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Nickel in PDB 6u2y: Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions, PDB code: 6u2y 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) 46.07 / 1.50
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.132, 104.132, 98.927, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 16.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions (pdb code 6u2y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions, PDB code: 6u2y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6u2y

Go back to Nickel Binding Sites List in 6u2y
Nickel binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:19.3
occ:0.99
 NE2 A:HIS246 2.1 18.3 1.0
O A:HOH445 2.1 38.9 1.0
NE2 A:HIS110 2.1 20.3 1.0
OD2 A:ASP109 2.1 19.3 1.0
O3 A:MX1300 2.3 23.7 1.0
N1 A:MX1300 2.5 25.7 1.0
CG A:ASP109 3.0 17.6 1.0
CE1 A:HIS246 3.0 18.4 1.0
CD2 A:HIS246 3.1 18.2 1.0
CE1 A:HIS110 3.1 18.3 1.0
CD2 A:HIS110 3.1 19.9 1.0
C7 A:MX1300 3.1 21.7 1.0
C4 A:MX1300 3.2 24.2 1.0
OD1 A:ASP109 3.2 18.0 1.0
C3 A:MX1300 3.4 29.0 1.0
NI A:NI302 3.6 18.3 1.0
O5 A:MX1300 4.0 30.3 1.0
ND1 A:HIS246 4.1 19.3 1.0
O32 A:MX1300 4.2 29.4 1.0
ND1 A:HIS110 4.2 16.9 1.0
CG A:HIS246 4.2 18.0 1.0
CG A:HIS110 4.2 17.6 1.0
C2 A:MX1300 4.3 28.9 1.0
NE2 A:HIS105 4.3 16.4 1.0
O4 A:MX1300 4.3 22.7 1.0
CE1 A:HIS105 4.3 18.5 1.0
CB A:ASP109 4.3 16.6 1.0
O2 A:MX1300 4.5 31.4 1.0
C5 A:MX1300 4.5 27.3 1.0
OG A:SER206 4.6 16.3 0.7
C1 A:MX1300 4.6 29.9 1.0
NE2 A:HIS181 4.8 16.3 1.0

Nickel binding site 2 out of 2 in 6u2y

Go back to Nickel Binding Sites List in 6u2y
Nickel binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase L1 From Stenotrophomonas Maltophilia in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:18.3
occ:1.00
 O A:HOH445 1.8 38.9 1.0
ND1 A:HIS107 2.0 16.6 1.0
NE2 A:HIS181 2.1 16.3 1.0
NE2 A:HIS105 2.1 16.4 1.0
O32 A:MX1300 2.6 29.4 1.0
CE1 A:HIS107 3.0 18.0 1.0
CD2 A:HIS181 3.0 17.5 1.0
CD2 A:HIS105 3.1 16.9 1.0
CG A:HIS107 3.1 15.6 1.0
CE1 A:HIS105 3.1 18.5 1.0
CE1 A:HIS181 3.1 18.0 1.0
CB A:HIS107 3.4 14.7 1.0
O3 A:MX1300 3.4 23.7 1.0
NI A:NI301 3.6 19.3 1.0
C1 A:MX1300 3.8 29.9 1.0
N1 A:MX1300 3.9 25.7 1.0
OD1 A:ASP109 4.1 18.0 1.0
NE2 A:HIS107 4.1 17.1 1.0
O5 A:MX1300 4.1 30.3 1.0
ND1 A:HIS105 4.1 17.9 1.0
CD2 A:HIS110 4.2 19.9 1.0
CD2 A:HIS107 4.2 19.6 1.0
CG A:HIS181 4.2 15.6 1.0
CG A:HIS105 4.2 17.3 1.0
ND1 A:HIS181 4.2 18.5 1.0
C7 A:MX1300 4.2 21.7 1.0
NE2 A:HIS110 4.3 20.3 1.0
C9 A:MX1300 4.4 30.4 1.0
C4 A:MX1300 4.5 24.2 1.0
C2 A:MX1300 4.5 28.9 1.0
O31 A:MX1300 4.7 26.4 0.6
C3 A:MX1300 4.8 29.0 1.0
CA A:HIS107 4.9 15.9 1.0
OD2 A:ASP109 4.9 19.3 1.0
CG A:ASP109 4.9 17.6 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 in the Complex with the Hydrolyzed Moxalactam and Two Ni Ions To Be Published.
Page generated: Thu Oct 10 08:54:39 2024

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