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Magnesium in PDB 4ex4: The Structure of Glcb From Mycobacterium Leprae

Enzymatic activity of The Structure of Glcb From Mycobacterium Leprae

All present enzymatic activity of The Structure of Glcb From Mycobacterium Leprae:
2.3.3.9;

Protein crystallography data

The structure of The Structure of Glcb From Mycobacterium Leprae, PDB code: 4ex4 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.610, 59.740, 118.460, 90.00, 100.97, 90.00
R / Rfree (%) 18.1 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Glcb From Mycobacterium Leprae (pdb code 4ex4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Structure of Glcb From Mycobacterium Leprae, PDB code: 4ex4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4ex4

Go back to Magnesium Binding Sites List in 4ex4
Magnesium binding site 1 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:4.2
occ:1.00
 OD2 A:ASP467 2.2 14.3 1.0
OE1 A:GLU439 2.2 12.6 1.0
O A:HOH1156 2.2 17.2 1.0
O A:HOH983 2.3 6.6 1.0
O A:HOH1158 2.4 24.2 1.0
O A:HOH1157 2.4 15.9 1.0
CD A:GLU439 3.1 12.4 1.0
CG A:ASP467 3.3 14.4 1.0
OE2 A:GLU439 3.4 12.6 1.0
CB A:ASP467 3.7 15.0 1.0
NH1 A:ARG340 3.8 12.5 1.0
NZ A:LYS404 4.1 10.0 1.0
OD2 A:ASP275 4.2 13.8 1.0
OD1 A:ASP467 4.3 13.7 1.0
CG A:GLU439 4.4 12.4 1.0
CB A:ALA640 4.4 17.0 1.0
OE1 A:GLU274 4.5 10.7 1.0
CE A:MET437 4.7 14.6 1.0
N A:ASP467 4.7 17.6 1.0
CB A:GLU439 4.8 12.5 1.0
CZ A:ARG340 4.8 12.3 1.0
CA A:ASP467 4.9 15.8 1.0
CA A:GLY464 5.0 20.6 1.0
CG A:ASP275 5.0 12.9 1.0

Magnesium binding site 2 out of 6 in 4ex4

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Magnesium binding site 2 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:16.7
occ:1.00
 O A:HIS379 2.2 16.7 1.0
O A:LEU390 2.2 16.9 1.0
O A:ASN387 2.4 18.3 1.0
O A:HOH990 2.5 12.3 1.0
O A:ASN296 2.5 15.6 1.0
O A:LYS297 2.8 16.9 1.0
C A:HIS379 3.3 16.6 1.0
C A:LEU390 3.3 17.9 1.0
C A:LYS297 3.3 16.9 1.0
CA A:LYS297 3.4 17.3 1.0
C A:ASN296 3.5 15.4 1.0
C A:ASN387 3.6 17.8 1.0
N A:LYS297 3.9 16.2 1.0
N A:LEU390 4.0 17.6 1.0
N A:GLY380 4.0 16.7 1.0
O A:GLY388 4.0 17.1 1.0
CA A:GLY380 4.1 17.0 1.0
O A:LYS382 4.1 21.1 1.0
C A:GLY388 4.1 16.9 1.0
CA A:GLY388 4.2 16.9 1.0
CA A:LEU390 4.2 17.8 1.0
N A:THR391 4.2 18.8 1.0
CA A:HIS379 4.2 16.1 1.0
CB A:HIS379 4.3 15.5 1.0
N A:GLY388 4.3 17.2 1.0
CA A:THR391 4.4 18.6 1.0
N A:GLY298 4.4 16.2 1.0
CB A:ASN387 4.5 18.7 1.0
CG2 A:THR391 4.6 20.0 1.0
O A:HOH1030 4.6 17.5 1.0
CA A:ASN387 4.6 18.4 1.0
CB A:LYS297 4.7 18.3 1.0
N A:PRO389 4.7 16.7 1.0
C A:GLY380 4.8 17.6 1.0
CA A:ASN296 4.9 14.6 1.0
C A:PRO389 4.9 17.8 1.0

Magnesium binding site 3 out of 6 in 4ex4

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Magnesium binding site 3 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.4
occ:1.00
 O A:HOH1067 2.3 23.4 1.0
O A:HOH1059 2.5 24.2 1.0
O A:HOH1181 2.5 29.3 1.0
O A:HOH1179 2.6 29.5 1.0
O A:ASN392 2.6 19.2 1.0
O A:THR391 2.7 19.0 1.0
C A:THR391 3.5 18.7 1.0
C A:ASN392 3.6 18.6 1.0
NH2 A:ARG334 3.7 18.2 1.0
O A:HOH974 3.8 12.5 1.0
CA A:ASN392 3.9 18.1 1.0
O A:HOH1110 3.9 39.1 1.0
O A:HOH1184 3.9 28.9 1.0
N A:ASN392 4.0 18.0 1.0
O A:HOH1288 4.1 32.2 1.0
OG1 A:THR391 4.2 20.1 1.0
CG A:ARG394 4.6 27.1 1.0
O A:HOH1001 4.6 21.3 1.0
CA A:THR391 4.7 18.6 1.0
O A:HOH1007 4.7 19.0 1.0
N A:SER393 4.7 18.9 1.0
CZ A:ARG334 4.8 18.2 1.0
O A:SER393 4.8 21.1 1.0
CB A:THR391 4.8 19.6 1.0
OD2 A:ASP318 4.8 23.9 1.0
C A:SER393 4.9 21.1 1.0
N A:THR391 5.0 18.8 1.0
CD A:ARG394 5.0 28.5 1.0

Magnesium binding site 4 out of 6 in 4ex4

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Magnesium binding site 4 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:6.3
occ:1.00
 OD2 B:ASP467 2.0 18.7 1.0
O B:HOH1037 2.1 13.3 1.0
OE1 B:GLU439 2.1 13.2 1.0
O B:HOH999 2.2 15.3 1.0
O B:HOH1171 2.3 20.5 1.0
O B:HOH1172 2.4 18.1 1.0
CG B:ASP467 3.1 17.7 1.0
CD B:GLU439 3.1 13.1 1.0
OE2 B:GLU439 3.5 12.5 1.0
CB B:ASP467 3.6 17.6 1.0
OD2 B:ASP275 3.8 17.3 1.0
NH2 B:ARG340 3.9 11.8 1.0
NZ B:LYS404 4.2 12.3 1.0
OD1 B:ASP467 4.2 17.3 1.0
O B:HOH1332 4.2 26.9 1.0
CG B:GLU439 4.4 13.2 1.0
CB B:ALA640 4.4 19.7 1.0
CE B:MET437 4.6 12.8 1.0
OE1 B:GLU274 4.6 13.3 1.0
N B:ASP467 4.7 18.2 1.0
CB B:GLU439 4.7 13.5 1.0
CA B:ASP467 4.7 17.9 1.0
CG B:ASP275 4.8 16.0 1.0
CA B:GLY464 4.9 18.3 1.0
CZ B:ARG340 4.9 11.4 1.0
O B:GLY464 5.0 19.0 1.0

Magnesium binding site 5 out of 6 in 4ex4

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Magnesium binding site 5 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.0
occ:1.00
 O B:HIS379 2.3 12.4 1.0
O B:LEU390 2.3 13.8 1.0
O B:ASN387 2.3 13.8 1.0
O B:ASN296 2.5 12.7 1.0
O B:HOH1104 2.5 12.6 1.0
O B:LYS297 2.7 13.9 1.0
C B:LYS297 3.2 13.6 1.0
CA B:LYS297 3.3 13.5 1.0
C B:HIS379 3.3 12.3 1.0
C B:LEU390 3.4 13.7 1.0
C B:ASN387 3.5 13.9 1.0
C B:ASN296 3.5 12.2 1.0
N B:LYS297 3.9 12.8 1.0
N B:LEU390 3.9 13.5 1.0
O B:GLY388 4.0 13.6 1.0
N B:GLY380 4.1 12.5 1.0
C B:GLY388 4.1 13.4 1.0
O B:LYS382 4.1 18.1 1.0
CA B:GLY380 4.2 12.9 1.0
CA B:GLY388 4.2 13.3 1.0
N B:GLY388 4.2 13.4 1.0
CA B:LEU390 4.3 13.4 1.0
CB B:HIS379 4.3 11.9 1.0
N B:THR391 4.3 14.0 1.0
CA B:HIS379 4.3 12.1 1.0
CG2 B:THR391 4.3 14.2 1.0
N B:GLY298 4.4 13.4 1.0
CB B:ASN387 4.4 14.1 1.0
CA B:THR391 4.4 14.1 1.0
CA B:ASN387 4.5 14.1 1.0
O B:HOH911 4.5 10.5 1.0
CB B:LYS297 4.6 13.6 1.0
N B:PRO389 4.7 13.1 1.0
CA B:ASN296 4.8 11.7 1.0
O B:HOH1085 4.9 20.1 1.0
C B:PRO389 4.9 13.8 1.0
C B:GLY380 4.9 13.5 1.0

Magnesium binding site 6 out of 6 in 4ex4

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Magnesium binding site 6 out of 6 in the The Structure of Glcb From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Glcb From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:26.7
occ:1.00
 O B:HOH1220 2.1 18.6 1.0
O B:HOH1024 2.4 18.0 1.0
O B:HOH949 2.4 15.2 1.0
O B:THR391 2.4 14.1 1.0
O B:HOH929 2.6 20.7 1.0
O B:ASN392 2.6 16.2 1.0
C B:THR391 3.3 14.1 1.0
C B:ASN392 3.5 14.8 1.0
O B:HOH1105 3.7 30.6 1.0
CA B:ASN392 3.7 14.3 1.0
NH2 B:ARG334 3.7 15.3 1.0
N B:ASN392 3.8 14.1 1.0
O B:HOH926 4.0 13.9 1.0
O B:HOH1076 4.1 23.3 1.0
OG1 B:THR391 4.3 14.6 1.0
CG B:ARG394 4.4 23.2 1.0
CA B:THR391 4.5 14.1 1.0
O B:HOH1036 4.5 13.9 1.0
O B:HOH1069 4.5 13.5 1.0
O B:SER393 4.7 15.1 1.0
NH1 B:ARG394 4.7 32.6 1.0
N B:SER393 4.7 14.8 1.0
OD2 B:ASP318 4.8 17.3 1.0
CZ B:ARG334 4.8 15.6 1.0
CB B:THR391 4.8 14.2 1.0
N B:THR391 4.8 14.0 1.0
C B:SER393 4.9 15.6 1.0
CD B:ARG394 4.9 26.4 1.0
OD1 B:ASP318 4.9 16.3 1.0

Reference:

M.C.Clifton, D.Fox Iii, Seattle Structural Genomics Center For Infectious Disease. The Structure of Glcb From Mycobacterium Leprae To Be Published.
Page generated: Mon Aug 11 12:31:40 2025

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