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Calcium in PDB 3fl8: Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative

Enzymatic activity of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative

All present enzymatic activity of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative:
1.5.1.3;

Protein crystallography data

The structure of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative, PDB code: 3fl8 was solved by C.R.Bourne, W.W.Barrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.178, 135.920, 168.652, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative (pdb code 3fl8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative, PDB code: 3fl8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3fl8

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Calcium binding site 1 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:31.4
occ:1.00
 OD1 A:ASP110 2.4 19.3 1.0
O A:HOH266 2.5 26.7 1.0
O A:HOH209 2.6 34.4 1.0
O A:HOH178 2.7 19.7 1.0
O A:TYR108 2.7 20.2 1.0
OD2 A:ASP110 3.0 19.9 1.0
CG A:ASP110 3.0 24.1 1.0
C A:TYR108 3.7 20.3 1.0
CA A:TYR108 4.1 19.0 1.0
O A:HOH602 4.2 24.7 1.0
CB A:ASP110 4.5 21.6 1.0
O A:HOH1284 4.5 36.1 1.0
CB A:TYR108 4.6 18.8 1.0
O A:VAL109 4.6 19.2 1.0
C A:VAL109 4.7 18.4 1.0
N A:VAL109 4.7 25.3 1.0
N A:ASP110 4.8 16.5 1.0
CG2 A:VAL3 5.0 15.6 1.0
CA A:ASP110 5.0 20.3 1.0

Calcium binding site 2 out of 8 in 3fl8

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Calcium binding site 2 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca300

b:22.8
occ:1.00
 OE2 H:GLU147 2.4 31.2 1.0
O B:HOH168 2.5 14.7 1.0
O B:HOH204 2.5 22.3 1.0
O B:TYR108 2.6 14.2 1.0
OD1 B:ASP110 2.6 17.5 1.0
O B:HOH186 2.7 25.7 1.0
OD2 B:ASP110 2.8 21.4 1.0
CG B:ASP110 3.0 24.2 1.0
CD H:GLU147 3.2 24.9 1.0
C B:TYR108 3.5 15.8 1.0
OE1 H:GLU147 3.8 26.1 1.0
CA B:TYR108 3.9 17.3 1.0
CG H:GLU147 4.2 22.3 1.0
CB B:TYR108 4.3 15.8 1.0
O B:HOH184 4.4 24.3 1.0
CG2 B:VAL3 4.5 18.5 1.0
CB B:ASP110 4.5 18.1 1.0
N B:VAL109 4.6 18.1 1.0
C B:VAL109 4.7 16.7 1.0
O B:MET1 4.7 23.0 1.0
N B:ASP110 4.8 11.0 1.0
O B:VAL109 4.8 15.0 1.0
CB B:VAL3 4.8 16.5 1.0
O B:HOH316 4.8 29.2 1.0

Calcium binding site 3 out of 8 in 3fl8

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Calcium binding site 3 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca300

b:16.9
occ:1.00
 O C:HOH183 2.3 22.0 1.0
O C:TYR108 2.5 18.1 1.0
O C:HOH168 2.6 8.9 1.0
O C:HOH175 2.6 20.1 1.0
OE2 A:GLU147 2.6 30.5 1.0
OD1 C:ASP110 2.6 21.0 1.0
OD2 C:ASP110 2.8 22.9 1.0
CG C:ASP110 3.0 27.7 1.0
CD A:GLU147 3.4 22.9 1.0
C C:TYR108 3.4 16.7 1.0
CA C:TYR108 3.9 19.1 1.0
OE1 A:GLU147 4.0 26.8 1.0
CG A:GLU147 4.2 23.9 1.0
CB C:TYR108 4.2 17.0 1.0
CG2 C:VAL3 4.4 17.4 1.0
O C:HOH176 4.5 17.7 1.0
CB C:ASP110 4.5 15.0 1.0
N C:VAL109 4.5 18.1 1.0
O A:HOH326 4.6 25.0 1.0
C C:VAL109 4.6 16.4 1.0
CB C:VAL3 4.7 18.5 1.0
N C:ASP110 4.7 15.1 1.0
O C:MET1 4.7 16.7 1.0
O C:VAL109 4.8 16.8 1.0
O A:HOH174 4.9 17.4 1.0
O C:HOH172 4.9 17.6 1.0
CA C:VAL109 5.0 16.0 1.0

Calcium binding site 4 out of 8 in 3fl8

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Calcium binding site 4 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca300

b:25.3
occ:1.00
 O D:HOH171 2.4 16.2 1.0
O D:TYR108 2.5 18.7 1.0
O D:HOH461 2.6 23.5 1.0
OD1 D:ASP110 2.6 15.8 1.0
O D:HOH1241 2.9 30.2 1.0
OD2 D:ASP110 2.9 21.7 1.0
CG D:ASP110 3.1 25.7 1.0
C D:TYR108 3.5 16.5 1.0
CA D:TYR108 3.9 18.4 1.0
O D:HOH1434 4.2 35.4 1.0
CB D:TYR108 4.2 15.6 1.0
CG2 D:VAL3 4.5 16.5 1.0
O D:HOH469 4.5 24.6 1.0
CB D:ASP110 4.6 18.6 1.0
N D:VAL109 4.6 17.2 1.0
C D:VAL109 4.7 15.2 1.0
O D:MET1 4.7 27.2 1.0
CB D:VAL3 4.8 15.0 1.0
O D:VAL109 4.8 14.1 1.0
N D:ASP110 4.8 12.6 1.0

Calcium binding site 5 out of 8 in 3fl8

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Calcium binding site 5 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca300

b:26.2
occ:1.00
 OE2 D:GLU147 2.4 27.3 1.0
O E:HOH201 2.5 18.7 1.0
O E:HOH167 2.5 17.6 1.0
O E:TYR108 2.5 19.1 1.0
O D:HOH177 2.5 19.6 1.0
OD1 E:ASP110 2.6 22.6 1.0
OD2 E:ASP110 2.7 22.9 1.0
CG E:ASP110 3.0 25.1 1.0
CD D:GLU147 3.2 25.9 1.0
C E:TYR108 3.5 20.2 1.0
CG D:GLU147 3.8 24.3 1.0
CA E:TYR108 4.0 18.8 1.0
OE1 D:GLU147 4.0 34.2 1.0
O D:HOH272 4.1 31.6 1.0
CB E:TYR108 4.3 16.1 1.0
CG2 E:VAL3 4.3 17.4 1.0
CB E:ASP110 4.5 18.5 1.0
O E:HOH1259 4.6 32.8 1.0
N E:VAL109 4.6 24.0 1.0
CB E:VAL3 4.6 18.6 1.0
C E:VAL109 4.6 18.3 1.0
O E:HOH223 4.7 25.4 1.0
O E:MET1 4.7 30.3 1.0
N E:ASP110 4.8 16.1 1.0
O E:VAL109 4.8 17.0 1.0
O E:HOH447 4.8 16.6 1.0
CB D:GLU147 5.0 27.6 1.0

Calcium binding site 6 out of 8 in 3fl8

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Calcium binding site 6 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca300

b:27.6
occ:1.00
 OE2 G:GLU147 2.3 33.2 1.0
O F:HOH452 2.5 23.8 1.0
OD1 F:ASP110 2.5 20.4 1.0
O F:HOH174 2.6 27.7 1.0
O F:HOH755 2.6 31.6 1.0
O F:TYR108 2.6 21.3 1.0
OD2 F:ASP110 2.8 20.8 1.0
CG F:ASP110 2.9 25.9 1.0
CD G:GLU147 3.2 27.1 1.0
C F:TYR108 3.6 16.3 1.0
OE1 G:GLU147 3.7 32.6 1.0
CA F:TYR108 4.1 18.8 1.0
NZ F:LYS160 4.1 32.5 1.0
CG G:GLU147 4.3 25.5 1.0
CB F:ASP110 4.4 20.0 1.0
CB F:TYR108 4.4 16.5 1.0
CG2 F:VAL3 4.6 19.3 1.0
C F:VAL109 4.6 16.7 1.0
O F:VAL109 4.7 20.4 1.0
N F:VAL109 4.7 21.9 1.0
N F:ASP110 4.8 15.0 1.0
O F:MET1 4.8 34.7 1.0
CB F:VAL3 4.9 19.9 1.0
CA F:ASP110 5.0 21.5 1.0

Calcium binding site 7 out of 8 in 3fl8

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Calcium binding site 7 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca300

b:29.2
occ:1.00
 O G:HOH174 2.4 19.4 1.0
O G:HOH173 2.5 30.1 1.0
O G:TYR108 2.5 21.6 1.0
OD1 G:ASP110 2.7 17.5 1.0
O G:HOH179 2.7 29.8 1.0
OD2 G:ASP110 2.8 27.9 1.0
CG G:ASP110 3.0 27.8 1.0
C G:TYR108 3.5 17.5 1.0
CA G:TYR108 3.9 22.3 1.0
CB G:TYR108 4.2 17.7 1.0
CG2 G:VAL3 4.4 20.1 1.0
CB G:ASP110 4.5 15.9 1.0
N G:VAL109 4.6 20.3 1.0
O G:MET1 4.6 40.0 1.0
O G:HOH182 4.7 23.0 1.0
C G:VAL109 4.7 18.8 1.0
CB G:VAL3 4.7 17.5 1.0
O G:VAL109 4.8 16.1 1.0
N G:ASP110 4.8 16.5 1.0

Calcium binding site 8 out of 8 in 3fl8

Go back to Calcium Binding Sites List in 3fl8
Calcium binding site 8 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with RAB1, A Tmp-Dihydrophthalazine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca300

b:40.9
occ:1.00
 OD1 H:ASP110 2.5 18.1 1.0
O H:HOH203 2.5 25.6 1.0
O H:TYR108 2.6 24.5 1.0
O H:HOH478 2.7 36.4 1.0
O H:HOH169 2.9 27.8 1.0
CG H:ASP110 3.1 27.6 1.0
OD2 H:ASP110 3.2 26.4 1.0
C H:TYR108 3.4 22.5 1.0
CA H:TYR108 3.8 20.1 1.0
O H:VAL109 4.4 21.1 1.0
CB H:TYR108 4.4 17.5 1.0
N H:VAL109 4.4 24.9 1.0
C H:VAL109 4.4 20.0 1.0
CB H:ASP110 4.5 22.5 1.0
O H:HOH436 4.6 35.6 1.0
N H:ASP110 4.7 17.9 1.0
NZ H:LYS160 4.8 42.7 1.0
CA H:ASP110 4.9 21.3 1.0
CA H:VAL109 4.9 23.2 1.0

Reference:

C.R.Bourne, R.A.Bunce, P.C.Bourne, K.D.Berlin, E.W.Barrow, W.W.Barrow. Crystal Structure of Bacillus Anthracis Dihydrofolate Reductase with the Dihydrophthalazine-Based Trimethoprim Derivative RAB1 Provides A Structural Explanation of Potency and Selectivity. Antimicrob.Agents Chemother. V. 53 3065 2009.
ISSN: ISSN 0066-4804
PubMed: 19364848
DOI: 10.1128/AAC.01666-08
Page generated: Sat Jul 13 10:10:37 2024

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