Magnesium in PDB 7tm9: Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae, PDB code: 7tm9 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) 46.09 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.95, 240.6, 101.479, 90, 105.13, 90
R / Rfree (%) 17.2 / 21.1

Other elements in 7tm9:

The structure of Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae also contains other interesting chemical elements:

Zinc (Zn) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae (pdb code 7tm9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae, PDB code: 7tm9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7tm9

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Magnesium binding site 1 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:14.0
occ:1.00
 OE2 A:GLU337 2.0 6.7 1.0
O A:HOH601 2.1 9.9 1.0
OD2 A:ASP66 2.1 9.3 1.0
OG1 A:THR170 2.2 6.2 1.0
O A:HOH641 2.2 10.3 1.0
O A:HOH734 2.3 11.8 1.0
CD A:GLU337 3.0 10.5 1.0
CB A:THR170 3.1 7.1 1.0
CG A:ASP66 3.2 13.8 1.0
OE1 A:GLU337 3.4 11.6 1.0
OD2 A:ASP168 3.5 15.8 1.0
CB A:ASP66 3.7 9.3 1.0
N A:THR170 4.0 9.0 1.0
CG2 A:THR170 4.1 8.4 1.0
O A:HOH630 4.2 17.4 1.0
CA A:THR170 4.2 8.1 1.0
OD1 A:ASP66 4.2 13.8 1.0
O A:HOH649 4.3 8.8 1.0
CG A:GLU337 4.4 4.5 1.0
CB A:ALA339 4.4 13.9 1.0
OG A:SEP117 4.4 23.9 1.0
O3P A:SEP117 4.5 25.2 1.0
CG A:ASP168 4.5 15.6 1.0
ZN A:ZN502 4.6 34.7 1.0
CB A:SEP117 4.7 14.0 1.0
CA A:ALA339 4.7 8.1 1.0
O A:ALA339 4.7 16.7 1.0
OD2 A:ASP384 4.8 10.6 1.0
CD A:PRO171 5.0 9.9 1.0

Magnesium binding site 2 out of 8 in 7tm9

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Magnesium binding site 2 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:10.7
occ:1.00
 OE2 B:GLU337 1.9 11.1 1.0
OD2 B:ASP66 2.0 9.8 1.0
OG1 B:THR170 2.0 4.2 1.0
O B:HOH981 2.2 8.1 1.0
O B:HOH1069 2.2 6.7 1.0
O B:HOH1122 2.4 9.1 1.0
CD B:GLU337 3.0 10.4 1.0
CG B:ASP66 3.1 9.4 1.0
CB B:THR170 3.1 7.3 1.0
OE1 B:GLU337 3.4 5.2 1.0
CB B:ASP66 3.7 9.6 1.0
OD2 B:ASP168 3.9 12.8 1.0
CG2 B:THR170 4.0 4.1 1.0
N B:THR170 4.1 4.8 1.0
OD1 B:ASP66 4.1 11.8 1.0
CA B:THR170 4.2 4.2 1.0
O B:HOH1092 4.2 6.9 1.0
CG B:GLU337 4.3 8.9 1.0
O B:HOH988 4.3 14.4 1.0
OG B:SEP117 4.4 27.2 1.0
ZN B:ZN502 4.5 32.9 1.0
CB B:ALA339 4.5 11.9 1.0
OD2 B:ASP384 4.6 10.6 1.0
CB B:SEP117 4.6 11.0 1.0
O B:ALA339 4.7 9.7 1.0
O2P B:SEP117 4.7 15.3 1.0
CA B:ALA339 4.7 10.7 1.0
CG B:ASP168 4.8 12.7 1.0
CA B:ASP66 5.0 10.7 1.0

Magnesium binding site 3 out of 8 in 7tm9

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Magnesium binding site 3 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:8.2
occ:1.00
 OD2 C:ASP66 2.0 10.6 1.0
OE2 C:GLU337 2.1 11.7 1.0
O C:HOH872 2.2 6.6 1.0
OG1 C:THR170 2.2 7.6 1.0
O C:HOH704 2.2 9.6 1.0
O C:HOH706 2.3 8.7 1.0
CG C:ASP66 3.0 18.8 1.0
CD C:GLU337 3.1 9.8 1.0
CB C:THR170 3.2 8.4 1.0
OE1 C:GLU337 3.5 9.1 1.0
CB C:ASP66 3.7 11.0 1.0
OD2 C:ASP168 3.9 14.2 1.0
OD1 C:ASP66 4.1 22.4 1.0
O C:HOH610 4.1 19.4 1.0
CG2 C:THR170 4.1 4.9 1.0
N C:THR170 4.2 6.3 1.0
CA C:THR170 4.3 8.1 1.0
CG C:GLU337 4.4 5.2 1.0
O C:HOH658 4.4 6.0 1.0
ZN C:ZN502 4.4 39.1 1.0
OD2 C:ASP384 4.5 12.3 1.0
O3P C:SEP117 4.5 21.1 1.0
OG C:SEP117 4.5 31.0 1.0
CB C:ALA339 4.6 13.6 1.0
CB C:SEP117 4.6 14.0 1.0
CG C:ASP168 4.7 13.0 1.0
O C:ALA339 4.7 13.9 1.0
CA C:ALA339 4.8 11.6 1.0
CA C:ASP66 5.0 10.9 1.0

Magnesium binding site 4 out of 8 in 7tm9

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Magnesium binding site 4 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:8.3
occ:1.00
 OE2 D:GLU337 2.0 7.9 1.0
OD2 D:ASP66 2.1 10.5 1.0
O D:HOH726 2.2 7.1 1.0
O D:HOH684 2.2 8.8 1.0
OG1 D:THR170 2.2 7.3 1.0
O D:HOH647 2.2 9.3 1.0
CD D:GLU337 3.0 8.8 1.0
CG D:ASP66 3.2 15.3 1.0
CB D:THR170 3.2 8.8 1.0
OE1 D:GLU337 3.4 8.2 1.0
CB D:ASP66 3.7 10.9 1.0
OD2 D:ASP168 3.8 19.3 1.0
N D:THR170 4.1 3.7 1.0
CG2 D:THR170 4.2 8.1 1.0
OD1 D:ASP66 4.2 10.6 1.0
CA D:THR170 4.3 7.8 1.0
O D:HOH662 4.3 16.3 1.0
CG D:GLU337 4.4 5.5 1.0
O D:HOH711 4.4 8.8 1.0
O3P D:SEP117 4.4 14.3 1.0
OG D:SEP117 4.5 22.4 1.0
CB D:ALA339 4.5 8.3 1.0
ZN D:ZN502 4.6 33.3 1.0
CG D:ASP168 4.6 19.9 1.0
CB D:SEP117 4.6 10.5 1.0
O D:ALA339 4.6 14.2 1.0
CA D:ALA339 4.7 11.7 1.0
OD2 D:ASP384 4.7 8.3 1.0

Magnesium binding site 5 out of 8 in 7tm9

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Magnesium binding site 5 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:7.2
occ:1.00
 OD2 E:ASP66 2.0 6.8 1.0
OE2 E:GLU337 2.1 6.6 1.0
OG1 E:THR170 2.1 6.3 1.0
O E:HOH685 2.2 11.2 1.0
O E:HOH845 2.2 12.6 1.0
O E:HOH644 2.3 6.9 1.0
CG E:ASP66 3.0 7.8 1.0
CD E:GLU337 3.1 8.8 1.0
CB E:THR170 3.2 6.3 1.0
OE1 E:GLU337 3.5 9.4 1.0
CB E:ASP66 3.7 8.6 1.0
OD2 E:ASP168 3.8 13.9 1.0
OD1 E:ASP66 4.1 8.2 1.0
N E:THR170 4.1 7.8 1.0
CG2 E:THR170 4.1 5.9 1.0
O E:HOH604 4.2 20.1 1.0
OG E:SEP117 4.2 15.4 1.0
CA E:THR170 4.3 4.9 1.0
O E:HOH713 4.3 5.6 1.0
CB E:SEP117 4.4 5.9 1.0
CG E:GLU337 4.4 5.8 1.0
O2P E:SEP117 4.5 21.1 1.0
CB E:ALA339 4.5 10.0 1.0
ZN E:ZN502 4.5 31.9 1.0
CG E:ASP168 4.7 15.6 1.0
OD2 E:ASP384 4.7 8.9 1.0
O E:ALA339 4.7 15.4 1.0
CA E:ALA339 4.8 12.0 1.0
P E:SEP117 4.9 25.8 1.0
CA E:ASP66 5.0 9.5 1.0

Magnesium binding site 6 out of 8 in 7tm9

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Magnesium binding site 6 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:13.1
occ:1.00
 OE2 F:GLU337 1.9 12.8 1.0
OG1 F:THR170 2.1 7.3 1.0
O F:HOH652 2.1 9.5 1.0
O F:HOH644 2.2 13.1 1.0
OD2 F:ASP66 2.2 11.1 1.0
O F:HOH756 2.3 12.3 1.0
CD F:GLU337 3.0 13.7 1.0
CB F:THR170 3.1 9.1 1.0
CG F:ASP66 3.2 14.5 1.0
OE1 F:GLU337 3.5 12.8 1.0
OD2 F:ASP168 3.7 9.6 1.0
CB F:ASP66 3.8 11.1 1.0
N F:THR170 4.0 5.0 1.0
CG2 F:THR170 4.1 8.7 1.0
O F:HOH656 4.1 16.3 1.0
CA F:THR170 4.2 6.3 1.0
O F:HOH730 4.2 11.6 1.0
OD1 F:ASP66 4.2 19.1 1.0
CG F:GLU337 4.3 11.2 1.0
CB F:ALA339 4.4 14.5 1.0
OG F:SEP117 4.5 22.4 1.0
O1P F:SEP117 4.5 20.4 1.0
CG F:ASP168 4.6 9.0 1.0
CB F:SEP117 4.6 10.6 1.0
ZN F:ZN502 4.6 37.1 1.0
O F:ALA339 4.7 15.1 1.0
CA F:ALA339 4.7 14.5 1.0
OD2 F:ASP384 4.7 16.2 1.0

Magnesium binding site 7 out of 8 in 7tm9

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Magnesium binding site 7 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg503

b:8.5
occ:1.00
 OE2 G:GLU337 1.9 7.9 1.0
OD2 G:ASP66 2.1 8.8 1.0
OG1 G:THR170 2.1 7.2 1.0
O G:HOH859 2.2 8.8 1.0
O G:HOH678 2.3 8.6 1.0
O G:HOH630 2.5 10.5 1.0
CD G:GLU337 2.9 7.3 1.0
CB G:THR170 3.0 5.3 1.0
CG G:ASP66 3.1 13.4 1.0
OE1 G:GLU337 3.3 9.3 1.0
CB G:ASP66 3.7 6.8 1.0
CG2 G:THR170 3.9 6.5 1.0
OD2 G:ASP168 4.0 7.8 1.0
N G:THR170 4.1 5.0 1.0
OD1 G:ASP66 4.2 12.2 1.0
CG G:GLU337 4.2 7.0 1.0
CA G:THR170 4.2 6.0 1.0
O G:HOH740 4.3 3.5 1.0
OG G:SEP117 4.4 19.4 1.0
O G:HOH628 4.4 12.5 1.0
O3P G:SEP117 4.5 13.9 1.0
CB G:ALA339 4.6 12.4 1.0
ZN G:ZN502 4.6 30.1 1.0
CB G:SEP117 4.6 12.8 1.0
O G:ALA339 4.7 13.3 1.0
CA G:ALA339 4.7 8.8 1.0
OD2 G:ASP384 4.8 11.7 1.0
CG G:ASP168 4.8 10.9 1.0
CA G:ASP66 5.0 6.7 1.0

Magnesium binding site 8 out of 8 in 7tm9

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Magnesium binding site 8 out of 8 in the Crystal Structure of Bacterial Alkaline Phosphatase 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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg503

b:12.1
occ:1.00
 OE2 H:GLU337 2.1 10.4 1.0
OD2 H:ASP66 2.1 12.4 1.0
OG1 H:THR170 2.1 7.9 1.0
O H:HOH637 2.1 9.2 1.0
O H:HOH611 2.2 12.2 1.0
O H:HOH833 2.2 13.5 1.0
CB H:THR170 3.1 6.9 1.0
CD H:GLU337 3.1 8.5 1.0
CG H:ASP66 3.2 17.5 1.0
OE1 H:GLU337 3.6 5.9 1.0
OD2 H:ASP168 3.6 20.7 1.0
CB H:ASP66 3.8 17.5 1.0
CG2 H:THR170 4.0 5.6 1.0
O H:HOH657 4.0 23.0 1.0
N H:THR170 4.1 9.7 1.0
OD1 H:ASP66 4.2 17.5 1.0
O H:HOH702 4.2 7.9 1.0
CA H:THR170 4.2 4.6 1.0
OG H:SEP117 4.3 21.0 1.0
CG H:GLU337 4.4 6.2 1.0
O1P H:SEP117 4.5 14.6 1.0
CB H:ALA339 4.5 13.9 1.0
OD2 H:ASP384 4.5 11.6 1.0
ZN H:ZN502 4.6 37.4 1.0
CG H:ASP168 4.6 13.0 1.0
CB H:SEP117 4.7 18.7 1.0
CA H:ALA339 4.8 11.3 1.0
O H:ALA339 4.8 17.2 1.0
NZ H:LYS343 5.0 18.0 1.0
P H:SEP117 5.0 25.9 1.0

Reference:

L.Liu, S.Lovell, K.P.Battaile, L.Tillery, R.Shek, J.K.Craig, L.K.Barrett, W.C.Van Voorhis. Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae To Be Published.
Page generated: Thu Apr 6 22:59:01 2023

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