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Sodium in PDB 8ctr: Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp

Enzymatic activity of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp

All present enzymatic activity of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp:
1.1.1.133;

Protein crystallography data

The structure of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp, PDB code: 8ctr was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 45.35 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.55, 71.69, 81.23, 89.96, 66.58, 83.08
R / Rfree (%) 16.2 / 18.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp (pdb code 8ctr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp, PDB code: 8ctr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8ctr

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Sodium binding site 1 out of 4 in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:28.0
occ:1.00
 O D:HOH704 2.2 44.8 1.0
O A:HOH574 2.3 27.8 1.0
O D:HOH441 2.3 28.2 1.0
O D:HOH524 2.4 36.2 1.0
O D:HOH482 2.4 36.2 1.0
O A:HOH416 4.2 26.3 1.0
O A:HOH612 4.2 28.0 1.0
O D:HOH413 4.2 27.7 1.0
O D:HOH534 4.3 29.7 1.0
O A:HOH463 4.3 53.7 1.0
OD1 D:ASP56 4.3 29.0 1.0
OD1 A:ASP56 4.4 28.1 1.0
O A:GLY96 4.6 19.8 1.0
O D:GLY96 4.6 18.9 1.0
NH1 A:ARG145 4.8 18.3 0.4
O A:LEU95 4.8 21.1 1.0
O D:LEU95 4.8 21.8 1.0
NH1 D:ARG145 4.9 20.8 0.4

Sodium binding site 2 out of 4 in 8ctr

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Sodium binding site 2 out of 4 in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:25.9
occ:1.00
 O B:HOH572 2.3 33.1 1.0
O C:HOH461 2.3 26.4 1.0
O B:HOH721 2.4 50.4 1.0
O B:HOH464 2.4 28.3 1.0
O C:HOH719 2.5 45.5 1.0
O C:HOH491 2.5 32.1 1.0
O C:HOH584 4.1 29.2 1.0
O C:HOH674 4.2 50.2 1.0
O B:HOH474 4.2 28.8 1.0
O C:HOH421 4.3 24.6 1.0
O B:HOH423 4.3 25.7 1.0
OD1 C:ASP56 4.4 24.7 1.0
OD1 B:ASP56 4.4 25.7 1.0
O C:GLY96 4.7 15.1 1.0
O B:GLY96 4.7 17.3 1.0
O C:LEU95 4.8 17.2 1.0
O B:HOH555 4.9 39.8 1.0
O B:LEU95 4.9 19.9 1.0
NH1 C:ARG145 5.0 17.5 0.6
NH1 B:ARG145 5.0 16.9 0.6

Sodium binding site 3 out of 4 in 8ctr

Go back to Sodium Binding Sites List in 8ctr
Sodium binding site 3 out of 4 in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:17.7
occ:1.00
 O B:HOH450 1.9 17.5 1.0
O A:HOH471 1.9 16.4 1.0
O A:HOH459 2.1 16.9 1.0
O B:HOH452 2.1 16.9 1.0
O A:HOH527 2.1 19.3 1.0
O B:HOH508 2.1 18.8 1.0
OE2 B:GLU190 3.9 19.9 1.0
OE2 A:GLU190 4.0 19.8 1.0
OE2 B:GLU15 4.0 18.0 1.0
OE2 A:GLU15 4.0 18.3 1.0
OE2 A:GLU292 4.1 16.5 1.0
OE2 B:GLU292 4.2 16.3 1.0
O A:HOH559 4.2 18.5 1.0
OE1 B:GLU292 4.3 17.6 1.0
O B:HOH560 4.3 17.5 1.0
OE1 A:GLU292 4.3 17.3 1.0
OE1 B:GLU15 4.3 18.1 1.0
OE1 A:GLU15 4.3 15.6 1.0
CD B:GLU15 4.5 19.1 1.0
CD A:GLU15 4.6 17.2 1.0
CD B:GLU292 4.6 18.4 1.0
CD A:GLU292 4.6 16.1 1.0
O B:HOH441 4.7 24.3 1.0
O A:HOH464 4.7 21.8 1.0
NH2 A:ARG288 4.9 16.0 1.0
NH2 B:ARG288 5.0 18.1 1.0
CD B:GLU190 5.0 21.4 1.0

Sodium binding site 4 out of 4 in 8ctr

Go back to Sodium Binding Sites List in 8ctr
Sodium binding site 4 out of 4 in the Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:19.1
occ:1.00
 O D:HOH477 2.0 19.8 1.0
O D:HOH451 2.1 16.7 1.0
O D:HOH541 2.1 20.4 1.0
OE2 D:GLU15 4.0 19.3 1.0
OE2 D:GLU190 4.0 20.1 1.0
OE2 D:GLU292 4.2 17.2 1.0
O D:HOH544 4.2 18.9 1.0
OE1 D:GLU292 4.3 18.8 1.0
OE1 D:GLU15 4.4 15.9 1.0
CD D:GLU15 4.6 16.8 1.0
CD D:GLU292 4.7 21.5 1.0
O D:HOH440 4.8 23.8 1.0
NH2 D:ARG288 5.0 17.4 1.0

Reference:

M.J.Bolejack, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Dtdp-4-Dehydrorhamnose Reductase From Klebsiella Pneumoniae with Bound Nadp To Be Published.
Page generated: Wed Oct 9 11:08:21 2024

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