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Magnesium in PDB 6j35: Crystal Structure of Ligand-Free of Pula-G680L Mutant From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Ligand-Free of Pula-G680L Mutant From Klebsiella Pneumoniae, PDB code: 6j35 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) 38.72 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.159, 80.203, 127.301, 94.92, 103.01, 112.03
R / Rfree (%) 16.4 / 19

Other elements in 6j35:

The structure of Crystal Structure of Ligand-Free of Pula-G680L Mutant From Klebsiella Pneumoniae also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ligand-Free of Pula-G680L Mutant From Klebsiella Pneumoniae (pdb code 6j35). 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 Ligand-Free of Pula-G680L Mutant From Klebsiella Pneumoniae, PDB code: 6j35:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6j35

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Magnesium binding site 1 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:11.3
occ:1.00
 OD1 A:ASP481 2.3 14.4 1.0
OE2 A:GLU487 2.3 15.3 1.0
O A:HOH1342 2.3 14.3 1.0
O A:LEU482 2.3 18.1 1.0
O A:HOH1492 2.4 14.6 1.0
OE2 A:GLU568 2.4 15.2 1.0
CD A:GLU568 3.2 16.3 1.0
CD A:GLU487 3.2 17.3 1.0
OE1 A:GLU568 3.4 16.3 1.0
CG A:ASP481 3.5 16.8 1.0
C A:LEU482 3.5 15.3 1.0
N A:LEU482 3.6 16.6 1.0
CG A:GLU487 3.9 15.4 1.0
OG A:SER388 4.0 13.7 1.0
C A:ASP481 4.1 15.1 1.0
CA A:LEU482 4.1 17.2 1.0
OD2 A:ASP481 4.2 14.3 1.0
OE1 A:GLU487 4.2 15.3 1.0
O A:HOH1305 4.2 17.0 1.0
CA A:ASP481 4.3 13.6 1.0
O A:HOH1581 4.3 18.6 1.0
N A:GLY569 4.4 16.0 1.0
CG A:LEU482 4.4 16.1 1.0
CB A:ASP481 4.5 14.0 1.0
N A:ALA483 4.6 15.3 1.0
O A:VAL485 4.6 13.2 1.0
CG A:GLU568 4.6 14.8 1.0
CA A:GLU568 4.8 13.8 1.0
O A:ASP481 4.8 16.2 1.0
CA A:ALA483 4.8 16.4 1.0
CB A:LEU482 4.9 18.2 1.0
CD1 A:LEU482 5.0 18.9 1.0

Magnesium binding site 2 out of 9 in 6j35

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Magnesium binding site 2 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:11.0
occ:1.00
 OD1 A:ASP553 2.3 15.3 1.0
O A:HOH1600 2.3 17.0 1.0
O A:TYR555 2.4 15.1 1.0
OD1 A:ASP893 2.4 23.1 1.0
O A:ALA550 2.4 18.4 1.0
O A:HOH1456 2.5 15.1 1.0
O A:HOH1709 2.6 19.2 1.0
CG A:ASP553 3.4 17.4 1.0
C A:ALA550 3.5 16.3 1.0
C A:TYR555 3.5 12.6 1.0
CG A:ASP893 3.6 20.8 1.0
OD2 A:ASP553 3.8 15.3 1.0
CA A:ALA550 3.9 17.9 1.0
OD2 A:ASP893 4.1 19.8 1.0
N A:TYR555 4.1 15.1 1.0
CA A:TYR555 4.2 14.3 1.0
CB A:ALA550 4.2 16.1 1.0
O A:ASP553 4.3 14.8 1.0
CB A:TYR555 4.4 15.4 1.0
N A:ASN556 4.6 16.9 1.0
N A:ASP553 4.7 11.5 1.0
N A:GLN551 4.7 17.7 1.0
ND2 A:ASN556 4.7 18.0 1.0
C A:ASP553 4.7 14.6 1.0
CB A:ASP553 4.7 12.9 1.0
CB A:ASP893 4.8 16.1 1.0
CB A:ASN556 4.8 14.3 1.0
O A:ASP893 4.8 13.6 1.0
CA A:ASP893 4.8 15.8 1.0
O A:HOH1771 4.8 22.4 1.0
O A:THR484 4.9 25.2 1.0
CA A:ASN556 4.9 14.2 1.0
CA A:ASP553 4.9 12.4 1.0

Magnesium binding site 3 out of 9 in 6j35

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Magnesium binding site 3 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:20.7
occ:1.00
 O A:HOH1443 2.1 17.4 1.0
O A:ASP1003 2.1 20.0 1.0
OE1 A:GLN1070 2.1 20.1 1.0
OD2 A:ASP994 2.1 17.6 1.0
O A:VAL1006 2.2 18.1 1.0
OG A:SER1001 2.3 19.0 1.0
CD A:GLN1070 3.2 21.3 1.0
CG A:ASP994 3.2 18.4 1.0
C A:ASP1003 3.2 17.8 1.0
C A:VAL1006 3.3 19.8 1.0
CB A:SER1001 3.4 17.5 1.0
CB A:ASP994 3.8 20.4 1.0
N A:ASP1003 3.8 18.9 1.0
NE2 A:GLN1070 3.8 21.4 1.0
CA A:ASP1003 4.0 19.3 1.0
CA A:SER1001 4.0 16.0 1.0
OD1 A:ASP1007 4.1 19.3 1.0
N A:SER1004 4.2 18.6 1.0
N A:VAL1006 4.2 17.8 1.0
O A:ASP994 4.2 18.7 1.0
N A:ASP1007 4.2 18.6 1.0
OD1 A:ASP994 4.2 18.6 1.0
CA A:ASP1007 4.2 19.8 1.0
CA A:SER1004 4.3 20.7 1.0
O A:HOH1274 4.3 30.0 1.0
CB A:ASP1003 4.3 17.3 1.0
CG A:GLN1070 4.3 20.0 1.0
CA A:VAL1006 4.4 18.6 1.0
C A:SER1001 4.5 19.7 1.0
C A:SER1004 4.5 19.7 1.0
N A:LEU1002 4.5 18.8 1.0
CB A:GLN1070 4.6 18.1 1.0
N A:ARG1005 4.8 18.9 1.0
O A:SER1004 4.8 18.6 1.0
C A:ASP994 4.9 20.1 1.0
CG2 A:VAL1006 4.9 16.9 1.0
CA A:ASP994 5.0 16.4 1.0

Magnesium binding site 4 out of 9 in 6j35

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Magnesium binding site 4 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:28.3
occ:1.00
 O A:HOH1845 2.0 25.6 1.0
O A:HOH1886 2.1 27.1 1.0
O A:HOH1253 2.1 22.2 1.0
O A:HOH1270 2.2 26.3 1.0
O A:HOH1259 2.2 23.3 1.0
O A:HOH1245 2.2 23.6 1.0
NE A:ARG715 4.0 19.5 1.0
OE1 A:GLU639 4.1 21.9 1.0
NH2 A:ARG715 4.1 21.5 1.0
OD1 A:ASP714 4.1 24.6 1.0
OD2 A:ASP714 4.2 23.6 1.0
OE1 A:GLN712 4.2 24.3 1.0
OE1 A:GLU633 4.2 22.5 1.0
OE2 A:GLU639 4.3 22.8 1.0
O A:HOH1366 4.4 30.0 1.0
NE2 A:GLN712 4.4 28.3 1.0
OE2 A:GLU633 4.5 21.5 1.0
O A:ASN711 4.5 28.1 1.0
CZ A:ARG715 4.5 20.2 1.0
CG A:ASP714 4.6 25.1 1.0
CD A:GLU639 4.6 22.3 1.0
CD A:GLN712 4.7 26.3 1.0
ND2 A:ASN711 4.7 38.7 1.0
CD A:GLU633 4.8 24.0 1.0

Magnesium binding site 5 out of 9 in 6j35

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Magnesium binding site 5 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:32.4
occ:1.00
 O A:HOH1312 2.2 30.0 1.0
O A:THR150 2.3 31.8 1.0
O A:ASP162 2.4 31.1 1.0
OD1 A:ASP148 2.4 33.7 1.0
OD2 A:ASP148 2.5 35.4 1.0
OD1 A:ASP162 2.7 35.7 1.0
CG A:ASP148 2.7 37.1 1.0
CG A:ASP162 3.4 35.2 1.0
C A:THR150 3.4 37.2 1.0
C A:ASP162 3.5 32.6 1.0
CB A:THR150 3.5 36.0 1.0
CA A:THR150 3.9 34.8 1.0
OD2 A:ASP162 3.9 37.9 1.0
O A:HOH1683 3.9 30.0 1.0
CA A:ASP162 4.0 31.5 1.0
N A:THR150 4.1 32.9 1.0
CB A:ASP148 4.2 35.4 1.0
OE2 A:GLU45 4.3 35.1 1.0
CB A:ASP162 4.3 33.5 1.0
CG2 A:THR150 4.3 33.0 1.0
O A:HOH1233 4.4 28.3 1.0
NE2 A:GLN48 4.4 39.6 1.0
OG1 A:THR150 4.5 35.4 1.0
N A:SER163 4.6 31.2 1.0
N A:VAL151 4.6 34.2 1.0
CA A:SER163 4.9 28.1 1.0

Magnesium binding site 6 out of 9 in 6j35

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Magnesium binding site 6 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:11.0
occ:1.00
 O B:HOH1673 2.3 17.1 1.0
O B:TYR555 2.4 15.1 1.0
OD1 B:ASP553 2.4 16.4 1.0
OD1 B:ASP893 2.4 23.6 1.0
O B:HOH1565 2.5 13.5 1.0
O B:ALA550 2.5 15.5 1.0
O B:HOH1743 2.5 18.0 1.0
CG B:ASP553 3.5 16.3 1.0
C B:TYR555 3.5 13.6 1.0
C B:ALA550 3.5 18.3 1.0
CG B:ASP893 3.6 19.3 1.0
OD2 B:ASP553 3.9 14.1 1.0
CA B:ALA550 3.9 16.9 1.0
N B:TYR555 4.1 13.2 1.0
OD2 B:ASP893 4.1 18.6 1.0
CA B:TYR555 4.2 11.9 1.0
CB B:ALA550 4.3 15.5 1.0
O B:ASP553 4.3 14.2 1.0
CB B:TYR555 4.4 15.0 1.0
N B:ASN556 4.6 14.2 1.0
O B:HOH1608 4.6 30.0 1.0
ND2 B:ASN556 4.6 15.6 1.0
N B:ASP553 4.7 14.6 1.0
C B:ASP553 4.7 14.4 1.0
N B:GLN551 4.7 18.1 1.0
O B:ASP893 4.7 15.7 1.0
O B:THR484 4.7 22.2 1.0
CB B:ASP553 4.8 13.4 1.0
CB B:ASN556 4.8 13.8 1.0
CB B:ASP893 4.8 15.8 1.0
CA B:ASP893 4.8 14.5 1.0
CA B:ASN556 4.9 16.3 1.0
O B:HOH1584 4.9 20.6 1.0
CA B:ASP553 4.9 12.2 1.0

Magnesium binding site 7 out of 9 in 6j35

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Magnesium binding site 7 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:18.8
occ:1.00
 OD2 B:ASP994 2.0 15.5 1.0
O B:ASP1003 2.0 17.3 1.0
O B:HOH1346 2.1 17.2 1.0
OE1 B:GLN1070 2.1 20.3 1.0
O B:VAL1006 2.1 18.4 1.0
OG B:SER1001 2.2 15.5 1.0
CG B:ASP994 3.1 16.1 1.0
C B:ASP1003 3.2 17.1 1.0
CD B:GLN1070 3.2 22.4 1.0
C B:VAL1006 3.3 20.6 1.0
CB B:SER1001 3.3 18.6 1.0
CB B:ASP994 3.8 19.8 1.0
N B:ASP1003 3.8 16.1 1.0
NE2 B:GLN1070 3.8 22.1 1.0
CA B:ASP1003 3.9 17.6 1.0
CA B:SER1001 4.0 16.7 1.0
O B:ASP994 4.1 17.6 1.0
N B:VAL1006 4.1 18.7 1.0
OD1 B:ASP994 4.1 17.6 1.0
N B:ASP1007 4.2 17.7 1.0
N B:SER1004 4.2 18.4 1.0
OD1 B:ASP1007 4.2 18.5 1.0
O B:HOH1271 4.2 30.0 1.0
CA B:ASP1007 4.2 18.5 1.0
CB B:ASP1003 4.3 17.3 1.0
CA B:SER1004 4.3 21.5 1.0
CA B:VAL1006 4.3 18.6 1.0
CG B:GLN1070 4.4 19.9 1.0
C B:SER1001 4.5 20.9 1.0
N B:LEU1002 4.5 19.2 1.0
C B:SER1004 4.5 18.6 1.0
CB B:GLN1070 4.6 19.1 1.0
O B:SER1004 4.8 18.4 1.0
C B:ASP994 4.9 17.6 1.0
N B:ARG1005 4.9 18.9 1.0
CG2 B:VAL1006 4.9 20.5 1.0
CA B:ASP994 4.9 16.0 1.0
C B:LEU1002 5.0 18.5 1.0

Magnesium binding site 8 out of 9 in 6j35

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Magnesium binding site 8 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:26.5
occ:1.00
 O B:THR150 2.2 25.4 1.0
O B:ASP162 2.3 30.0 1.0
O B:HOH1823 2.4 24.7 1.0
OD1 B:ASP148 2.5 25.4 1.0
OD1 B:ASP162 2.5 30.0 1.0
OD2 B:ASP148 2.6 25.6 1.0
CG B:ASP148 2.9 28.4 1.0
CG B:ASP162 3.3 33.6 1.0
C B:THR150 3.3 27.1 1.0
C B:ASP162 3.3 30.4 1.0
CB B:THR150 3.6 28.0 1.0
CA B:ASP162 3.9 30.0 1.0
CA B:THR150 3.9 29.3 1.0
OD2 B:ASP162 3.9 33.3 1.0
O B:HOH1931 4.0 30.0 1.0
O B:HOH1574 4.1 30.0 1.0
N B:THR150 4.1 26.4 1.0
CB B:ASP162 4.2 32.0 1.0
CG2 B:THR150 4.2 27.4 1.0
O B:HOH1224 4.2 30.0 1.0
OE2 B:GLU45 4.4 27.0 1.0
CB B:ASP148 4.4 23.7 1.0
N B:VAL151 4.4 27.1 1.0
N B:SER163 4.5 28.7 1.0
OG1 B:THR150 4.7 27.6 1.0
CA B:VAL151 4.8 25.5 1.0
CA B:SER163 4.9 28.5 1.0
OE1 B:GLN48 4.9 34.6 1.0

Magnesium binding site 9 out of 9 in 6j35

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Magnesium binding site 9 out of 9 in the Crystal Structure of Ligand-Free of Pula-G680L Mutant 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-G680L Mutant From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:26.3
occ:1.00
 O B:HOH1333 2.1 26.0 1.0
O B:HOH1256 2.1 19.4 1.0
O B:HOH1677 2.1 23.9 1.0
O B:HOH1332 2.2 24.4 1.0
O B:HOH1966 2.2 24.0 1.0
O B:HOH1328 2.2 24.3 1.0
OE1 B:GLU639 4.0 19.8 1.0
OE1 B:GLU633 4.1 20.5 1.0
NE B:ARG715 4.1 19.2 1.0
OE2 B:GLU639 4.1 19.6 1.0
NH2 B:ARG715 4.2 18.6 1.0
O B:HOH1713 4.2 30.0 1.0
OD1 B:ASP714 4.2 26.1 1.0
NE2 B:GLN712 4.2 22.1 1.0
OD2 B:ASP714 4.3 25.6 1.0
ND2 B:ASN711 4.3 42.5 1.0
OE2 B:GLU633 4.5 19.5 1.0
CD B:GLU639 4.5 20.7 1.0
OE1 B:GLN712 4.5 32.2 1.0
O B:ASN711 4.6 29.9 1.0
CZ B:ARG715 4.7 19.8 1.0
CG B:ASP714 4.7 24.1 1.0
CD B:GLU633 4.7 22.3 1.0
CD B:GLN712 4.8 27.7 1.0

Reference:

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
Page generated: Tue Oct 1 04:32:50 2024

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