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Magnesium in PDB 6mgj: Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme, PDB code: 6mgj was solved by P.J.Stogios, T.Skarina, B.Nocek, G.Arnal, H.Brumer, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.78 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 239.094, 226.674, 187.224, 90.00, 114.07, 90.00
R / Rfree (%) 14.9 / 17.7

Other elements in 6mgj:

The structure of Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme (pdb code 6mgj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme, PDB code: 6mgj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6mgj

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:20.2
occ:1.00
 O A:HOH1247 2.1 21.2 1.0
OE2 A:GLU412 2.2 26.0 1.0
OD1 A:ASP410 2.3 26.0 1.0
OD2 A:ASP410 2.4 26.9 1.0
O A:HOH1637 2.5 33.1 1.0
O A:ILE55 2.5 21.3 1.0
CG A:ASP410 2.7 26.7 1.0
O A:HOH1732 2.9 43.6 1.0
CD A:GLU412 3.2 24.0 1.0
C A:ILE55 3.6 19.6 1.0
N A:ILE55 3.8 17.7 1.0
CG A:GLU412 3.8 19.9 1.0
O A:HOH901 4.1 22.6 1.0
OE1 A:GLU412 4.2 28.2 1.0
CB A:ASP410 4.2 23.8 1.0
CA A:ILE55 4.3 18.9 1.0
O A:HOH1009 4.3 23.2 1.0
O A:HOH1030 4.3 23.2 1.0
O A:HOH1046 4.3 23.1 1.0
O A:HOH1335 4.5 23.3 1.0
O A:HOH1306 4.6 36.8 1.0
N A:ILE56 4.6 19.3 1.0
CA A:GLY54 4.7 19.2 1.0
C A:GLY54 4.7 20.2 1.0
OE2 A:GLU161 4.7 24.0 1.0
CG1 A:ILE56 4.8 19.7 1.0
CA A:ILE56 4.8 22.3 1.0
O A:HOH1304 4.9 30.0 1.0
CB A:ILE55 4.9 20.1 1.0

Magnesium binding site 2 out of 9 in 6mgj

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:17.9
occ:0.97
 O B:HOH1217 2.1 20.3 1.0
O B:HOH1291 2.2 24.5 1.0
OE2 B:GLU412 2.4 29.6 1.0
OD2 B:ASP410 2.4 23.2 1.0
OD1 B:ASP410 2.4 22.1 1.0
O B:ILE55 2.5 17.9 1.0
CG B:ASP410 2.7 21.4 1.0
O B:HOH1766 3.0 37.9 1.0
CD B:GLU412 3.3 23.5 1.0
C B:ILE55 3.6 19.4 1.0
CG B:GLU412 3.7 23.4 1.0
N B:ILE55 3.8 17.9 1.0
O B:HOH1201 4.2 28.6 1.0
CB B:ASP410 4.3 19.2 1.0
CA B:ILE55 4.3 18.1 1.0
OE1 B:GLU412 4.3 26.9 1.0
MG B:MG802 4.3 26.9 0.6
O B:HOH911 4.3 22.4 1.0
O B:HOH1137 4.4 23.0 1.0
O B:HOH1031 4.4 17.3 1.0
N B:ILE56 4.6 18.2 1.0
OE2 B:GLU161 4.6 21.3 1.0
CA B:GLY54 4.7 18.4 1.0
C B:GLY54 4.7 18.1 1.0
O B:HOH1409 4.7 37.6 1.0
CG1 B:ILE56 4.7 18.4 1.0
CA B:ILE56 4.8 19.6 1.0
CB B:ILE55 4.9 16.6 1.0

Magnesium binding site 3 out of 9 in 6mgj

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.9
occ:0.61
 O B:HOH1209 1.9 32.4 1.0
O B:LEU329 2.4 17.3 1.0
OE2 B:GLU412 2.4 29.6 1.0
O B:HOH1201 2.5 28.6 1.0
O B:LEU411 2.6 19.4 1.0
CD B:GLU412 2.9 23.5 1.0
O B:HOH911 3.1 22.4 1.0
OE1 B:GLU412 3.4 26.9 1.0
C B:LEU329 3.5 16.5 1.0
O B:HOH1308 3.8 24.7 1.0
C B:LEU411 3.8 18.5 1.0
O B:HOH1391 3.9 20.0 1.0
CA B:ALA330 3.9 18.1 1.0
CG B:GLU412 4.0 23.4 1.0
O B:HOH1409 4.0 37.6 1.0
N B:ALA330 4.1 16.0 1.0
OD1 B:ASP410 4.1 22.1 1.0
MG B:MG801 4.3 17.9 1.0
CA B:GLU412 4.3 18.5 1.0
O B:HOH1766 4.3 37.9 1.0
OE2 B:GLU276 4.4 33.9 1.0
CB B:ALA330 4.5 15.4 1.0
N B:GLU412 4.6 18.2 1.0
CD B:GLU276 4.6 30.3 1.0
O B:HOH1291 4.7 24.5 1.0
N B:LEU411 4.7 20.7 1.0
CB B:GLU412 4.7 20.3 1.0
CA B:LEU329 4.7 18.2 1.0
N B:LEU329 4.7 18.0 1.0
CG B:GLU276 4.8 22.7 1.0
CA B:LEU411 4.9 19.6 1.0

Magnesium binding site 4 out of 9 in 6mgj

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg801

b:17.7
occ:0.95
 O C:HOH1158 2.1 20.4 1.0
OE2 C:GLU412 2.2 28.3 1.0
OD1 C:ASP410 2.4 24.4 1.0
OD2 C:ASP410 2.5 24.7 1.0
O C:ILE55 2.5 20.0 1.0
O C:HOH1656 2.6 26.3 1.0
CG C:ASP410 2.7 25.3 1.0
O C:HOH1755 2.9 40.3 1.0
CD C:GLU412 3.2 25.6 1.0
C C:ILE55 3.6 18.6 1.0
N C:ILE55 3.8 16.7 1.0
CG C:GLU412 3.9 20.3 1.0
O C:HOH904 4.1 7.1 0.5
OE1 C:GLU412 4.1 25.3 1.0
CB C:ASP410 4.3 23.1 1.0
CA C:ILE55 4.3 18.9 1.0
O C:HOH1168 4.3 27.1 1.0
O C:HOH1186 4.4 22.1 1.0
O C:HOH1001 4.4 20.5 1.0
O C:HOH1064 4.4 19.8 1.0
O C:HOH1566 4.4 42.7 1.0
N C:ILE56 4.6 16.0 1.0
OE2 C:GLU161 4.7 19.8 1.0
CG1 C:ILE56 4.7 20.7 1.0
CA C:GLY54 4.7 17.7 1.0
C C:GLY54 4.7 17.5 1.0
CA C:ILE56 4.8 17.8 1.0
O C:HOH904 4.8 10.7 0.5
CB C:ILE55 4.9 21.5 1.0

Magnesium binding site 5 out of 9 in 6mgj

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:15.8
occ:0.81
 O D:HOH1123 2.1 20.1 1.0
OE2 D:GLU412 2.2 28.9 1.0
OD1 D:ASP410 2.4 26.4 1.0
OD2 D:ASP410 2.4 27.4 1.0
O D:HOH1644 2.5 28.5 1.0
O D:ILE55 2.5 21.8 1.0
CG D:ASP410 2.7 25.9 1.0
O D:HOH1693 2.9 36.7 1.0
CD D:GLU412 3.2 25.6 1.0
C D:ILE55 3.7 19.0 1.0
N D:ILE55 3.8 18.7 1.0
CG D:GLU412 3.9 21.3 1.0
O D:HOH901 4.1 6.8 0.5
OE1 D:GLU412 4.1 27.1 1.0
CB D:ASP410 4.2 22.1 1.0
O D:HOH1262 4.3 27.9 1.0
CA D:ILE55 4.4 17.6 1.0
O D:HOH1200 4.4 25.1 1.0
O D:HOH996 4.4 24.0 1.0
O D:HOH977 4.4 19.4 1.0
O D:HOH1570 4.6 44.5 1.0
OE2 D:GLU161 4.7 22.4 1.0
N D:ILE56 4.7 19.5 1.0
CA D:GLY54 4.7 21.7 1.0
C D:GLY54 4.7 20.9 1.0
CG1 D:ILE56 4.8 18.8 1.0
CA D:ILE56 4.8 20.5 1.0
O D:HOH901 4.8 10.7 0.5
CB D:ILE55 5.0 19.6 1.0

Magnesium binding site 6 out of 9 in 6mgj

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:19.6
occ:0.92
 OE2 E:GLU412 2.2 26.9 1.0
OD2 E:ASP410 2.4 29.3 1.0
OD1 E:ASP410 2.4 28.4 1.0
O E:HOH913 2.4 21.2 1.0
O E:HOH1639 2.5 28.1 1.0
O E:ILE55 2.5 22.6 1.0
CG E:ASP410 2.7 28.1 1.0
O E:HOH1682 2.9 38.8 1.0
CD E:GLU412 3.2 26.5 1.0
C E:ILE55 3.6 22.4 1.0
N E:ILE55 3.8 20.5 1.0
CG E:GLU412 3.9 24.0 1.0
O E:HOH904 4.0 11.3 0.5
OE1 E:GLU412 4.2 28.5 1.0
O E:HOH1434 4.2 32.2 1.0
CB E:ASP410 4.2 25.1 1.0
CA E:ILE55 4.3 21.1 1.0
O E:HOH983 4.3 20.0 1.0
O E:HOH1176 4.4 26.0 1.0
O E:HOH1138 4.5 22.1 1.0
O E:HOH1395 4.6 46.8 1.0
N E:ILE56 4.6 20.4 1.0
OE2 E:GLU161 4.6 23.8 1.0
CA E:GLY54 4.7 19.9 1.0
C E:GLY54 4.7 21.2 1.0
O E:HOH904 4.7 12.5 0.5
CG1 E:ILE56 4.7 25.1 1.0
CA E:ILE56 4.8 20.2 1.0
CB E:ILE55 5.0 20.2 1.0
CE1 E:HIS274 5.0 25.6 1.0

Magnesium binding site 7 out of 9 in 6mgj

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg801

b:15.0
occ:0.89
 O F:HOH1159 2.1 20.5 1.0
OE2 F:GLU412 2.2 23.9 1.0
OD1 F:ASP410 2.3 23.7 1.0
OD2 F:ASP410 2.4 26.6 1.0
O F:HOH1626 2.5 27.8 1.0
O F:ILE55 2.5 20.6 1.0
CG F:ASP410 2.7 24.4 1.0
O F:HOH1789 3.0 35.0 1.0
CD F:GLU412 3.3 23.8 1.0
C F:ILE55 3.6 19.3 1.0
N F:ILE55 3.9 18.4 1.0
CG F:GLU412 3.9 16.5 1.0
O F:HOH901 4.1 25.9 1.0
OE1 F:GLU412 4.2 24.0 1.0
CB F:ASP410 4.2 22.9 1.0
O F:HOH1121 4.3 20.8 1.0
CA F:ILE55 4.4 15.9 1.0
O F:HOH1061 4.4 18.7 1.0
O F:HOH1220 4.4 22.9 1.0
O F:HOH1276 4.5 27.0 1.0
O F:HOH1519 4.6 36.7 1.0
N F:ILE56 4.7 17.0 1.0
OE2 F:GLU161 4.7 22.1 1.0
CG1 F:ILE56 4.7 21.7 1.0
CA F:GLY54 4.8 18.8 1.0
O F:HOH1165 4.8 30.5 1.0
C F:GLY54 4.8 18.9 1.0
CA F:ILE56 4.8 16.1 1.0

Magnesium binding site 8 out of 9 in 6mgj

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


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 the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg801

b:21.5
occ:0.94
 OE1 G:GLU412 2.2 28.6 1.0
OD2 G:ASP410 2.4 24.3 1.0
OD1 G:ASP410 2.4 25.4 1.0
O G:ILE55 2.5 21.0 1.0
O G:HOH1042 2.5 22.5 1.0
O G:HOH1663 2.6 26.0 1.0
CG G:ASP410 2.7 25.1 1.0
O G:HOH1727 3.0 39.9 1.0
CD G:GLU412 3.1 26.4 1.0
C G:ILE55 3.6 20.7 1.0
CG G:GLU412 3.8 21.4 1.0
N G:ILE55 3.8 18.0 1.0
OE2 G:GLU412 4.0 28.5 1.0
O G:HOH901 4.2 7.6 0.5
CB G:ASP410 4.2 22.6 1.0
CA G:ILE55 4.3 17.9 1.0
O G:HOH1210 4.4 26.1 1.0
O G:HOH1117 4.5 29.0 1.0
O G:HOH1113 4.5 21.9 1.0
O G:HOH1035 4.5 23.2 1.0
N G:ILE56 4.6 19.6 1.0
O G:HOH1192 4.6 38.9 1.0
CA G:ILE56 4.8 18.7 1.0
CA G:GLY54 4.8 20.1 1.0
C G:GLY54 4.8 21.1 1.0
CG1 G:ILE56 4.8 16.7 1.0
O G:HOH901 4.8 11.0 0.5
OE2 G:GLU161 4.8 21.1 1.0
CB G:ILE55 4.9 18.5 1.0
O G:LEU411 5.0 18.9 1.0

Magnesium binding site 9 out of 9 in 6mgj

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg801

b:17.1
occ:0.97
 O H:HOH1324 2.1 19.7 1.0
OE2 H:GLU412 2.2 26.2 1.0
OD1 H:ASP410 2.3 27.6 1.0
OD2 H:ASP410 2.4 28.6 1.0
O H:ILE55 2.5 21.8 1.0
O H:HOH1683 2.5 26.8 1.0
CG H:ASP410 2.7 26.6 1.0
O H:HOH1776 2.9 38.6 1.0
CD H:GLU412 3.2 23.3 1.0
C H:ILE55 3.6 20.3 1.0
N H:ILE55 3.9 21.1 1.0
CG H:GLU412 3.9 16.4 1.0
O H:HOH907 4.0 21.3 1.0
OE1 H:GLU412 4.1 26.5 1.0
O H:HOH1139 4.2 25.8 1.0
CB H:ASP410 4.2 23.5 1.0
CA H:ILE55 4.3 18.5 1.0
O H:HOH970 4.3 20.8 1.0
O H:HOH1055 4.4 23.6 1.0
O H:HOH965 4.5 22.4 1.0
N H:ILE56 4.6 19.8 1.0
O H:HOH1597 4.7 34.7 1.0
OE2 H:GLU161 4.7 22.2 1.0
CG1 H:ILE56 4.8 20.6 1.0
CA H:GLY54 4.8 16.9 1.0
C H:GLY54 4.8 19.1 1.0
CA H:ILE56 4.8 20.2 1.0
O H:HOH1326 4.8 29.7 1.0
CB H:ILE55 5.0 19.9 1.0
CE1 H:HIS274 5.0 21.4 1.0

Reference:

G.Arnal, P.J.Stogios, J.Asohan, T.Skarina, A.Savchenko, H.Brumer. Structural Enzymology Reveals the Molecular Basis of Substrate Regiospecificity and Processivity of An Exemplar Bacterial Glycoside Hydrolase Family 74ENDO-Xyloglucanase. Biochem. J. V. 475 3963 2018.
ISSN: ESSN 1470-8728
PubMed: 30463871
DOI: 10.1042/BCJ20180763
Page generated: Tue Oct 1 11:39:10 2024

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