Chlorine in PDB 8ezi: A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn

Enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn

All present enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn:
5.1.2.1;

Protein crystallography data

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn, PDB code: 8ezi was solved by S.Gatreddi, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.79 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.011, 79.092, 121.171, 90, 90, 90
R / Rfree (%) 18.3 / 22.1

Other elements in 8ezi:

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Magnesium (Mg) 2 atoms
Nickel (Ni) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn (pdb code 8ezi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn, PDB code: 8ezi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8ezi

Go back to Chlorine Binding Sites List in 8ezi
Chlorine binding site 1 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl512

b:24.8
occ:1.00
 O B:HOH770 2.8 15.2 1.0
O1 B:EDO502 3.3 26.3 1.0
N B:LEU395 3.3 17.4 1.0
O B:HOH769 3.7 31.3 1.0
C1 B:EDO502 3.8 12.5 1.0
CA B:THR394 3.9 18.9 1.0
CD1 B:ILE13 4.0 13.8 1.0
CB B:THR394 4.0 18.5 1.0
CB B:LEU395 4.0 26.3 1.0
C B:THR394 4.1 15.6 1.0
CB B:ILE13 4.1 19.0 1.0
C2 B:EDO502 4.2 24.2 1.0
CA B:LEU395 4.2 21.7 1.0
CG2 B:ILE13 4.3 21.3 1.0
CG B:LEU395 4.3 36.0 1.0
CD1 B:LEU395 4.5 27.1 1.0
O B:HOH651 4.5 23.1 1.0
CG1 B:ILE13 4.6 20.4 1.0
CG2 B:THR394 4.8 18.6 1.0
N B:ASP396 4.9 16.1 1.0

Chlorine binding site 2 out of 3 in 8ezi

Go back to Chlorine Binding Sites List in 8ezi
Chlorine binding site 2 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl513

b:55.5
occ:1.00
 O B:HOH700 3.6 22.8 1.0
NH2 B:ARG405 3.9 19.0 1.0
C B:HIS370 3.9 20.0 1.0
O B:HIS370 4.0 22.6 1.0
O B:LEU367 4.0 22.7 1.0
N B:HIS371 4.1 18.1 1.0
O B:VAL368 4.1 25.6 1.0
N B:HIS370 4.3 20.3 1.0
CA B:HIS371 4.5 18.1 1.0
CA B:HIS370 4.5 20.9 1.0
C B:HIS369 4.7 26.8 1.0
O B:HOH714 4.7 28.6 1.0
C B:VAL368 4.7 26.2 1.0
CB B:HIS371 4.8 14.0 1.0
CZ B:ARG405 5.0 23.7 1.0

Chlorine binding site 3 out of 3 in 8ezi

Go back to Chlorine Binding Sites List in 8ezi
Chlorine binding site 3 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl514

b:48.3
occ:1.00
 N B:LYS36 3.3 24.5 1.0
CG B:LYS36 3.5 30.9 1.0
O B:HOH635 3.5 23.9 1.0
CB B:LYS36 3.8 31.0 1.0
CD B:LYS36 3.8 32.3 1.0
O B:HIS34 3.8 20.0 1.0
OD1 B:ASN35 4.0 22.8 1.0
O B:HOH669 4.0 28.3 1.0
OH B:TYR33 4.0 25.6 1.0
CE B:LYS36 4.1 30.9 1.0
CA B:LYS36 4.1 28.1 1.0
CA B:ASN35 4.1 17.2 1.0
C B:ASN35 4.2 19.8 1.0
CE1 B:TYR33 4.4 19.8 1.0
CZ B:TYR33 4.6 26.0 1.0
C B:HIS34 4.8 18.5 1.0
CG B:ASN35 4.9 24.1 1.0
N B:ASN35 5.0 20.8 1.0

Reference:

S.Gatreddi, D.Sui, R.P.Hausinger, J.Hu. Irreversible Inactivation of Lactate Racemase By Sodium Borohydride Reveals Reactivity of the Nickel-Pincer Nucleotide Cofactor Acs Catalysis 1441 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C05461
Page generated: Tue Jul 30 09:06:08 2024

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