Magnesium in PDB 7mj1: Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad

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

All present enzymatic activity of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad:
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 Nad, PDB code: 7mj1 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) 41.76 / 3.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.445, 120.445, 213.589, 90, 90, 90
R / Rfree (%) 24.3 / 26.9

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 Nad (pdb code 7mj1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad, PDB code: 7mj1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mj1

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Magnesium binding site 1 out of 4 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad


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 Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:67.4
occ:1.00
 O A:SER223 2.5 78.4 1.0
O A:GLY188 2.9 62.2 1.0
O A:VAL191 3.1 74.3 1.0
OD1 A:ASP192 3.4 100.5 1.0
C A:SER223 3.5 80.0 1.0
OH B:TYR238 3.9 78.7 1.0
CA A:ASP192 4.0 92.6 1.0
C A:GLY188 4.0 63.9 1.0
CE1 B:TYR238 4.0 74.8 1.0
C A:VAL191 4.0 75.9 1.0
CA A:GLY224 4.2 71.2 1.0
N A:GLY224 4.2 73.7 1.0
CG A:ASP192 4.4 101.6 1.0
CZ B:TYR238 4.4 77.2 1.0
N A:ASP192 4.4 88.0 1.0
CA A:SER223 4.5 83.5 1.0
CA A:GLY188 4.7 65.6 1.0
CB A:ASP192 4.8 99.3 1.0
N A:LYS193 4.8 86.9 1.0
CB A:SER223 4.8 83.6 1.0
C A:ASP192 4.8 91.3 1.0
O A:LYS193 4.9 77.1 1.0

Magnesium binding site 2 out of 4 in 7mj1

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Magnesium binding site 2 out of 4 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad


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 Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:76.9
occ:1.00
 O C:VAL191 2.3 59.8 1.0
O C:SER223 2.5 96.2 1.0
O C:GLY188 2.8 69.2 1.0
C C:SER223 3.5 97.6 1.0
C C:VAL191 3.5 59.2 1.0
C C:GLY188 4.0 71.1 1.0
CA C:ASP192 4.1 116.9 1.0
N C:GLY224 4.2 105.0 1.0
N C:ASP192 4.2 113.0 1.0
CA C:GLY224 4.3 105.4 1.0
OD1 C:ASP192 4.3 115.0 1.0
CA C:SER223 4.4 97.5 1.0
OH D:TYR238 4.5 112.9 1.0
CB C:SER223 4.5 95.5 1.0
O C:LYS193 4.6 64.1 1.0
N C:VAL191 4.6 55.3 1.0
CA C:VAL191 4.6 55.8 1.0
C C:ASP192 4.7 119.3 1.0
CA C:GLY188 4.7 69.0 1.0
N C:LYS193 4.8 66.2 1.0
CE2 D:TYR238 4.9 105.2 1.0
CZ D:TYR238 4.9 107.3 1.0
SD D:MET242 5.0 89.5 1.0

Magnesium binding site 3 out of 4 in 7mj1

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Magnesium binding site 3 out of 4 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad


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 Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:90.7
occ:1.00
 O2N C:NAD302 2.0 116.6 1.0
O1A C:NAD302 2.0 117.0 1.0
OD1 C:ASP151 2.5 103.2 1.0
OD2 C:ASP151 2.6 106.0 1.0
CG C:ASP151 2.8 104.2 1.0
PN C:NAD302 3.1 119.8 1.0
O1N C:NAD302 3.3 117.7 1.0
PA C:NAD302 3.3 122.5 1.0
O3 C:NAD302 3.6 121.5 1.0
NH2 C:ARG159 3.7 138.1 1.0
N C:THR126 4.0 95.1 1.0
CA C:GLY125 4.0 80.8 1.0
O5B C:NAD302 4.3 120.6 1.0
CB C:ASP151 4.3 103.2 1.0
O2A C:NAD302 4.4 118.9 1.0
CG2 C:THR126 4.4 97.3 1.0
OG1 C:THR126 4.4 99.0 1.0
O5D C:NAD302 4.5 123.7 1.0
C C:GLY125 4.6 80.2 1.0
O C:ALA124 4.8 67.9 1.0
CB C:THR126 4.9 96.9 1.0
CA C:ASP151 4.9 101.0 1.0
CZ C:ARG159 5.0 138.9 1.0

Magnesium binding site 4 out of 4 in 7mj1

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Magnesium binding site 4 out of 4 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:112.5
occ:1.00
 OD1 E:ASP151 2.1 125.7 1.0
O2A E:NAI302 2.2 104.7 1.0
CG E:ASP151 2.3 129.9 1.0
O2N E:NAI302 2.3 102.6 1.0
OD2 E:ASP151 2.3 136.4 1.0
PN E:NAI302 3.4 101.5 1.0
PA E:NAI302 3.5 104.9 1.0
CB E:ASP151 3.5 121.7 1.0
CA E:GLY125 3.7 116.2 1.0
O E:ALA124 3.7 110.1 1.0
O3 E:NAI302 3.7 99.8 1.0
NH1 E:ARG159 4.0 161.8 1.0
O1N E:NAI302 4.0 102.3 1.0
O E:ASP151 4.1 129.2 1.0
N E:THR126 4.2 107.5 1.0
CA E:ASP151 4.2 113.8 1.0
C E:ASP151 4.3 121.3 1.0
O5B E:NAI302 4.4 107.6 1.0
C E:GLY125 4.5 115.8 1.0
C E:ALA124 4.6 107.0 1.0
O1A E:NAI302 4.6 102.7 1.0
N E:GLY125 4.7 108.5 1.0
OG1 E:THR126 4.7 123.4 1.0
O5D E:NAI302 4.8 103.2 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: Thu Oct 3 00:58:25 2024

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