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Zinc in PDB 6u0y: Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia, PDB code: 6u0y was solved by Y.Kim, N.Maltseva, M.Endres, A.Joachimiak, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.63 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.033, 97.229, 91.725, 90.00, 105.55, 90.00
R / Rfree (%) 16.8 / 19.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (pdb code 6u0y). 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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia, PDB code: 6u0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6u0y

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Zinc binding site 1 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:27.9
occ:0.86
 NE2 A:HIS181 2.1 23.3 1.0
ND1 A:HIS107 2.2 22.1 1.0
O1 A:EDO305 2.2 31.9 1.0
NE2 A:HIS105 2.2 30.6 1.0
O2 A:EDO305 2.4 29.2 1.0
CE1 A:HIS107 3.1 24.9 1.0
CE1 A:HIS181 3.1 26.7 1.0
CE1 A:HIS105 3.1 26.7 1.0
CD2 A:HIS181 3.1 19.6 1.0
C2 A:EDO305 3.2 30.9 1.0
CG A:HIS107 3.2 21.9 1.0
CD2 A:HIS105 3.2 22.4 1.0
C1 A:EDO305 3.2 32.4 1.0
ZN A:ZN302 3.5 41.4 0.6
CB A:HIS107 3.6 23.3 1.0
NE2 A:HIS107 4.2 22.0 1.0
ND1 A:HIS181 4.2 22.5 1.0
ND1 A:HIS105 4.2 27.2 1.0
OD1 A:ASP109 4.3 28.1 1.0
CG A:HIS181 4.3 20.5 1.0
CG A:HIS105 4.3 25.2 1.0
CD2 A:HIS107 4.3 22.5 1.0
CD2 A:HIS110 4.4 26.0 1.0
NE2 A:HIS110 4.6 29.2 1.0

Zinc binding site 2 out of 8 in 6u0y

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Zinc binding site 2 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:41.4
occ:0.57
 NE2 A:HIS110 2.1 29.2 1.0
NE2 A:HIS246 2.5 38.6 1.0
O1 A:EDO305 2.9 31.9 1.0
CD2 A:HIS110 2.9 26.0 1.0
OD2 A:ASP109 3.0 38.4 1.0
CE1 A:HIS110 3.3 30.4 1.0
OD1 A:ASP109 3.3 28.1 1.0
CG A:ASP109 3.4 36.1 1.0
CD2 A:HIS246 3.4 37.2 1.0
ZN A:ZN301 3.5 27.9 0.9
CE1 A:HIS246 3.5 34.3 1.0
C1 A:EDO305 3.9 32.4 1.0
CE1 A:HIS105 4.0 26.7 1.0
NE2 A:HIS105 4.1 30.6 1.0
CG A:HIS110 4.2 27.6 1.0
ND1 A:HIS110 4.3 24.7 1.0
O2 A:EDO305 4.3 29.2 1.0
ND1 A:HIS246 4.6 36.2 1.0
CG A:HIS246 4.6 31.4 1.0
CB A:ASP109 4.6 24.0 1.0
OG A:SER206 4.6 22.4 0.3
NE2 A:HIS181 4.7 23.3 1.0
C2 A:EDO305 4.8 30.9 1.0

Zinc binding site 3 out of 8 in 6u0y

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Zinc binding site 3 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:30.3
occ:0.78
 O B:HOH402 2.1 37.9 1.0
NE2 B:HIS181 2.1 25.0 1.0
ND1 B:HIS107 2.2 30.4 1.0
NE2 B:HIS105 2.2 30.9 1.0
O2 B:EDO302 2.5 48.7 1.0
O B:HOH468 2.8 34.2 1.0
CD2 B:HIS181 3.1 25.3 1.0
CE1 B:HIS181 3.1 29.0 1.0
CE1 B:HIS107 3.1 28.2 1.0
CE1 B:HIS105 3.1 27.8 1.0
CD2 B:HIS105 3.2 24.8 1.0
CG B:HIS107 3.2 22.0 1.0
ZN B:ZN301 3.4 34.6 0.7
CB B:HIS107 3.5 20.6 1.0
C2 B:EDO302 3.7 60.2 1.0
O1 B:EDO302 3.8 59.7 1.0
ND1 B:HIS105 4.2 31.3 1.0
ND1 B:HIS181 4.2 25.3 1.0
CG B:HIS181 4.2 24.2 1.0
NE2 B:HIS107 4.2 27.6 1.0
CG B:HIS105 4.3 22.9 1.0
OD1 B:ASP109 4.3 30.9 1.0
CD2 B:HIS110 4.3 25.4 1.0
CD2 B:HIS107 4.3 24.4 1.0
C1 B:EDO302 4.3 65.4 1.0
NE2 B:HIS110 4.5 28.7 1.0
OD2 B:ASP109 4.8 37.7 1.0
O B:HOH485 5.0 37.2 1.0
CG B:ASP109 5.0 34.6 1.0

Zinc binding site 4 out of 8 in 6u0y

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Zinc binding site 4 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:34.6
occ:0.74
 O B:HOH468 2.2 34.2 1.0
NE2 B:HIS246 2.2 30.8 1.0
NE2 B:HIS110 2.2 28.7 1.0
OD2 B:ASP109 2.3 37.7 1.0
O B:HOH402 2.3 37.9 1.0
O1 B:EDO302 2.4 59.7 1.0
CD2 B:HIS110 3.0 25.4 1.0
CG B:ASP109 3.1 34.6 1.0
CE1 B:HIS246 3.1 24.9 1.0
CD2 B:HIS246 3.2 29.1 1.0
CE1 B:HIS110 3.3 27.9 1.0
OD1 B:ASP109 3.3 30.9 1.0
ZN B:ZN300 3.4 30.3 0.8
C1 B:EDO302 3.8 65.4 1.0
O2 B:EDO302 4.0 48.7 1.0
NE2 B:HIS105 4.1 30.9 1.0
CE1 B:HIS105 4.2 27.8 1.0
O B:HOH485 4.2 37.2 1.0
CG B:HIS110 4.2 24.4 1.0
C2 B:EDO302 4.2 60.2 1.0
ND1 B:HIS246 4.3 26.8 1.0
ND1 B:HIS110 4.3 24.4 1.0
CG B:HIS246 4.3 26.4 1.0
CB B:ASP109 4.4 24.6 1.0
OG B:SER206 4.6 38.9 1.0
NE2 B:HIS181 4.7 25.0 1.0

Zinc binding site 5 out of 8 in 6u0y

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Zinc binding site 5 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:34.9
occ:0.75
 O C:HOH406 2.0 38.4 1.0
ND1 C:HIS107 2.1 33.5 1.0
NE2 C:HIS181 2.1 32.9 1.0
NE2 C:HIS105 2.3 36.4 1.0
O C:HOH568 2.6 45.5 1.0
CE1 C:HIS107 3.0 31.7 1.0
O C:HOH560 3.0 41.6 1.0
CD2 C:HIS181 3.1 29.3 1.0
CE1 C:HIS181 3.1 31.8 1.0
CG C:HIS107 3.1 27.4 1.0
CE1 C:HIS105 3.2 37.6 1.0
CD2 C:HIS105 3.2 34.2 1.0
ZN C:ZN302 3.5 44.8 0.6
CB C:HIS107 3.5 25.4 1.0
O C:HOH562 4.0 50.6 1.0
NE2 C:HIS107 4.1 28.5 1.0
OD1 C:ASP109 4.1 37.4 1.0
ND1 C:HIS181 4.2 28.2 1.0
CD2 C:HIS107 4.2 31.6 1.0
CG C:HIS181 4.2 27.4 1.0
ND1 C:HIS105 4.3 38.4 1.0
CG C:HIS105 4.3 32.9 1.0
CD2 C:HIS110 4.3 34.4 1.0
NE2 C:HIS110 4.5 32.6 1.0
O C:HOH468 4.7 44.4 1.0
OD2 C:ASP109 4.8 40.4 1.0
CG C:ASP109 5.0 33.6 1.0
CA C:HIS107 5.0 25.6 1.0

Zinc binding site 6 out of 8 in 6u0y

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Zinc binding site 6 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:44.8
occ:0.58
 O C:HOH560 2.0 41.6 1.0
O C:HOH562 2.2 50.6 1.0
NE2 C:HIS110 2.2 32.6 1.0
OD2 C:ASP109 2.3 40.4 1.0
NE2 C:HIS246 2.4 40.3 1.0
O C:HOH406 2.6 38.4 1.0
CG C:ASP109 3.1 33.6 1.0
CD2 C:HIS110 3.1 34.4 1.0
CE1 C:HIS110 3.2 37.8 1.0
OD1 C:ASP109 3.3 37.4 1.0
CE1 C:HIS246 3.4 36.4 1.0
CD2 C:HIS246 3.4 38.9 1.0
ZN C:ZN301 3.5 34.9 0.8
O C:HOH468 3.9 44.4 1.0
O C:HOH568 4.0 45.5 1.0
NE2 C:HIS105 4.2 36.4 1.0
CE1 C:HIS105 4.2 37.6 1.0
CG C:HIS110 4.3 31.6 1.0
ND1 C:HIS110 4.3 31.6 1.0
CB C:ASP109 4.5 31.0 1.0
ND1 C:HIS246 4.5 39.0 1.0
CG C:HIS246 4.5 37.8 1.0
NE2 C:HIS181 4.6 32.9 1.0

Zinc binding site 7 out of 8 in 6u0y

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Zinc binding site 7 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:36.8
occ:0.72
 O2 D:EDO302 1.9 38.8 1.0
ND1 D:HIS107 2.1 35.7 1.0
NE2 D:HIS181 2.2 37.2 1.0
NE2 D:HIS105 2.3 38.8 1.0
O1 D:EDO302 2.4 48.0 1.0
C2 D:EDO302 3.0 49.3 1.0
CE1 D:HIS107 3.1 35.5 1.0
CG D:HIS107 3.1 30.8 1.0
CD2 D:HIS181 3.2 31.9 1.0
CE1 D:HIS105 3.2 40.9 1.0
CD2 D:HIS105 3.2 36.5 1.0
CE1 D:HIS181 3.3 35.8 1.0
C1 D:EDO302 3.3 46.4 1.0
ZN D:ZN301 3.4 71.6 0.7
CB D:HIS107 3.4 31.9 1.0
OD1 D:ASP109 4.2 35.3 1.0
NE2 D:HIS107 4.2 31.9 1.0
CD2 D:HIS107 4.2 32.6 1.0
ND1 D:HIS105 4.3 39.0 1.0
CD2 D:HIS110 4.3 41.3 1.0
CG D:HIS181 4.3 33.8 1.0
CG D:HIS105 4.3 33.0 1.0
ND1 D:HIS181 4.3 32.5 1.0
NE2 D:HIS110 4.5 45.2 1.0
OD2 D:ASP109 4.9 45.6 1.0
CA D:HIS107 4.9 29.2 1.0
CG D:ASP109 5.0 37.9 1.0

Zinc binding site 8 out of 8 in 6u0y

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Zinc binding site 8 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia


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 Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:71.6
occ:0.68
 NE2 D:HIS110 2.3 45.2 1.0
NE2 D:HIS246 2.3 41.5 1.0
OD2 D:ASP109 2.3 45.6 1.0
O2 D:EDO302 2.6 38.8 1.0
CD2 D:HIS110 3.1 41.3 1.0
CG D:ASP109 3.1 37.9 1.0
OD1 D:ASP109 3.1 35.3 1.0
CD2 D:HIS246 3.3 41.3 1.0
CE1 D:HIS246 3.3 42.5 1.0
CE1 D:HIS110 3.3 43.5 1.0
ZN D:ZN300 3.4 36.8 0.7
C2 D:EDO302 3.5 49.3 1.0
C1 D:EDO302 4.1 46.4 1.0
NE2 D:HIS105 4.2 38.8 1.0
O1 D:EDO302 4.2 48.0 1.0
CE1 D:HIS105 4.3 40.9 1.0
CG D:HIS110 4.3 39.5 1.0
ND1 D:HIS110 4.3 41.3 1.0
ND1 D:HIS246 4.4 45.2 1.0
CG D:HIS246 4.4 39.0 1.0
CB D:ASP109 4.5 32.3 1.0
NE2 D:HIS181 4.7 37.2 1.0

Reference:

Y.Kim, N.Maltseva, M.Endres, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia To Be Published.
Page generated: Tue Oct 29 08:21:08 2024

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