Magnesium in PDB 6j33: Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae

The structure of Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae, PDB code: 6j33 was solved by N.Saka, H.Iwamoto, N.Takahashi, K.Mizutani, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.357, 80.276, 127.741, 96.70, 102.30, 112.10
R / Rfree (%)	12.8 / 15.4

The structure of Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae (pdb code 6j33). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 22 binding sites of Magnesium where determined in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae, PDB code: 6j33:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:20.7 occ:1.00 OE1 A:GLN1070 2.0 27.1 1.0 O A:ASP1003 2.0 22.9 1.0 OD2 A:ASP994 2.1 19.0 1.0 O A:HOH1403 2.1 20.7 1.0 O A:VAL1006 2.1 20.3 1.0 OG A:SER1001 2.2 22.1 1.0 CD A:GLN1070 3.1 28.1 1.0 C A:ASP1003 3.2 22.9 1.0 CG A:ASP994 3.2 18.4 1.0 C A:VAL1006 3.3 19.9 1.0 CB A:SER1001 3.3 21.5 1.0 CB A:ASP994 3.8 18.1 1.0 NE2 A:GLN1070 3.8 27.7 1.0 N A:ASP1003 3.9 23.6 1.0 CA A:ASP1003 4.0 22.5 1.0 CA A:SER1001 4.0 21.7 1.0 N A:SER1004 4.1 23.1 1.0 N A:ASP1007 4.1 20.4 1.0 N A:VAL1006 4.1 23.1 1.0 OD1 A:ASP1007 4.1 23.3 1.0 OD1 A:ASP994 4.2 18.7 1.0 O A:ASP994 4.2 19.6 1.0 CA A:ASP1007 4.2 20.3 1.0 CA A:SER1004 4.2 26.2 1.0 O A:ACT1114 4.3 39.3 1.0 CG A:GLN1070 4.3 26.6 1.0 CA A:VAL1006 4.3 21.7 1.0 CB A:ASP1003 4.4 22.5 1.0 C A:SER1004 4.4 27.1 1.0 C A:SER1001 4.5 22.5 1.0 CB A:GLN1070 4.5 28.1 1.0 N A:LEU1002 4.6 21.7 1.0 N A:ARG1005 4.8 26.8 0.4 N A:ARG1005 4.8 27.5 0.6 O A:SER1004 4.8 28.7 1.0 OXT A:ACT1114 4.8 44.3 1.0 CG2 A:VAL1006 4.9 21.2 1.0 C A:ASP994 4.9 17.9 1.0 C A:ACT1114 5.0 42.5 1.0 CA A:ASP994 5.0 18.8 1.0 CG A:ASP1007 5.0 23.9 1.0

Magnesium binding site 2 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:18.9 occ:1.00 O A:HOH2488 2.1 23.5 1.0 O A:HOH1439 2.1 19.0 1.0 O A:HOH2444 2.1 21.7 1.0 O A:HOH1434 2.1 17.6 1.0 O A:HOH1555 2.1 18.0 1.0 O A:HOH1274 2.1 20.3 1.0 NE A:ARG715 4.0 18.0 1.0 OE1 A:GLU639 4.0 18.8 1.0 OD2 A:ASP714 4.1 21.4 1.0 OE1 A:GLU633 4.2 22.2 1.0 O A:HOH2467 4.3 66.2 1.0 OE1 A:GLN712 4.3 16.3 1.0 NH2 A:ARG715 4.3 17.8 1.0 O A:HOH2273 4.3 20.9 1.0 OD1 A:ASP714 4.3 20.0 1.0 OE2 A:GLU639 4.3 18.4 1.0 OE2 A:GLU633 4.4 22.0 1.0 O A:ASN711 4.5 15.9 0.5 NE2 A:GLN712 4.6 16.9 1.0 CD A:GLU639 4.6 17.8 1.0 CZ A:ARG715 4.6 16.7 1.0 CG A:ASP714 4.7 19.7 1.0 CD A:GLU633 4.7 21.5 1.0 CD A:GLN712 4.8 16.0 1.0 O A:ASN711 4.8 15.9 0.5 CD A:ARG715 5.0 17.8 1.0 ND2 A:ASN711 5.0 23.5 0.5

Magnesium binding site 3 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:29.3 occ:1.00 O A:ASP162 2.3 29.0 1.0 O A:THR150 2.3 24.2 1.0 OD1 A:ASP148 2.5 34.9 1.0 O A:HOH1818 2.5 36.6 1.0 OD1 A:ASP162 2.5 38.2 1.0 OD2 A:ASP148 2.5 37.8 1.0 CG A:ASP148 2.8 36.2 1.0 CG A:ASP162 3.2 37.9 1.0 C A:ASP162 3.3 30.1 1.0 C A:THR150 3.5 23.8 1.0 OD2 A:ASP162 3.7 40.4 1.0 CB A:THR150 3.8 24.6 1.0 CA A:ASP162 3.8 31.4 1.0 O A:HOH2030 4.0 40.4 1.0 CA A:THR150 4.0 24.3 1.0 CB A:ASP162 4.1 34.4 1.0 O A:HOH2477 4.1 46.4 1.0 N A:THR150 4.2 25.9 1.0 O A:HOH1279 4.3 59.4 1.0 NE2 A:GLN48 4.3 46.8 1.0 O A:HOH1370 4.3 25.0 1.0 CB A:ASP148 4.3 35.4 1.0 OE2 A:GLU45 4.4 27.4 1.0 CG2 A:THR150 4.4 24.7 1.0 N A:SER163 4.5 29.6 1.0 N A:VAL151 4.6 23.3 1.0 O A:HOH1232 4.6 59.4 1.0 OG1 A:THR150 4.9 26.1 1.0 CA A:SER163 4.9 28.9 1.0 CA A:VAL151 4.9 24.4 1.0

Magnesium binding site 4 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:38.3 occ:1.00 O A:ALA93 2.2 24.6 1.0 O B:HOH1573 2.3 25.8 1.0 O B:HOH1207 2.3 38.4 1.0 O A:HOH2300 2.3 38.7 1.0 O A:HOH2312 2.4 45.3 1.0 OH A:TYR78 2.8 29.1 1.0 OH B:TYR78 3.3 29.2 1.0 C A:ALA93 3.4 23.8 1.0 CZ A:TYR78 3.9 26.8 1.0 CA A:ALA93 4.1 24.3 1.0 O A:HOH1315 4.1 30.0 1.0 CE1 A:TYR78 4.2 26.2 1.0 O B:HOH1740 4.4 22.5 1.0 N A:ASP94 4.4 23.2 1.0 N A:TRP95 4.4 21.6 1.0 CB A:ALA93 4.6 25.3 1.0 O B:HOH1503 4.6 35.5 1.0 CA A:ASP94 4.6 23.7 1.0 CZ B:TYR78 4.7 26.8 1.0 O B:HOH1285 4.7 41.4 1.0 O B:ALA93 4.7 26.8 1.0 O B:HOH2615 4.8 50.5 1.0 CB B:TRP80 4.8 24.0 1.0 CD1 B:TRP80 4.8 26.3 1.0 C A:ASP94 4.9 21.9 1.0 O A:HOH2360 4.9 40.3 1.0 CG B:TRP80 5.0 25.1 1.0

Magnesium binding site 5 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:11.2 occ:1.00 O A:TYR555 2.3 12.6 1.0 OD1 A:ASP893 2.3 13.8 0.7 O A:HOH1924 2.3 16.4 1.0 O A:HOH1443 2.4 23.4 1.0 OD1 A:ASP553 2.5 13.0 1.0 O A:HOH1759 2.5 13.5 1.0 O A:ALA550 2.5 14.7 1.0 C A:TYR555 3.5 11.7 1.0 CG A:ASP553 3.5 13.1 1.0 CG A:ASP893 3.5 15.2 0.7 C A:ALA550 3.5 13.8 1.0 CA A:ALA550 3.9 13.9 1.0 OD2 A:ASP553 3.9 13.8 1.0 N A:TYR555 4.1 12.6 1.0 OD2 A:ASP893 4.1 17.8 0.7 CA A:TYR555 4.2 12.9 1.0 CB A:ALA550 4.2 15.6 1.0 CB A:TYR555 4.4 13.0 1.0 O A:ASP553 4.5 13.8 1.0 O A:HOH1354 4.5 59.5 1.0 N A:ASN556 4.6 11.7 1.0 CB A:ASP893 4.6 14.4 0.3 ND2 A:ASN556 4.7 15.5 1.0 CB A:ASP893 4.7 14.8 0.7 N A:ASP553 4.7 12.8 1.0 O A:ASP893 4.7 14.4 1.0 C A:ASP553 4.7 13.1 1.0 CA A:ASP893 4.8 13.7 0.7 CB A:ASN556 4.8 13.3 1.0 N A:GLN551 4.8 14.2 1.0 O A:HOH2048 4.8 21.8 1.0 CA A:ASP893 4.8 13.2 0.3 O A:THR484 4.8 19.5 0.8 CB A:ASP553 4.8 12.8 1.0 CA A:ASN556 4.8 13.1 1.0 CA A:ASP553 5.0 12.8 1.0 C A:ASP893 5.0 13.2 1.0

Magnesium binding site 6 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:11.1 occ:1.00 OD1 A:ASP481 2.1 13.3 1.0 O A:HOH1487 2.2 13.9 1.0 O A:HOH1613 2.2 14.2 1.0 O A:LEU482 2.2 18.6 0.5 OE2 A:GLU568 2.2 12.8 1.0 O A:LEU482 2.2 14.5 0.5 OE2 A:GLU487 2.2 13.1 1.0 CD A:GLU568 3.1 13.9 1.0 CD A:GLU487 3.2 13.6 1.0 CG A:ASP481 3.3 12.8 1.0 C A:LEU482 3.3 13.9 0.5 OE1 A:GLU568 3.4 13.3 1.0 C A:LEU482 3.4 15.5 0.5 N A:LEU482 3.5 13.4 0.5 N A:LEU482 3.6 14.1 0.5 CG A:GLU487 3.8 13.6 1.0 CA A:LEU482 4.0 14.0 0.5 OG A:SER388 4.0 14.1 1.0 OD2 A:ASP481 4.0 13.3 1.0 C A:ASP481 4.0 12.6 1.0 CA A:LEU482 4.1 14.6 0.5 OE1 A:GLU487 4.2 13.9 1.0 CA A:ASP481 4.3 12.7 1.0 N A:GLY569 4.3 12.0 1.0 O A:HOH1571 4.3 14.9 1.0 CB A:ASP481 4.3 13.1 1.0 O A:HOH1584 4.4 13.7 1.0 CB A:LEU482 4.4 17.1 0.5 N A:ALA483 4.4 14.0 1.0 CG A:LEU482 4.5 14.5 0.5 CG A:GLU568 4.5 13.2 1.0 O A:VAL485 4.6 15.6 0.8 O A:VAL485 4.6 14.2 0.2 CA A:GLU568 4.7 12.9 1.0 CA A:ALA483 4.8 14.3 1.0 O A:ASP481 4.8 13.3 1.0 CD1 A:LEU482 4.9 15.4 0.5 CB A:LEU482 4.9 16.0 0.5 CB A:GLU568 4.9 12.7 1.0 CG A:LEU482 4.9 16.4 0.5

Magnesium binding site 7 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:38.4 occ:0.43 OE2 A:GLU404 2.2 33.1 0.6 O A:HOH1239 2.2 50.7 1.0 O A:HOH2204 2.7 36.7 1.0 CD A:GLU404 3.1 31.3 0.6 O A:HOH1871 3.1 45.4 1.0 O A:LYS402 3.3 17.4 1.0 CG A:GLU404 3.4 27.4 0.6 N A:GLU404 3.6 19.3 0.6 N A:GLU404 3.6 19.2 0.4 O A:HOH2346 3.7 49.8 1.0 CA A:GLU404 4.0 20.7 0.6 CA A:GLU404 4.0 20.2 0.4 C A:PRO403 4.0 18.7 1.0 OE1 A:GLU404 4.1 32.1 0.6 NZ A:LYS582 4.3 24.2 1.0 CB A:GLU404 4.3 23.2 0.6 CB A:GLU404 4.3 22.3 0.4 O A:HOH1911 4.3 34.6 1.0 CA A:PRO403 4.4 17.1 1.0 C A:LYS402 4.4 15.7 1.0 O A:PRO403 4.5 19.0 1.0 CE A:LYS582 4.6 20.5 1.0 O A:SER399 4.6 18.1 1.0 CG A:GLU404 4.9 26.2 0.4 N A:PRO403 4.9 16.0 1.0 O A:HOH1984 5.0 45.3 1.0

Magnesium binding site 8 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:36.4 occ:0.45 O A:HOH2334 1.9 50.7 1.0 O A:HOH2096 2.1 25.6 1.0 O A:HOH2129 2.1 48.9 1.0 O A:HOH2447 2.3 52.2 1.0 O A:HOH1889 2.8 38.2 1.0 O A:HOH2582 3.5 38.7 1.0 OG A:SER489 3.7 19.0 0.6 O A:HOH1695 4.1 25.4 1.0 O A:HOH1785 4.1 27.4 1.0 O A:HOH1915 4.1 21.3 1.0 O A:HOH1273 4.1 56.3 1.0 O A:THR573 4.2 17.6 1.0 NZ A:LYS448 4.3 16.4 1.0 CB A:SER489 4.5 18.7 0.6 CB A:SER489 4.6 19.9 0.4 CE A:LYS448 4.8 16.4 1.0

Magnesium binding site 9 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


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 Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1109 b:35.7 occ:0.55 O A:THR226 2.3 31.8 1.0 O A:HOH2109 2.3 38.9 1.0 O A:HOH2244 2.4 33.3 1.0 O A:HOH1271 2.9 34.7 1.0 C A:THR226 3.4 31.7 1.0 N A:THR226 3.9 31.0 1.0 O A:ALA244 4.1 25.9 1.0 O A:HOH2580 4.2 56.2 1.0 CA A:THR226 4.2 31.2 1.0 N A:THR227 4.3 32.9 1.0 O A:HOH1424 4.4 34.9 1.0 CA A:THR227 4.5 33.8 1.0 N A:ALA244 4.5 27.8 1.0 C A:PRO225 4.7 31.8 1.0 CB A:PRO225 4.7 32.6 1.0 OG1 A:THR227 4.7 35.9 1.0 CB A:ALA244 4.8 27.4 1.0 CA A:PRO225 4.9 32.0 1.0 C A:ALA244 4.9 25.8 1.0

Magnesium binding site 10 out of 22 in the Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Ligand-Free of Pula From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1110 b:26.3 occ:0.43 O A:HOH2142 2.0 41.0 1.0 O A:HOH1521 2.1 41.6 1.0 O A:HOH1995 2.3 29.5 1.0 N A:ASP902 2.7 15.0 1.0 O A:ASP907 3.0 15.2 1.0 CB A:ASP902 3.4 17.3 1.0 CA A:ASP902 3.5 15.4 1.0 C A:VAL901 3.6 14.8 1.0 CA A:VAL901 3.7 14.5 1.0 CA A:ASN908 3.7 13.0 1.0 O A:ASP902 3.8 15.3 1.0 C A:ASP902 4.0 15.1 1.0 C A:ASN908 4.0 13.4 1.0 C A:ASP907 4.0 14.5 1.0 CG1 A:VAL901 4.1 15.7 1.0 O A:ASN908 4.3 13.3 1.0 N A:ASN908 4.3 14.1 1.0 O A:ARG900 4.5 13.7 1.0 CB A:VAL901 4.5 14.1 1.0 CD2 A:LEU942 4.5 16.4 0.6 N A:ASN909 4.6 13.5 1.0 CB A:LEU881 4.6 14.1 1.0 CD1 A:LEU881 4.7 18.0 1.0 O A:LEU881 4.7 14.3 1.0 CB A:ASN908 4.7 13.3 1.0 N A:VAL901 4.7 13.2 1.0 CG A:ASP902 4.8 18.5 1.0 O A:VAL901 4.8 17.0 1.0 C A:ARG900 5.0 13.1 1.0

N.Saka, D.Malle, H.Iwamoto, N.Takahashi, K.Mizutani, B.Mikami. Relationship Between the Induced-Fit Loop and the Activity of Klebsiella Pneumoniae Pullulanase. Acta Crystallogr D Struct V. 75 792 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31478902
DOI: 10.1107/S2059798319010660