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Magnesium in PDB 8soq: S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad

Enzymatic activity of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad

All present enzymatic activity of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad:
2.5.1.143;

Protein crystallography data

The structure of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad, PDB code: 8soq was solved by S.Chatterjee, J.A.Rankin, J.Hu, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.15 / 3.10
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.91, 120.91, 212.64, 90, 90, 90
R / Rfree (%) 23.6 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad (pdb code 8soq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad, PDB code: 8soq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8soq

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Magnesium binding site 1 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:116.1
occ:1.00
 O12 A:DND303 1.8 125.1 1.0
OD1 A:ASP151 2.6 94.6 1.0
O13 A:DND303 2.9 146.3 1.0
PN A:DND303 3.3 128.0 1.0
NH1 A:ARG159 3.3 78.6 1.0
OD2 A:ASP151 3.4 102.2 1.0
CG A:ASP151 3.4 90.3 1.0
O3P A:DND303 3.8 142.4 1.0
PA A:DND303 3.9 165.1 1.0
NH2 A:ARG159 4.0 68.8 1.0
CZ A:ARG159 4.1 81.6 1.0
O11 A:DND303 4.2 134.8 1.0
O5D A:DND303 4.3 115.9 1.0
C5B A:DND303 4.3 143.0 1.0
O5B A:DND303 4.5 160.3 1.0
O A:ALA124 4.7 94.0 1.0
CB A:ASP151 4.8 69.5 1.0
CA A:GLY125 4.9 90.7 1.0

Magnesium binding site 2 out of 7 in 8soq

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Magnesium binding site 2 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:77.5
occ:1.00
 O A:GLY188 2.7 64.0 1.0
O A:VAL191 2.7 69.9 1.0
O A:SER223 2.8 53.3 1.0
C A:GLY188 3.7 68.3 1.0
C A:VAL191 3.9 65.5 1.0
C A:SER223 4.0 61.8 1.0
CA A:GLY224 4.1 54.5 1.0
CA A:GLY188 4.2 56.1 1.0
O A:LYS193 4.5 57.2 1.0
N A:GLY224 4.5 56.9 1.0
CG2 A:VAL191 4.5 56.0 1.0
OH B:TYR238 4.6 55.0 1.0
CA A:ASP192 4.6 72.6 1.0
N A:ASP192 4.7 71.8 1.0
C A:GLY224 4.8 54.3 1.0
N A:GLY189 4.8 67.1 1.0
CE1 B:TYR238 4.8 50.1 1.0
N A:VAL191 4.9 67.0 1.0
O A:GLY224 4.9 57.7 1.0
CA A:VAL191 4.9 61.7 1.0

Magnesium binding site 3 out of 7 in 8soq

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Magnesium binding site 3 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:149.2
occ:1.00
 O12 B:DND302 2.3 118.2 1.0
O13 B:DND302 3.0 144.9 1.0
PN B:DND302 3.6 151.1 1.0
O5B B:DND302 3.7 120.6 1.0
PA B:DND302 3.8 151.6 1.0
OD2 B:ASP151 3.9 103.8 1.0
O3P B:DND302 3.9 145.9 1.0
OD1 B:ASP151 4.1 107.1 1.0
O3B B:DND302 4.3 105.8 0.4
CG B:ASP151 4.4 98.2 1.0
O11 B:DND302 4.5 127.8 1.0
O5D B:DND302 4.7 123.4 1.0
C3B B:DND302 5.0 111.2 0.4

Magnesium binding site 4 out of 7 in 8soq

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Magnesium binding site 4 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:118.4
occ:1.00
 O12 C:DND302 2.1 149.4 1.0
OD1 C:ASP151 3.2 102.2 1.0
NH1 C:ARG159 3.3 99.3 1.0
NH2 C:ARG159 3.3 80.0 1.0
O13 C:DND302 3.5 196.6 1.0
PN C:DND302 3.5 171.7 1.0
O5B C:DND302 3.7 153.2 1.0
CZ C:ARG159 3.8 100.9 1.0
PA C:DND302 4.1 210.2 1.0
O3P C:DND302 4.1 173.3 1.0
CG C:ASP151 4.2 88.2 1.0
O5D C:DND302 4.3 145.9 1.0
OD2 C:ASP151 4.4 91.3 1.0
O C:ALA124 4.6 61.3 1.0
O11 C:DND302 4.6 131.9 1.0

Magnesium binding site 5 out of 7 in 8soq

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Magnesium binding site 5 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:167.6
occ:1.00
 O12 D:DND303 2.4 158.2 1.0
OD2 D:ASP151 2.5 126.3 1.0
OD1 D:ASP151 2.5 112.6 1.0
CG D:ASP151 2.8 105.9 1.0
O13 D:DND303 3.4 171.8 1.0
NH1 D:ARG159 3.4 116.5 1.0
PN D:DND303 3.8 157.8 1.0
CB D:ASP151 4.3 84.0 1.0
CZ D:ARG159 4.3 111.1 1.0
O3P D:DND303 4.4 164.8 1.0
NH2 D:ARG159 4.4 99.5 1.0
O11 D:DND303 4.5 156.4 1.0
PA D:DND303 4.5 171.7 1.0
N D:THR126 4.9 93.0 1.0
CA D:GLY125 4.9 112.3 1.0
CG2 D:THR126 4.9 98.1 1.0
O5D D:DND303 5.0 153.2 1.0

Magnesium binding site 6 out of 7 in 8soq

Go back to Magnesium Binding Sites List in 8soq
Magnesium binding site 6 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:72.4
occ:1.00
 O D:SER223 2.5 81.0 0.3
O D:LYS193 2.8 62.0 1.0
CA D:GLY224 3.3 70.8 0.3
CA D:GLY224 3.4 71.2 0.7
C D:SER223 3.5 83.5 0.3
CG2 D:VAL195 3.5 55.0 1.0
O D:SER223 3.5 84.2 0.7
C D:GLY224 3.6 65.7 0.7
C D:GLY224 3.6 68.7 0.3
O D:GLY188 3.6 78.6 1.0
O D:GLY224 3.6 63.0 0.7
O D:VAL191 3.8 67.0 1.0
N D:GLY224 3.8 76.4 0.3
O D:GLY224 3.9 62.7 0.3
C D:LYS193 4.0 59.3 1.0
CB D:VAL195 4.1 50.8 1.0
N D:VAL195 4.1 52.9 1.0
CG2 D:VAL191 4.2 63.9 1.0
N D:ILE225 4.3 61.9 1.0
CA D:GLY188 4.3 74.3 1.0
C D:SER223 4.4 84.9 0.7
N D:GLY224 4.4 73.6 0.7
C D:GLY188 4.4 73.8 1.0
SD C:MET242 4.4 69.3 1.0
N D:LYS193 4.4 80.5 1.0
C D:PRO194 4.7 54.0 1.0
C D:VAL191 4.7 68.0 1.0
CA D:PRO194 4.7 54.1 1.0
CA D:VAL195 4.7 46.4 1.0
CE C:MET242 4.8 66.8 1.0
N D:PRO194 4.8 60.3 1.0
CA D:SER223 4.9 82.4 0.3
CG1 D:ILE225 4.9 59.5 1.0
CA D:LYS193 4.9 64.6 1.0
CE1 C:TYR238 4.9 65.7 1.0

Magnesium binding site 7 out of 7 in 8soq

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Magnesium binding site 7 out of 7 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Authentic Substrate Naad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:167.8
occ:1.00
 O12 E:DND302 1.9 140.1 1.0
OD1 E:ASP151 2.5 147.4 1.0
OD2 E:ASP151 2.7 160.3 1.0
CG E:ASP151 3.0 147.3 1.0
O13 E:DND302 3.1 152.8 1.0
PN E:DND302 3.2 139.3 1.0
O5B E:DND302 3.8 168.2 1.0
PA E:DND302 3.8 165.1 1.0
O3P E:DND302 3.8 149.9 1.0
O11 E:DND302 4.0 143.6 1.0
O5D E:DND302 4.4 148.4 1.0
CB E:ASP151 4.5 144.7 1.0
CA E:GLY125 4.8 130.6 1.0
N E:THR126 4.9 153.3 1.0
O E:ALA124 4.9 135.3 1.0

Reference:

S.Chatterjee, J.L.Nevarez, J.A.Rankin, J.Hu, R.P.Hausinger. Structure of the Larb-Substrate Complex and Identification of A Reaction Intermediate During Nickel-Pincer Nucleotide Cofactor Biosynthesis. Biochemistry V. 62 3096 2023.
ISSN: ISSN 0006-2960
PubMed: 37831946
DOI: 10.1021/ACS.BIOCHEM.3C00242
Page generated: Fri Aug 15 15:48:34 2025

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