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Magnesium in PDB 5cjn: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate, PDB code: 5cjn was solved by H.-L.Huang, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.65 / 2.19
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.807, 78.807, 223.823, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate (pdb code 5cjn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate, PDB code: 5cjn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cjn

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:12.7
occ:1.00
 OD2 A:ASP462 2.0 15.8 1.0
O A:HOH1030 2.0 10.0 1.0
OE2 A:GLU434 2.1 16.1 1.0
O A:HOH912 2.1 18.9 1.0
O A:HOH1059 2.1 11.0 1.0
O A:HOH1242 2.5 25.2 1.0
CG A:ASP462 3.0 16.4 1.0
CD A:GLU434 3.1 12.2 1.0
CB A:ASP462 3.3 18.5 1.0
OE1 A:GLU434 3.5 12.3 1.0
CE A:MET432 3.7 11.2 1.0
NZ A:LYS399 4.0 13.1 1.0
O A:HOH908 4.0 22.6 1.0
OD2 A:ASP274 4.1 14.0 1.0
OD1 A:ASP462 4.1 10.5 1.0
NH1 A:ARG339 4.2 15.9 1.0
O A:HOH1272 4.3 20.1 1.0
O03 A:52F809 4.4 27.5 1.0
CG A:GLU434 4.4 12.7 1.0
OE1 A:GLU273 4.5 10.2 1.0
CB A:ALA635 4.5 16.1 1.0
CA A:ASP462 4.7 15.4 1.0
CB A:GLU434 4.7 10.0 1.0
OD2 A:ASP633 4.7 20.8 1.0
CG A:ASP274 4.9 16.2 1.0
C04 A:52F809 4.9 26.1 1.0
O A:HOH1138 4.9 14.7 1.0
SD A:MET432 5.0 32.7 1.0

Magnesium binding site 2 out of 8 in 5cjn

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:42.0
occ:1.00
 O A:HOH1318 2.0 18.1 1.0
O A:HOH1310 2.5 27.4 1.0
O A:HOH1434 3.5 43.6 1.0
O A:HOH1027 3.7 23.2 1.0
O A:HOH1343 3.8 35.2 1.0
O A:HOH1141 3.9 24.3 1.0
CG A:GLU493 4.0 14.8 1.0
CB A:GLU493 4.1 13.2 1.0
CD A:GLU493 4.2 22.1 1.0
O A:HOH961 4.2 16.4 1.0
OE2 A:GLU493 4.3 23.6 1.0
OE1 A:GLU493 4.8 17.9 1.0
CD2 A:LEU490 4.8 16.3 1.0
CE A:LYS513 4.9 14.5 1.0
CD A:LYS513 5.0 15.9 1.0

Magnesium binding site 3 out of 8 in 5cjn

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:25.4
occ:1.00
 O A:HIS374 2.6 19.3 1.0
O A:LYS377 2.7 28.2 1.0
O A:ASN382 2.7 34.6 1.0
O A:ASN295 2.7 15.4 1.0
O A:LEU385 2.9 39.5 1.0
O A:PRO384 3.0 47.4 1.0
O A:GLY383 3.3 40.7 1.0
O A:LYS296 3.4 29.3 1.0
C A:HIS374 3.7 19.5 1.0
C A:LYS377 3.7 32.2 1.0
CA A:LYS296 3.7 21.6 1.0
C A:LYS296 3.8 24.6 1.0
C A:ASN295 3.8 19.5 1.0
C A:ASN382 3.8 38.4 1.0
C A:PRO384 3.9 47.6 1.0
C A:GLY383 4.0 40.8 1.0
C A:LEU385 4.1 37.1 1.0
CA A:GLY375 4.3 19.3 1.0
N A:LYS296 4.3 18.7 1.0
CA A:ALA378 4.3 33.8 1.0
N A:GLY375 4.4 17.1 1.0
N A:ALA378 4.4 40.8 1.0
CB A:ASN382 4.5 36.9 1.0
N A:LYS377 4.6 23.9 1.0
CA A:GLY383 4.6 36.1 1.0
CA A:HIS374 4.6 18.4 1.0
CA A:LYS377 4.7 25.9 1.0
N A:GLY383 4.7 32.1 1.0
N A:LEU385 4.7 49.0 1.0
O A:HOH1256 4.7 28.3 1.0
N A:PRO384 4.7 43.6 1.0
C A:GLY375 4.7 21.0 1.0
CB A:HIS374 4.8 19.1 1.0
CA A:PRO384 4.8 44.6 1.0
N A:GLY297 4.8 21.9 1.0
CA A:ASN382 4.8 39.6 1.0
CA A:LEU385 4.8 47.2 1.0
CB A:ALA378 4.9 33.3 1.0

Magnesium binding site 4 out of 8 in 5cjn

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:38.4
occ:1.00
 O A:HOH1135 2.2 20.1 1.0
O A:HOH958 2.5 23.9 1.0
O A:HOH1061 3.7 37.5 1.0
OE1 A:GLN564 3.7 24.3 1.0
CB A:SER538 4.0 17.2 1.0
O A:THR111 4.0 29.9 1.0
O A:HOH1011 4.1 18.0 1.0
CD A:GLN564 4.2 21.7 1.0
CB A:ALA113 4.4 17.3 1.0
O A:HOH1403 4.4 36.8 1.0
CG1 A:VAL560 4.4 19.7 1.0
NE2 A:GLN564 4.5 21.6 1.0
CA A:ALA561 4.6 17.5 1.0
N A:ALA561 4.6 14.4 1.0
CB A:ALA561 4.7 19.6 1.0
OG A:SER538 4.7 18.4 1.0
N A:GLY507 4.7 20.8 1.0
OG A:SER506 4.8 34.1 1.0
C A:THR111 4.8 26.8 1.0
N A:ALA113 4.9 19.2 1.0

Magnesium binding site 5 out of 8 in 5cjn

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:36.8
occ:1.00
 N A:GLY222 3.6 37.6 1.0
CA A:THR221 3.7 28.8 1.0
OG1 A:THR321 4.0 31.9 1.0
CB A:THR221 4.1 26.8 1.0
C A:THR221 4.2 26.5 1.0
CG2 A:THR221 4.3 28.6 1.0
O A:TYR220 4.3 26.5 1.0
O A:ASN319 4.7 31.4 1.0
CA A:GLY222 4.7 33.3 1.0
N A:THR321 4.7 31.2 1.0
O A:GLY222 4.7 37.3 1.0
C A:TYR320 4.7 33.0 1.0
CA A:TYR320 4.9 31.2 1.0
N A:THR221 4.9 26.5 1.0
O A:HOH938 4.9 37.1 1.0
CB A:THR321 4.9 36.6 1.0

Magnesium binding site 6 out of 8 in 5cjn

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:31.4
occ:1.00
 O A:HOH1339 2.1 31.8 1.0
O A:HOH1357 2.2 38.8 1.0
O A:HOH1185 2.5 38.4 1.0
O A:HOH1124 2.9 26.0 1.0
CD A:LYS443 3.3 26.9 1.0
CB A:ALA502 3.8 23.4 1.0
CA A:ALA499 3.9 19.5 1.0
CG A:LYS443 4.0 23.0 1.0
CE A:LYS443 4.1 30.9 1.0
CB A:LYS443 4.2 21.6 1.0
CB A:ALA499 4.3 16.2 1.0
OE1 A:GLU94 4.3 40.2 1.0
NZ A:LYS443 4.3 36.1 1.0
N A:ALA499 4.6 17.0 1.0
O A:HOH1369 4.6 36.9 1.0
O A:ASP498 4.6 21.9 1.0
O A:ALA499 4.6 18.4 1.0
O A:HOH1068 4.8 32.9 1.0
NH2 A:ARG571 4.8 51.5 1.0
C A:ALA499 4.8 19.7 1.0
O A:HOH1063 4.8 35.5 1.0
C A:ASP498 4.9 23.1 1.0

Magnesium binding site 7 out of 8 in 5cjn

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg807

b:43.8
occ:1.00
 O A:HOH1265 2.4 30.0 1.0
O A:HOH1155 2.5 31.1 1.0
O A:HOH1402 3.0 38.9 1.0
O A:ALA703 4.1 22.7 1.0
O A:GLN704 4.3 20.1 1.0
CA A:GLN704 4.3 21.6 1.0
O A:HOH914 4.5 31.0 1.0
C A:GLN704 4.6 21.9 1.0
OD2 A:ASP65 4.7 28.7 1.0
O A:HOH1021 4.7 34.1 1.0
O A:HOH1157 4.8 27.0 1.0

Magnesium binding site 8 out of 8 in 5cjn

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 3-(3-Oxo-3,4-Dihydroquinoxalin-2-Yl)Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:39.0
occ:1.00
 O A:HOH928 2.0 29.2 1.0
O A:HOH1140 2.1 28.2 1.0
O A:HOH1293 2.1 28.9 1.0
O A:HOH1182 2.1 29.5 1.0
NE2 A:HIS235 2.4 23.8 1.0
CE1 A:HIS235 3.2 26.4 1.0
CD2 A:HIS235 3.4 24.4 1.0
O A:HOH956 4.2 39.7 1.0
OD2 A:ASP559 4.2 28.8 1.0
ND1 A:HIS235 4.4 23.6 1.0
CB A:ASP559 4.5 22.2 1.0
CG A:HIS235 4.5 23.6 1.0
O A:HOH1188 4.6 35.2 1.0
OD1 A:ASN234 4.6 26.3 1.0
CG A:ASP559 4.7 28.4 1.0

Reference:

H.L.Huang, I.V.Krieger, M.K.Parai, V.B.Gawandi, J.C.Sacchettini. Mycobacterium Tuberculosis Malate Synthase Structures with Fragments Reveal A Portal For Substrate/Product Exchange. J. Biol. Chem. V. 291 27421 2016.
ISSN: ESSN 1083-351X
PubMed: 27738104
DOI: 10.1074/JBC.M116.750877
Page generated: Sun Sep 29 02:10:45 2024

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