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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

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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

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