Atomistry » Nickel » PDB 6vwz-6z8m » 6wgq
Atomistry »
  Nickel »
    PDB 6vwz-6z8m »
      6wgq »

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: Thu Oct 10 08:57:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy