Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7mj2

Go back to Magnesium Binding Sites List in 7mj2
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg301

b:40.2
occ:1.00
O A:SER223 2.4 33.3 1.0
O B:HOH311 2.5 34.8 1.0
O A:VAL191 2.7 32.4 1.0
O A:GLY188 2.7 30.6 1.0
C A:SER223 3.5 35.7 1.0
C A:GLY188 3.8 28.7 1.0
CA A:GLY224 3.8 24.7 1.0
C A:VAL191 3.8 32.0 1.0
O A:LYS193 4.0 33.4 1.0
N A:GLY224 4.1 25.2 1.0
O A:GLY224 4.1 20.7 1.0
C A:GLY224 4.2 22.2 1.0
CA A:GLY188 4.2 26.6 1.0
CA A:ASP192 4.4 44.0 1.0
CG2 A:VAL191 4.4 27.1 1.0
CE1 B:TYR238 4.5 26.4 1.0
N A:ASP192 4.6 42.0 1.0
OH B:TYR238 4.7 28.8 1.0
OD1 A:ASP192 4.7 48.9 1.0
CA A:SER223 4.7 37.2 1.0
CE B:MET242 4.8 22.9 1.0
SD B:MET242 4.8 24.1 1.0
C A:ASP192 4.9 43.2 1.0
CA A:VAL191 4.9 30.4 1.0
N A:VAL191 4.9 30.3 1.0
N A:LYS193 4.9 36.5 1.0
N A:GLY189 4.9 23.9 1.0

Magnesium binding site 2 out of 3 in 7mj2

Go back to Magnesium Binding Sites List in 7mj2
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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:Mg301

b:30.0
occ:0.50
O C:HOH435 2.3 34.8 1.0
O C:HOH436 2.9 35.7 1.0
OD2 C:ASP192 2.9 48.9 1.0
OD1 C:ASP192 3.0 46.3 1.0
CG C:ASP192 3.1 46.8 1.0
O C:GLY189 3.8 37.2 1.0
CB C:ASP192 4.4 45.2 1.0
C C:LEU190 4.4 35.7 1.0
O C:LEU190 4.4 36.7 1.0
N C:VAL191 4.5 26.5 1.0
N C:ASP192 4.6 42.2 1.0
C C:VAL191 4.6 25.5 1.0
C C:GLY189 4.8 35.7 1.0
O C:VAL191 4.8 25.1 1.0
CA C:ASP192 4.8 42.8 1.0
CA C:LEU190 4.9 36.9 1.0

Magnesium binding site 3 out of 3 in 7mj2

Go back to Magnesium Binding Sites List in 7mj2
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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
D:Mg301

b:30.0
occ:0.50
O D:SER207 2.2 85.3 1.0
OG D:SER207 2.8 89.1 1.0
O D:GLY178 2.9 67.9 1.0
C D:SER207 2.9 90.2 1.0
CA D:SER207 2.9 92.2 1.0
N D:ALA213 3.3 48.1 1.0
CB D:THR212 3.3 55.4 1.0
CB D:SER207 3.4 93.7 1.0
CG2 D:THR212 3.8 54.6 1.0
N D:THR212 3.9 52.0 1.0
CA D:THR212 3.9 51.2 1.0
CA D:GLY210 4.0 74.7 1.0
C D:THR212 4.0 47.8 1.0
O D:GLY210 4.0 68.0 1.0
CB D:ALA213 4.0 46.5 1.0
C D:GLY210 4.0 71.5 1.0
N D:GLY210 4.0 80.0 1.0
C D:GLY178 4.2 66.8 1.0
CA D:ALA213 4.2 44.9 1.0
N D:PHE208 4.2 70.5 1.0
N D:SER207 4.3 97.7 1.0
O D:THR206 4.3 102.5 1.0
OG1 D:THR212 4.4 58.4 1.0
N D:MET211 4.7 84.2 1.0
C D:THR206 4.8 107.0 1.0
CA D:MET179 4.9 95.5 1.0
C D:PHE208 4.9 66.7 1.0
N D:MET179 5.0 90.9 1.0
C D:MET211 5.0 80.0 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 15:20:23 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy