Atomistry » Zinc » PDB 6mby-6mn4 » 6mgx
Atomistry »
  Zinc »
    PDB 6mby-6mn4 »
      6mgx »

Zinc in PDB 6mgx: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae, PDB code: 6mgx was solved by Y.Kim, C.Tesar, R.Jedrzejczak, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.03 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.715, 73.901, 78.068, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae (pdb code 6mgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae, PDB code: 6mgx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 1 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


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 the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:29.2
occ:1.00
ND1 A:HIS122 2.0 49.6 1.0
NE2 A:HIS189 2.1 49.0 1.0
NE2 A:HIS120 2.1 50.7 1.0
CD2 A:HIS189 2.8 46.3 1.0
CE1 A:HIS122 2.9 48.2 1.0
CE1 A:HIS120 3.0 48.3 1.0
CD2 A:HIS120 3.1 48.6 1.0
CG A:HIS122 3.1 47.2 1.0
O1 A:SO4304 3.2 48.5 1.0
O3 A:SO4304 3.2 40.1 1.0
CE1 A:HIS189 3.3 47.7 1.0
CB A:HIS122 3.6 44.6 1.0
S A:SO4304 3.7 48.6 1.0
ZN A:ZN302 3.9 28.9 1.0
SG A:CYS208 3.9 54.2 1.0
CG A:HIS189 4.0 45.6 1.0
NE2 A:HIS122 4.1 48.6 1.0
ND1 A:HIS120 4.1 47.8 1.0
CG A:HIS120 4.2 47.8 1.0
CD2 A:HIS122 4.2 48.3 1.0
ND1 A:HIS189 4.2 47.2 1.0
O2 A:SO4304 4.3 49.2 1.0
CB A:CYS208 4.3 54.3 1.0
CG2 A:THR190 4.4 34.6 1.0
OD2 A:ASP124 4.5 50.7 1.0
O A:HOH411 4.7 19.4 1.0

Zinc binding site 2 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 2 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


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 the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:28.9
occ:1.00
O3 A:SO4304 1.9 40.1 1.0
NE2 A:HIS250 2.2 54.3 1.0
SG A:CYS208 2.6 54.2 1.0
OD1 A:ASP124 2.8 50.5 1.0
CE1 A:HIS250 3.0 54.5 1.0
O A:HOH411 3.2 19.4 1.0
S A:SO4304 3.2 48.6 1.0
CD2 A:HIS250 3.3 54.0 1.0
CG A:ASP124 3.5 50.3 1.0
OD2 A:ASP124 3.6 50.7 1.0
O4 A:SO4304 3.6 48.4 1.0
CB A:CYS208 3.7 54.3 1.0
ZN A:ZN301 3.9 29.2 1.0
O1 A:SO4304 3.9 48.5 1.0
ND1 A:HIS250 4.1 54.5 1.0
O2 A:SO4304 4.2 49.2 1.0
CG A:HIS250 4.3 53.8 1.0
CB A:SER249 4.4 35.4 1.0
NE2 A:HIS189 4.5 49.0 1.0
OG A:SER249 4.8 35.6 1.0
CE1 A:HIS189 4.8 47.7 1.0
CA A:CYS208 4.8 53.5 1.0
CE1 A:HIS120 4.9 48.3 1.0
CB A:ASP124 4.9 50.0 1.0
NE2 A:HIS120 4.9 50.7 1.0

Zinc binding site 3 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 3 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


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 the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:25.8
occ:1.00
OE1 A:GLU152 1.9 54.5 1.0
OD2 A:ASP223 2.0 53.2 1.0
OE2 B:GLU227 2.0 58.4 1.0
O A:HOH407 2.3 33.2 1.0
CD B:GLU227 2.7 56.3 1.0
CD A:GLU152 2.7 53.6 1.0
OE1 B:GLU227 2.7 58.2 1.0
CG A:ASP223 2.8 52.2 1.0
OE2 A:GLU152 2.8 53.6 1.0
OD1 A:ASP223 2.9 54.1 1.0
CE1 B:HIS228 4.0 45.0 1.0
NE2 B:HIS228 4.1 45.4 1.0
CG B:GLU227 4.1 52.7 1.0
O A:HOH417 4.1 44.9 1.0
CG A:GLU152 4.1 51.7 1.0
CB A:ASP223 4.2 49.6 1.0
NE2 A:HIS122 4.7 48.6 1.0
CB B:GLU227 4.9 50.7 1.0

Zinc binding site 4 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 4 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


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 the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:29.1
occ:1.00
ND1 B:HIS122 2.1 49.0 1.0
NE2 B:HIS189 2.1 48.7 1.0
NE2 B:HIS120 2.2 35.1 1.0
CD2 B:HIS189 2.9 48.3 1.0
O3 B:SO4304 2.9 46.6 1.0
CD2 B:HIS120 3.1 35.2 1.0
CE1 B:HIS122 3.1 49.3 1.0
CG B:HIS122 3.1 48.3 1.0
CE1 B:HIS120 3.2 34.5 1.0
CE1 B:HIS189 3.3 49.5 1.0
CB B:HIS122 3.4 45.2 1.0
O2 B:SO4304 3.5 38.5 1.0
S B:SO4304 3.8 46.8 1.0
ZN B:ZN302 3.8 27.1 1.0
SG B:CYS208 3.9 39.8 1.0
CG B:HIS189 4.1 47.9 1.0
CB B:CYS208 4.2 39.1 1.0
CG B:HIS120 4.2 35.1 1.0
NE2 B:HIS122 4.2 49.5 1.0
ND1 B:HIS120 4.2 34.4 1.0
CD2 B:HIS122 4.2 49.1 1.0
ND1 B:HIS189 4.3 49.0 1.0
OD2 B:ASP124 4.4 44.8 1.0
CG2 B:THR190 4.5 41.4 1.0
O4 B:SO4304 4.6 47.6 1.0
O B:HOH415 4.8 50.5 1.0
CA B:HIS122 4.9 43.1 1.0
O1 B:SO4304 4.9 46.9 1.0

Zinc binding site 5 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 5 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:27.1
occ:1.00
O2 B:SO4304 1.8 38.5 1.0
NE2 B:HIS250 2.2 36.4 1.0
SG B:CYS208 2.5 39.8 1.0
OD1 B:ASP124 2.6 44.2 1.0
CE1 B:HIS250 3.0 36.6 1.0
S B:SO4304 3.0 46.8 1.0
CG B:ASP124 3.3 44.0 1.0
OD2 B:ASP124 3.3 44.8 1.0
CD2 B:HIS250 3.4 35.8 1.0
O B:HOH415 3.4 50.5 1.0
O1 B:SO4304 3.4 46.9 1.0
O B:HOH401 3.4 22.1 1.0
O3 B:SO4304 3.6 46.6 1.0
CB B:CYS208 3.7 39.1 1.0
ZN B:ZN301 3.8 29.1 1.0
O4 B:SO4304 4.1 47.6 1.0
ND1 B:HIS250 4.2 36.1 1.0
CG B:HIS250 4.4 35.7 1.0
CB B:SER249 4.5 35.0 1.0
NE2 B:HIS189 4.5 48.7 1.0
CB B:ASP124 4.6 42.5 1.0
NE2 B:HIS120 4.7 35.1 1.0
OG B:SER249 4.8 36.8 1.0
CE1 B:HIS120 4.8 34.5 1.0
CE B:LYS125 4.8 46.9 1.0
CE1 B:HIS189 4.8 49.5 1.0
CA B:CYS208 4.8 39.1 1.0

Zinc binding site 6 out of 6 in 6mgx

Go back to Zinc Binding Sites List in 6mgx
Zinc binding site 6 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:24.2
occ:1.00
OE2 B:GLU152 2.0 53.1 1.0
OD2 B:ASP223 2.1 51.2 1.0
O A:HOH421 2.2 16.9 1.0
OE1 A:GLU227 2.4 39.6 1.0
OE2 A:GLU227 2.5 38.9 1.0
CD B:GLU152 2.8 51.3 1.0
CD A:GLU227 2.8 38.4 1.0
CG B:ASP223 2.9 49.4 1.0
OE1 B:GLU152 3.0 51.2 1.0
OD1 B:ASP223 3.1 51.1 0.7
O B:HOH417 4.1 44.4 1.0
NE2 B:HIS122 4.2 49.5 1.0
NE2 A:HIS228 4.2 43.2 1.0
CG B:GLU152 4.3 49.4 1.0
CB B:ASP223 4.3 46.9 1.0
CG A:GLU227 4.3 36.8 1.0
CE1 A:HIS228 4.5 43.1 1.0
CD2 B:HIS122 4.8 49.1 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae To Be Published.
Page generated: Tue Oct 29 03:07:48 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