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Nickel in PDB 6wgq: The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T

Enzymatic activity of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T

All present enzymatic activity of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T:
3.5.2.6;

Protein crystallography data

The structure of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T, PDB code: 6wgq was solved by K.Tan, R.Wu, M.Endres, A.Joachimiak, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.419, 73.767, 109.512, 90.00, 92.40, 90.00
R / Rfree (%) 15.3 / 19.2

Other elements in 6wgq:

The structure of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T (pdb code 6wgq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T, PDB code: 6wgq:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 6wgq

Go back to Nickel Binding Sites List in 6wgq
Nickel binding site 1 out of 5 in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:18.4
occ:1.00
 O1 A:TRS409 1.9 19.6 1.0
O2 A:TRS410 2.0 15.4 1.0
O3 A:TRS408 2.0 18.0 1.0
O2 A:TRS409 2.1 19.6 1.0
O A:GLN377 2.1 16.9 1.0
N A:TRS408 2.1 17.9 1.0
C3 A:TRS408 2.9 16.4 1.0
NI A:NI405 2.9 18.3 1.0
C2 A:TRS409 2.9 18.4 1.0
C A:GLN377 3.0 17.7 1.0
C A:TRS408 3.0 18.2 1.0
NI A:NI402 3.0 20.1 1.0
NI A:NI403 3.1 19.6 1.0
C2 A:TRS410 3.1 14.8 1.0
OXT A:GLN377 3.1 17.5 1.0
C1 A:TRS409 3.1 19.4 1.0
C A:TRS409 3.4 23.7 1.0
O2 A:TRS407 3.5 17.6 1.0
O2 A:TRS408 3.6 22.4 1.0
N A:TRS409 3.8 20.9 1.0
O A:HOH618 3.8 22.8 1.0
C2 A:TRS408 3.8 16.9 1.0
O A:HOH573 4.2 25.7 1.0
C1 A:TRS408 4.2 23.3 1.0
O A:HOH739 4.3 26.6 1.0
O1 A:TRS408 4.3 25.4 1.0
C A:TRS410 4.4 16.6 1.0
CA A:GLN377 4.4 15.2 1.0
N A:TRS410 4.4 18.9 1.0
NZ A:LYS348 4.6 21.9 1.0
O3 A:TRS410 4.7 19.2 1.0
O1 A:TRS407 4.7 21.7 1.0
N A:GLN377 4.8 15.2 1.0
C3 A:TRS409 4.9 29.2 1.0
C2 A:TRS407 4.9 18.5 1.0
O A:LEU376 5.0 18.6 1.0

Nickel binding site 2 out of 5 in 6wgq

Go back to Nickel Binding Sites List in 6wgq
Nickel binding site 2 out of 5 in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:20.1
occ:1.00
 O2 A:TRS408 2.0 22.4 1.0
O2 A:TRS409 2.0 19.6 1.0
O2 A:TRS407 2.0 17.6 1.0
O1 A:TRS407 2.1 21.7 1.0
O3 A:TRS408 2.1 18.0 1.0
N A:TRS407 2.2 23.1 1.0
C A:TRS407 2.8 18.4 1.0
C2 A:TRS407 2.9 18.5 1.0
C3 A:TRS408 2.9 16.4 1.0
C1 A:TRS407 3.0 20.0 1.0
NI A:NI403 3.0 19.6 1.0
NI A:NI401 3.0 18.4 1.0
C2 A:TRS408 3.1 16.9 1.0
NI A:NI405 3.1 18.3 1.0
C2 A:TRS409 3.2 18.4 1.0
C A:TRS408 3.4 18.2 1.0
O2 A:TRS410 3.5 15.4 1.0
N A:TRS408 3.7 17.9 1.0
NZ A:LYS348 3.8 21.9 1.0
C3 A:TRS407 4.2 20.6 1.0
C A:TRS409 4.5 23.7 1.0
O1 A:TRS409 4.5 19.6 1.0
O A:HOH593 4.6 31.6 1.0
OXT A:GLN377 4.6 17.5 1.0
O3 A:TRS407 4.6 25.0 1.0
N A:TRS409 4.6 20.9 1.0
O3 A:TRS410 4.7 19.2 1.0
O A:GLN377 4.7 16.9 1.0
C1 A:TRS408 4.8 23.3 1.0
C2 A:TRS410 4.8 14.8 1.0
N A:TRS410 5.0 18.9 1.0

Nickel binding site 3 out of 5 in 6wgq

Go back to Nickel Binding Sites List in 6wgq
Nickel binding site 3 out of 5 in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:19.6
occ:1.00
 O2 A:TRS407 2.0 17.6 1.0
O2 A:TRS409 2.0 19.6 1.0
O2 A:TRS410 2.0 15.4 1.0
O3 A:TRS410 2.1 19.2 1.0
N A:TRS409 2.2 20.9 1.0
C2 A:TRS410 2.8 14.8 1.0
C2 A:TRS409 2.8 18.4 1.0
C A:TRS409 3.0 23.7 1.0
NI A:NI402 3.0 20.1 1.0
NI A:NI405 3.1 18.3 1.0
NI A:NI401 3.1 18.4 1.0
C2 A:TRS407 3.1 18.5 1.0
C3 A:TRS410 3.1 22.7 1.0
C A:TRS410 3.3 16.6 1.0
N A:TRS410 3.6 18.9 1.0
O3 A:TRS408 3.6 18.0 1.0
O1 A:TRS409 3.6 19.6 1.0
N A:TRS407 3.7 23.1 1.0
C1 A:TRS409 3.9 19.4 1.0
C A:TRS407 4.0 18.4 1.0
C3 A:TRS409 4.3 29.2 1.0
O3 A:TRS409 4.3 28.1 1.0
O2 A:TRS408 4.6 22.4 1.0
OXT A:GLN377 4.6 17.5 1.0
O A:GLN377 4.7 16.9 1.0
O1 A:TRS407 4.7 21.7 1.0
NZ A:LYS348 4.7 21.9 1.0
O3 A:TRS407 4.8 25.0 1.0
C1 A:TRS410 4.8 18.8 1.0
N A:TRS408 4.9 17.9 1.0
C3 A:TRS408 5.0 16.4 1.0

Nickel binding site 4 out of 5 in 6wgq

Go back to Nickel Binding Sites List in 6wgq
Nickel binding site 4 out of 5 in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:16.9
occ:1.00
 N A:TRS406 2.0 15.4 1.0
NE2 B:HIS202 2.0 18.2 1.0
NE2 A:HIS202 2.1 14.6 1.0
O1 A:TRS406 2.2 19.5 1.0
O3 A:TRS420 2.2 19.1 1.0
N A:TRS420 2.2 18.1 1.0
C1 A:TRS406 2.9 16.4 1.0
C A:TRS406 2.9 22.1 1.0
C3 A:TRS420 3.0 18.2 1.0
CD2 B:HIS202 3.0 15.8 1.0
CD2 A:HIS202 3.0 13.9 1.0
CE1 B:HIS202 3.0 15.6 1.0
CE1 A:HIS202 3.1 15.8 1.0
C A:TRS420 3.1 21.2 1.0
C2 A:TRS406 3.7 23.5 1.0
C2 A:TRS420 3.9 27.8 1.0
ND1 B:HIS202 4.1 14.7 1.0
ND1 A:HIS202 4.2 14.7 1.0
CG B:HIS202 4.2 18.5 1.0
CG A:HIS202 4.2 13.5 1.0
C3 A:TRS406 4.2 28.9 1.0
O3 A:TRS406 4.2 29.7 1.0
O2 A:TRS406 4.3 29.7 1.0
C1 A:TRS420 4.4 28.8 1.0
O2 A:TRS420 4.5 34.4 1.0
O1 A:TRS420 4.5 28.6 1.0
OE1 A:GLU211 4.5 26.4 1.0
OE1 B:GLU211 4.6 30.4 1.0
OE1 B:GLN73 4.8 26.4 1.0
OE2 B:GLU211 4.8 33.0 1.0
OE2 A:GLU211 4.8 32.4 1.0
OE1 A:GLN73 4.8 25.1 1.0

Nickel binding site 5 out of 5 in 6wgq

Go back to Nickel Binding Sites List in 6wgq
Nickel binding site 5 out of 5 in the The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:18.3
occ:1.00
 O2 A:TRS410 1.9 15.4 1.0
OXT A:GLN377 2.0 17.5 1.0
NZ A:LYS348 2.1 21.9 1.0
O3 A:TRS408 2.1 18.0 1.0
N A:TRS410 2.2 18.9 1.0
O2 A:TRS407 2.2 17.6 1.0
C2 A:TRS410 2.9 14.8 1.0
NI A:NI401 2.9 18.4 1.0
C A:GLN377 3.0 17.7 1.0
C A:TRS410 3.0 16.6 1.0
NI A:NI403 3.1 19.6 1.0
CE A:LYS348 3.1 21.3 1.0
NI A:NI402 3.1 20.1 1.0
C2 A:TRS407 3.2 18.5 1.0
O A:GLN377 3.3 16.9 1.0
C3 A:TRS408 3.3 16.4 1.0
CD A:LYS348 3.5 18.5 1.0
O2 A:TRS409 3.5 19.6 1.0
O3 A:TRS410 3.6 19.2 1.0
O1 A:TRS407 3.7 21.7 1.0
C3 A:TRS410 3.9 22.7 1.0
C A:TRS407 4.2 18.4 1.0
C1 A:TRS410 4.3 18.8 1.0
O1 A:TRS410 4.3 20.1 1.0
CA A:GLN377 4.3 15.2 1.0
C1 A:TRS407 4.4 20.0 1.0
N A:TRS408 4.5 17.9 1.0
C A:TRS408 4.5 18.2 1.0
O1 A:TRS409 4.5 19.6 1.0
N A:TRS407 4.6 23.1 1.0
O2 A:TRS408 4.7 22.4 1.0
C2 A:TRS409 4.8 18.4 1.0
CG A:LYS348 4.9 19.2 1.0
N A:TRS409 5.0 20.9 1.0

Reference:

K.Tan, R.Wu, M.Endres, A.Joachimiak. The Crystal Structure of A Beta-Lactamase From Shigella Flexneri 2A Str. 2457T To Be Published.
Page generated: Wed Dec 16 01:57:07 2020

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