Zinc in PDB 6mgy: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae, PDB code: 6mgy was solved by Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.56 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.869, 69.619, 68.789, 92.26, 103.36, 88.52
R / Rfree (%) 15.4 / 18.9

Other elements in 6mgy:

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae (pdb code 6mgy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae, PDB code: 6mgy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6mgy

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Zinc binding site 1 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.9
occ:1.00
O A:HOH484 1.9 30.3 1.0
NE2 A:HIS120 2.0 24.9 1.0
ND1 A:HIS122 2.1 29.2 1.0
NE2 A:HIS189 2.1 23.0 1.0
CE1 A:HIS120 2.9 25.6 1.0
CD2 A:HIS189 2.9 22.5 1.0
CE1 A:HIS122 3.0 26.3 1.0
CD2 A:HIS120 3.1 22.9 1.0
CG A:HIS122 3.1 23.6 1.0
CE1 A:HIS189 3.2 25.9 1.0
ZN A:ZN302 3.5 42.5 1.0
CB A:HIS122 3.5 19.3 1.0
SG A:CYS208 3.7 31.5 1.0
CB A:CYS208 4.0 23.8 1.0
ND1 A:HIS120 4.0 24.6 1.0
OD1 A:ASP124 4.1 28.8 1.0
NE2 A:HIS122 4.1 28.8 1.0
CG A:HIS120 4.1 19.7 1.0
CG A:HIS189 4.2 20.7 1.0
CD2 A:HIS122 4.2 26.9 1.0
O A:HOH533 4.2 42.6 1.0
ND1 A:HIS189 4.3 23.4 1.0
CG2 A:THR190 4.5 21.9 1.0
OD2 A:ASP124 4.6 31.7 1.0
CG A:ASP124 4.8 29.6 1.0
CA A:HIS122 5.0 19.0 1.0

Zinc binding site 2 out of 8 in 6mgy

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Zinc binding site 2 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:42.5
occ:1.00
NE2 A:HIS250 2.2 43.0 1.0
SG A:CYS208 2.3 31.5 1.0
OD2 A:ASP124 2.3 31.7 1.0
O A:HOH484 2.5 30.3 1.0
O A:HOH533 2.7 42.6 1.0
CD2 A:HIS250 3.0 39.3 1.0
CE1 A:HIS250 3.2 42.3 1.0
CG A:ASP124 3.4 29.6 1.0
CB A:CYS208 3.4 23.8 1.0
ZN A:ZN301 3.5 26.9 1.0
OD1 A:ASP124 3.7 28.8 1.0
CB A:SER249 4.2 27.3 1.0
NE2 A:HIS189 4.2 23.0 1.0
CG A:HIS250 4.2 40.1 1.0
ND1 A:HIS250 4.3 40.0 1.0
CE1 A:HIS189 4.5 25.9 1.0
OG A:SER249 4.6 26.8 1.0
NE2 A:HIS120 4.6 24.9 1.0
CE1 A:HIS120 4.6 25.6 1.0
CA A:CYS208 4.6 20.9 1.0
CB A:ASP124 4.7 23.9 1.0

Zinc binding site 3 out of 8 in 6mgy

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Zinc binding site 3 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:25.2
occ:1.00
O B:HOH465 1.9 27.1 1.0
ND1 B:HIS122 2.0 24.7 1.0
NE2 B:HIS120 2.0 22.3 1.0
NE2 B:HIS189 2.1 19.7 1.0
CD2 B:HIS189 3.0 19.3 1.0
CD2 B:HIS120 3.0 20.9 1.0
CE1 B:HIS122 3.0 26.7 1.0
CG B:HIS122 3.0 22.0 1.0
CE1 B:HIS120 3.0 22.6 1.0
CE1 B:HIS189 3.1 22.1 1.0
CB B:HIS122 3.4 19.7 1.0
ZN B:ZN302 3.7 31.9 1.0
SG B:CYS208 3.9 25.0 1.0
CB B:CYS208 4.1 23.0 1.0
OD2 B:ASP124 4.1 28.0 1.0
O B:HOH527 4.1 38.4 1.0
ND1 B:HIS120 4.1 22.4 1.0
CG B:HIS120 4.1 17.6 1.0
NE2 B:HIS122 4.1 27.9 1.0
CG B:HIS189 4.1 15.7 1.0
CD2 B:HIS122 4.1 22.4 1.0
ND1 B:HIS189 4.2 19.2 1.0
CG2 B:THR190 4.5 19.1 1.0
OD1 B:ASP124 4.7 30.2 1.0
CG B:ASP124 4.8 26.6 1.0
CA B:HIS122 4.8 17.7 1.0

Zinc binding site 4 out of 8 in 6mgy

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Zinc binding site 4 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:31.9
occ:1.00
NE2 B:HIS250 2.1 38.1 1.0
OD1 B:ASP124 2.2 30.2 1.0
SG B:CYS208 2.3 25.0 1.0
O B:HOH465 2.4 27.1 1.0
O B:HOH527 2.4 38.4 1.0
CD2 B:HIS250 3.1 33.1 1.0
CE1 B:HIS250 3.2 36.8 1.0
CG B:ASP124 3.3 26.6 1.0
CB B:CYS208 3.4 23.0 1.0
OD2 B:ASP124 3.7 28.0 1.0
ZN B:ZN301 3.7 25.2 1.0
CG B:HIS250 4.2 34.8 1.0
CB B:SER249 4.2 26.2 1.0
ND1 B:HIS250 4.2 34.5 1.0
NE2 B:HIS189 4.4 19.7 1.0
CA B:CYS208 4.6 17.7 1.0
CB B:ASP124 4.6 21.9 1.0
OG B:SER249 4.6 23.7 1.0
CE1 B:HIS189 4.6 22.1 1.0
NE2 B:HIS120 4.7 22.3 1.0
CE1 B:HIS120 4.7 22.6 1.0
O B:HOH539 4.8 33.6 1.0

Zinc binding site 5 out of 8 in 6mgy

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Zinc binding site 5 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:24.4
occ:1.00
O C:HOH413 1.9 28.3 1.0
ND1 C:HIS122 2.0 23.0 1.0
NE2 C:HIS120 2.0 22.9 1.0
NE2 C:HIS189 2.1 22.1 1.0
CE1 C:HIS120 2.9 22.9 1.0
CE1 C:HIS122 2.9 23.1 1.0
CD2 C:HIS120 3.0 21.1 1.0
CG C:HIS122 3.0 21.3 1.0
CD2 C:HIS189 3.1 20.9 1.0
CE1 C:HIS189 3.2 25.3 1.0
CB C:HIS122 3.4 17.1 1.0
ZN C:ZN302 3.7 36.0 1.0
SG C:CYS208 3.8 30.1 1.0
ND1 C:HIS120 4.1 21.1 1.0
NE2 C:HIS122 4.1 25.7 1.0
CB C:CYS208 4.1 29.0 1.0
OD2 C:ASP124 4.1 30.3 1.0
CD2 C:HIS122 4.1 23.5 1.0
CG C:HIS120 4.1 17.6 1.0
O C:HOH549 4.2 40.8 1.0
CG C:HIS189 4.2 18.3 1.0
ND1 C:HIS189 4.3 20.8 1.0
CG2 C:THR190 4.5 19.8 1.0
OD1 C:ASP124 4.7 31.6 1.0
CG C:ASP124 4.8 31.5 1.0
CA C:HIS122 4.9 16.2 1.0

Zinc binding site 6 out of 8 in 6mgy

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Zinc binding site 6 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From 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 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:36.0
occ:1.00
NE2 C:HIS250 2.1 33.4 1.0
SG C:CYS208 2.3 30.1 1.0
OD1 C:ASP124 2.3 31.6 1.0
O C:HOH413 2.3 28.3 1.0
O C:HOH549 2.5 40.8 1.0
CD2 C:HIS250 2.9 30.7 1.0
CE1 C:HIS250 3.3 32.0 1.0
CG C:ASP124 3.4 31.5 1.0
CB C:CYS208 3.4 29.0 1.0
ZN C:ZN301 3.7 24.4 1.0
OD2 C:ASP124 3.7 30.3 1.0
CG C:HIS250 4.1 30.8 1.0
CB C:SER249 4.2 24.9 1.0
ND1 C:HIS250 4.3 29.9 1.0
NE2 C:HIS189 4.4 22.1 1.0
CE1 C:HIS189 4.6 25.3 1.0
CE1 C:HIS120 4.6 22.9 1.0
CA C:CYS208 4.6 21.3 1.0
CB C:ASP124 4.7 21.7 1.0
OG C:SER249 4.7 25.7 1.0
NE2 C:HIS120 4.7 22.9 1.0
O C:HOH428 4.9 43.6 1.0

Zinc binding site 7 out of 8 in 6mgy

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Zinc binding site 7 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:43.7
occ:1.00
NE2 D:HIS250 2.1 48.9 1.0
SG D:CYS208 2.2 30.9 1.0
OD2 D:ASP124 2.4 38.8 1.0
O D:HOH426 2.4 28.4 1.0
O D:HOH500 2.4 42.0 1.0
CD2 D:HIS250 3.0 47.1 1.0
CE1 D:HIS250 3.2 47.9 1.0
CG D:ASP124 3.4 36.9 1.0
CB D:CYS208 3.4 31.1 1.0
ZN D:ZN302 3.7 29.7 1.0
OD1 D:ASP124 3.8 36.3 1.0
O D:HOH498 4.1 46.1 1.0
CB D:SER249 4.1 29.2 1.0
CG D:HIS250 4.2 47.3 1.0
ND1 D:HIS250 4.2 46.7 1.0
NE2 D:HIS189 4.3 26.7 1.0
OG D:SER249 4.5 31.5 1.0
CA D:CYS208 4.6 26.6 1.0
CE1 D:HIS189 4.6 28.2 1.0
CE1 D:HIS120 4.6 31.0 1.0
CB D:ASP124 4.6 26.3 1.0
NE2 D:HIS120 4.6 30.3 1.0

Zinc binding site 8 out of 8 in 6mgy

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Zinc binding site 8 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:29.7
occ:1.00
O D:HOH426 2.0 28.4 1.0
NE2 D:HIS120 2.0 30.3 1.0
ND1 D:HIS122 2.0 31.8 1.0
NE2 D:HIS189 2.1 26.7 1.0
CE1 D:HIS122 3.0 32.2 1.0
CE1 D:HIS120 3.0 31.0 1.0
CD2 D:HIS120 3.0 28.1 1.0
CD2 D:HIS189 3.0 24.5 1.0
CG D:HIS122 3.1 28.1 1.0
CE1 D:HIS189 3.2 28.2 1.0
CB D:HIS122 3.5 24.1 1.0
ZN D:ZN301 3.7 43.7 1.0
SG D:CYS208 3.8 30.9 1.0
CB D:CYS208 4.1 31.1 1.0
OD1 D:ASP124 4.1 36.3 1.0
ND1 D:HIS120 4.1 28.6 1.0
NE2 D:HIS122 4.1 32.9 1.0
CG D:HIS120 4.1 23.8 1.0
O D:HOH500 4.1 42.0 1.0
CD2 D:HIS122 4.2 31.6 1.0
CG D:HIS189 4.2 22.5 1.0
ND1 D:HIS189 4.2 23.8 1.0
CG2 D:THR190 4.5 21.4 1.0
OD2 D:ASP124 4.6 38.8 1.0
O D:HOH498 4.6 46.1 1.0
CG D:ASP124 4.8 36.9 1.0
CA D:HIS122 4.9 23.3 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae To Be Published.
Page generated: Wed Dec 16 12:19:37 2020

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