH436 4.4 21.7 1.0
MN A:MN303 4.5 13.3 0.9
C13 A:ZZ7301 4.5 16.6 1.0
SG A:CYS208 4.5 14.3 1.0
CB A:CYS208 4.6 12.9 1.0
C12 A:ZZ7301 4.8 15.9 1.0
O1 A:ZZ7301 4.9 15.0 1.0
CA A:HIS122 5.0 13.2 1.0
N1 A:ZZ7301 5.0 17.1 1.0

Manganese binding site 2 out of 5 in 4h0d

Go back to Manganese Binding Sites List in 4h0d
Manganese binding site 2 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:13.3
occ:0.87
 OD2 A:ASP124 2.1 15.9 1.0
NE2 A:HIS250 2.1 15.7 1.0
O1 A:ZZ7301 2.2 15.0 1.0
N3 A:ZZ7301 2.3 15.1 1.0
SG A:CYS208 2.5 14.3 1.0
O A:HOH402 2.8 14.9 1.0
C2 A:ZZ7301 3.0 16.9 1.0
CE1 A:HIS250 3.1 16.7 1.0
CD2 A:HIS250 3.1 15.1 1.0
C12 A:ZZ7301 3.1 15.9 1.0
CG A:ASP124 3.3 15.5 1.0
C13 A:ZZ7301 3.4 16.6 1.0
CB A:CYS208 3.5 12.9 1.0
OD1 A:ASP124 3.7 14.2 1.0
C16 A:ZZ7301 3.7 17.2 1.0
C6 A:ZZ7301 4.0 16.2 1.0
ND1 A:HIS250 4.2 15.7 1.0
O2 A:ZZ7301 4.2 17.3 1.0
CG A:HIS250 4.3 14.8 1.0
CB A:SER249 4.3 14.1 1.0
C14 A:ZZ7301 4.4 16.0 1.0
OXT A:ZZ7301 4.4 16.7 1.0
MN A:MN302 4.5 16.3 1.0
CB A:ASP124 4.5 14.2 1.0
S1 A:ZZ7301 4.6 18.7 1.0
CA A:CYS208 4.6 12.4 1.0
OG A:SER249 4.7 13.9 1.0
NE2 A:HIS189 4.8 12.8 1.0
C15 A:ZZ7301 4.8 16.9 1.0
CE1 A:HIS189 4.9 13.5 1.0

Manganese binding site 3 out of 5 in 4h0d

Go back to Manganese Binding Sites List in 4h0d
Manganese binding site 3 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn306

b:15.9
occ:0.18
 CE1 A:HIS228 2.0 13.8 0.5
O B:HOH427 2.2 20.5 1.0
NE2 A:HIS228 2.2 21.7 0.5
OD2 B:ASP223 2.3 25.4 1.0
OE1 A:GLU227 2.5 30.5 0.5
OE2 B:GLU152 2.6 32.5 1.0
NE2 A:HIS228 2.6 15.6 0.5
O A:HOH593 2.8 36.7 1.0
O2 B:FMT304 2.9 28.5 1.0
CG B:ASP223 3.0 27.2 1.0
CD2 A:HIS228 3.1 21.0 0.5
ND1 A:HIS228 3.1 12.5 0.5
CE1 A:HIS228 3.2 19.0 0.5
CD B:GLU152 3.4 26.5 1.0
CD A:GLU227 3.5 31.1 0.5
OD1 B:ASP223 3.6 28.3 1.0
CD2 A:HIS228 3.9 17.1 0.5
OE1 B:GLU152 3.9 24.1 1.0
C B:FMT304 4.0 37.9 1.0
CB B:ASP223 4.0 19.8 1.0
CG A:HIS228 4.1 13.4 0.5
OE2 A:GLU227 4.1 34.7 0.5
CG A:GLU227 4.2 18.8 0.5
CG A:HIS228 4.2 16.2 0.5
O B:HOH413 4.3 18.5 1.0
CG B:GLU152 4.3 18.1 1.0
ND1 A:HIS228 4.3 18.3 0.5
NE2 B:HIS122 4.4 17.6 1.0
O1 B:FMT304 4.5 43.2 1.0
OD2 A:ASP225 4.5 22.2 1.0
O B:HOH416 4.6 18.6 1.0
CG A:GLU227 4.6 23.5 0.5
CB A:GLU227 4.6 18.2 0.5
CB A:GLU227 4.7 19.6 0.5
OD1 A:ASP225 4.8 17.6 1.0

Manganese binding site 4 out of 5 in 4h0d

Go back to Manganese Binding Sites List in 4h0d
Manganese binding site 4 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:15.3
occ:1.00
 O B:HOH402 2.1 15.2 1.0
ND1 B:HIS122 2.1 13.2 1.0
NE2 B:HIS189 2.2 13.2 1.0
OXT B:ZZ7301 2.2 15.7 1.0
NE2 B:HIS120 2.2 13.4 1.0
CE1 B:HIS122 3.1 15.6 1.0
CG B:HIS122 3.1 11.8 1.0
CE1 B:HIS189 3.1 15.1 1.0
CD2 B:HIS189 3.1 13.3 1.0
CE1 B:HIS120 3.2 14.6 1.0
C15 B:ZZ7301 3.2 16.5 1.0
CD2 B:HIS120 3.3 13.2 1.0
CB B:HIS122 3.4 12.7 1.0
C14 B:ZZ7301 3.8 15.9 1.0
N3 B:ZZ7301 3.9 15.4 1.0
O4 B:ZZ7301 4.1 19.8 1.0
NE2 B:HIS122 4.2 17.6 1.0
CG2 B:THR190 4.2 14.5 1.0
ND1 B:HIS189 4.3 13.4 1.0
CD2 B:HIS122 4.3 15.7 1.0
CG B:HIS189 4.3 12.7 1.0
OD1 B:ASP124 4.3 14.7 1.0
ND1 B:HIS120 4.3 14.5 1.0
CG B:HIS120 4.4 13.5 1.0
MN B:MN303 4.5 15.0 1.0
C13 B:ZZ7301 4.5 15.4 1.0
O B:HOH426 4.5 20.8 1.0
SG B:CYS208 4.5 14.7 1.0
CB B:CYS208 4.6 14.5 1.0
C12 B:ZZ7301 4.8 16.1 1.0
CA B:HIS122 4.9 12.0 1.0
O1 B:ZZ7301 4.9 15.3 1.0

Manganese binding site 5 out of 5 in 4h0d

Go back to Manganese Binding Sites List in 4h0d
Manganese binding site 5 out of 5 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:15.0
occ:1.00
 OD2 B:ASP124 2.1 14.1 1.0
NE2 B:HIS250 2.2 14.5 1.0
O1 B:ZZ7301 2.2 15.3 1.0
N3 B:ZZ7301 2.4 15.4 1.0
SG B:CYS208 2.5 14.7 1.0
O B:HOH402 2.8 15.2 1.0
C2 B:ZZ7301 3.0 16.1 1.0
CD2 B:HIS250 3.1 16.4 1.0
C12 B:ZZ7301 3.2 16.1 1.0
CE1 B:HIS250 3.2 14.8 1.0
CG B:ASP124 3.2 14.9 1.0
C13 B:ZZ7301 3.4 15.4 1.0
CB B:CYS208 3.6 14.5 1.0
OD1 B:ASP124 3.7 14.7 1.0
C16 B:ZZ7301 3.7 15.1 1.0
C6 B:ZZ7301 4.0 15.0 1.0
O2 B:ZZ7301 4.2 16.5 1.0
ND1 B:HIS250 4.3 14.7 1.0
CB B:SER249 4.3 14.6 1.0
CG B:HIS250 4.3 15.7 1.0
OXT B:ZZ7301 4.4 15.7 1.0
C14 B:ZZ7301 4.4 15.9 1.0
MN B:MN302 4.5 15.3 1.0
CB B:ASP124 4.5 13.7 1.0
S1 B:ZZ7301 4.6 19.1 1.0
CA B:CYS208 4.6 14.1 1.0
OG B:SER249 4.7 15.0 1.0
NE2 B:HIS189 4.8 13.2 1.0
C15 B:ZZ7301 4.8 16.5 1.0
CE1 B:HIS189 4.9 15.1 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, T.A.Binkowski, J.Mire, J.Sacchettini, A.Joachimiak. New Delhi Metallo-Beta-Lactamase-1 Complexed with Mn From Klebsiella Pneumoniae To Be Published.
Page generated: Sat Oct 5 19:40:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy