Zinc in PDB 7mj2: Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn

Enzymatic activity of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn

All present enzymatic activity of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn:
2.5.1.143;

Protein crystallography data

The structure of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn, PDB code: 7mj2 was solved by S.Chatterjee, J.A.Rankin, S.Lagishetty, J.Hu, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.98 / 2.80
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.102, 120.102, 212.575, 90, 90, 90
R / Rfree (%) 21 / 24.4

Other elements in 7mj2:

The structure of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn (pdb code 7mj2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn, PDB code: 7mj2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7mj2

Go back to Zinc Binding Sites List in 7mj2
Zinc binding site 1 out of 2 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:58.0
occ:1.00
OE2 A:GLU180 2.0 52.2 1.0
OE1 A:GLU180 2.1 51.7 1.0
CD A:GLU180 2.3 53.0 1.0
O A:HOH438 2.4 40.2 1.0
O A:HOH422 2.7 34.8 1.0
CG A:GLU180 3.8 55.7 1.0
N A:VAL154 4.2 29.4 1.0
CG1 A:VAL154 4.3 29.1 1.0
N A:ALA182 4.4 26.1 1.0
CB A:VAL154 4.5 28.9 1.0
CB A:ALA124 4.5 20.9 1.0
O A:GLY178 4.6 28.4 1.0
N A:GLY181 4.6 31.5 1.0
CB A:ALA182 4.7 28.8 1.0
N A:LEU183 4.7 26.9 1.0
CB A:GLU180 4.8 54.4 1.0
CA A:GLY153 5.0 32.6 1.0
CA A:VAL154 5.0 30.0 1.0

Zinc binding site 2 out of 2 in 7mj2

Go back to Zinc Binding Sites List in 7mj2
Zinc binding site 2 out of 2 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:57.8
occ:1.00
OE2 C:GLU180 2.1 48.1 1.0
OE1 C:GLU180 2.2 51.6 1.0
O C:HOH434 2.2 30.3 1.0
CD C:GLU180 2.4 50.4 1.0
O C:HOH438 2.9 33.0 1.0
N C:ALA182 3.8 25.2 1.0
CG C:GLU180 3.9 52.2 1.0
CB C:ALA182 4.1 28.3 1.0
N C:GLY181 4.2 34.1 1.0
O C:GLY178 4.3 32.9 1.0
CA C:ALA182 4.5 25.6 1.0
N C:LEU183 4.5 25.8 1.0
CB C:VAL154 4.6 32.4 1.0
C C:GLY181 4.6 32.4 1.0
CA C:GLY181 4.7 31.8 1.0
CG1 C:VAL154 4.8 35.3 1.0
N C:VAL154 4.8 31.3 1.0
CB C:GLU180 4.8 50.9 1.0
N C:GLU180 4.9 48.7 1.0
C C:GLU180 4.9 45.3 1.0
CB C:ALA124 5.0 27.0 1.0
C C:ALA182 5.0 23.8 1.0

Reference:

J.A.Rankin, S.Chatterjee, Z.Tariq, S.Lagishetty, B.Desguin, J.Hu, R.P.Hausinger. The Larb Carboxylase/Hydrolase Forms A Transient Cysteinyl-Pyridine Intermediate During Nickel-Pincer Nucleotide Cofactor Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34548397
DOI: 10.1073/PNAS.2106202118
Page generated: Fri Nov 5 16:54:58 2021

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