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Magnesium in PDB 6j34: Crystal Structure of Maltotriose-Complex of Pula From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Maltotriose-Complex of Pula From Klebsiella Pneumoniae, PDB code: 6j34 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) 47.15 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.891, 60.119, 133.829, 90.00, 114.69, 90.00
R / Rfree (%) 13 / 16.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Maltotriose-Complex of Pula From Klebsiella Pneumoniae (pdb code 6j34). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Maltotriose-Complex of Pula From Klebsiella Pneumoniae, PDB code: 6j34:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6j34

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Magnesium binding site 1 out of 4 in the Crystal Structure of Maltotriose-Complex 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 Maltotriose-Complex of Pula From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1111

b:18.7
occ:1.00
 O A:ASP1003 2.0 18.8 1.0
OD2 A:ASP994 2.0 19.2 1.0
O A:HOH1433 2.0 18.5 1.0
O A:VAL1006 2.1 18.9 1.0
OE1 A:GLN1070 2.1 21.6 1.0
OG A:SER1001 2.2 20.4 1.0
C A:ASP1003 3.2 18.5 1.0
CG A:ASP994 3.2 21.2 1.0
CD A:GLN1070 3.2 21.6 1.0
C A:VAL1006 3.3 18.0 1.0
CB A:SER1001 3.3 20.7 1.0
NE2 A:GLN1070 3.8 24.4 1.0
CB A:ASP994 3.8 18.3 1.0
N A:ASP1003 3.8 18.1 1.0
CA A:ASP1003 4.0 18.0 1.0
CA A:SER1001 4.0 18.4 1.0
N A:VAL1006 4.1 19.5 1.0
N A:ASP1007 4.1 18.0 1.0
N A:SER1004 4.1 20.1 1.0
OD1 A:ASP994 4.1 18.4 1.0
OD1 A:ASP1007 4.2 22.5 1.0
CA A:ASP1007 4.2 19.9 1.0
O A:ASP994 4.2 20.5 1.0
CA A:SER1004 4.3 19.4 1.0
O A:HOH1276 4.3 27.9 1.0
CA A:VAL1006 4.3 18.9 1.0
CB A:ASP1003 4.3 18.8 1.0
CG A:GLN1070 4.4 21.7 1.0
C A:SER1001 4.4 20.5 1.0
C A:SER1004 4.5 19.2 1.0
N A:LEU1002 4.5 19.0 1.0
CB A:GLN1070 4.6 22.2 1.0
N A:ARG1005 4.8 19.1 1.0
CG2 A:VAL1006 4.8 20.9 1.0
O A:SER1004 4.8 20.4 1.0
C A:ASP994 5.0 18.8 1.0

Magnesium binding site 2 out of 4 in 6j34

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Magnesium binding site 2 out of 4 in the Crystal Structure of Maltotriose-Complex 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 Maltotriose-Complex of Pula From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1112

b:14.6
occ:1.00
 O A:HOH1657 2.3 20.7 1.0
O A:TYR555 2.4 17.1 1.0
O A:HOH1684 2.4 28.8 1.0
OD1 A:ASP553 2.4 18.4 1.0
OD1 A:ASP893 2.4 18.1 0.6
O A:ALA550 2.5 20.2 1.0
O A:HOH1549 2.5 18.4 1.0
CG A:ASP553 3.5 18.3 1.0
C A:ALA550 3.5 19.5 1.0
C A:TYR555 3.5 15.1 1.0
CG A:ASP893 3.6 16.9 0.6
CA A:ALA550 3.9 18.6 1.0
OD2 A:ASP553 3.9 18.1 1.0
N A:TYR555 4.1 17.2 1.0
OD2 A:ASP893 4.2 21.3 0.6
CA A:TYR555 4.2 15.8 1.0
CB A:ALA550 4.2 19.1 1.0
O A:HOH1308 4.4 66.6 1.0
CB A:TYR555 4.4 16.6 1.0
O A:ASP553 4.5 19.4 1.0
CB A:ASP893 4.6 18.3 0.4
N A:ASN556 4.6 15.7 1.0
ND2 A:ASN556 4.6 16.6 1.0
N A:ASP553 4.7 17.6 1.0
N A:GLN551 4.7 18.5 1.0
O A:ASP893 4.7 18.3 0.6
C A:ASP553 4.7 18.6 1.0
O A:ASP893 4.7 18.1 0.4
CB A:ASN556 4.7 16.3 1.0
O A:THR484 4.8 20.9 1.0
CA A:ASP893 4.8 17.7 0.4
CB A:ASP553 4.8 17.2 1.0
CB A:ASP893 4.8 17.9 0.6
CA A:ASP893 4.8 17.4 0.6
O A:HOH1688 4.8 28.6 1.0
CA A:ASN556 4.9 15.3 1.0
CA A:ASP553 4.9 17.0 1.0

Magnesium binding site 3 out of 4 in 6j34

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Magnesium binding site 3 out of 4 in the Crystal Structure of Maltotriose-Complex 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 Maltotriose-Complex of Pula From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1113

b:13.7
occ:1.00
 OD1 A:ASP481 2.1 16.8 1.0
O A:HOH1378 2.2 17.5 1.0
O A:HOH1510 2.2 18.6 1.0
OE2 A:GLU487 2.2 17.9 1.0
OE2 A:GLU568 2.2 16.7 1.0
O A:LEU482 2.3 17.2 1.0
CD A:GLU568 3.1 17.9 1.0
CD A:GLU487 3.2 18.6 1.0
CG A:ASP481 3.3 16.2 1.0
OE1 A:GLU568 3.3 18.9 1.0
C A:LEU482 3.4 17.6 1.0
N A:LEU482 3.7 17.0 1.0
CG A:GLU487 3.8 18.2 1.0
OG A:SER388 4.0 18.2 1.0
OD2 A:ASP481 4.1 16.6 1.0
C A:ASP481 4.1 16.1 1.0
OE1 A:GLU487 4.1 19.7 1.0
CA A:LEU482 4.2 16.6 1.0
CA A:ASP481 4.3 14.1 1.0
N A:GLY569 4.3 15.7 1.0
O A:HOH1490 4.3 16.8 1.0
CB A:ASP481 4.4 15.5 1.0
O A:HOH1428 4.4 18.9 1.0
N A:ALA483 4.5 16.1 1.0
CG A:GLU568 4.5 17.7 1.0
CG A:LEU482 4.6 20.2 1.0
O A:VAL485 4.6 18.5 1.0
CA A:ALA483 4.7 16.6 1.0
CA A:GLU568 4.7 14.9 1.0
O A:ASP481 4.8 16.7 1.0
CB A:GLU568 4.9 16.1 1.0
CB A:LEU482 4.9 19.2 1.0
CD1 A:LEU482 5.0 21.5 1.0

Magnesium binding site 4 out of 4 in 6j34

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Magnesium binding site 4 out of 4 in the Crystal Structure of Maltotriose-Complex 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 Maltotriose-Complex of Pula From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1114

b:26.4
occ:1.00
 O A:HOH1282 2.0 24.3 1.0
O A:HOH2229 2.1 26.6 1.0
O A:HOH1256 2.1 25.8 1.0
O A:HOH1304 2.1 23.5 1.0
O A:HOH2222 2.3 29.2 1.0
O A:HOH1317 2.3 21.8 1.0
OD2 A:ASP714 4.0 28.8 1.0
NE A:ARG715 4.0 22.4 1.0
OE1 A:GLU633 4.1 29.7 1.0
O A:HOH2148 4.2 62.5 1.0
OE1 A:GLU639 4.2 24.9 1.0
OD1 A:ASP714 4.3 26.6 1.0
OE2 A:GLU633 4.3 30.3 1.0
O A:HOH2213 4.3 53.9 1.0
OE1 A:GLN712 4.3 22.8 1.0
NH2 A:ARG715 4.3 23.4 1.0
OE2 A:GLU639 4.4 24.6 1.0
O A:HOH2087 4.4 24.0 1.0
CG A:ASP714 4.6 24.5 1.0
CD A:GLU633 4.6 30.2 1.0
O A:ASN711 4.6 23.7 0.6
CZ A:ARG715 4.7 23.0 1.0
O A:HOH2249 4.7 74.8 1.0
NE2 A:GLN712 4.7 21.8 1.0
CD A:GLU639 4.7 24.4 1.0
O A:ASN711 4.9 22.7 0.4
CD A:GLN712 4.9 22.1 1.0
CD A:ARG715 5.0 22.9 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 04:32:43 2024

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