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Calcium in PDB 3fl9: Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim

Enzymatic activity of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim

All present enzymatic activity of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim:
1.5.1.3;

Protein crystallography data

The structure of Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim, PDB code: 3fl9 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) 29.95 / 2.40
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.930, 67.610, 167.000, 90.00, 90.12, 90.00
R / Rfree (%) 23.7 / 30.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim (pdb code 3fl9). 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 Trimethoprim, PDB code: 3fl9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3fl9

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Calcium binding site 1 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:27.3
occ:1.00
 O A:HOH198 2.7 25.0 1.0
OD2 A:ASP110 2.8 25.2 1.0
O A:TYR108 2.8 25.2 1.0
OD1 A:ASP110 2.8 25.4 1.0
CG A:ASP110 3.2 25.4 1.0
C A:TYR108 3.9 24.5 1.0
CG2 A:VAL3 4.2 24.9 1.0
CA A:TYR108 4.3 24.2 1.0
CB A:TYR108 4.5 24.7 1.0
O A:VAL109 4.6 24.6 1.0
O A:HOH186 4.6 25.6 1.0
CB A:ASP110 4.6 24.9 1.0
O A:MET1 4.7 25.1 1.0
CB A:VAL3 4.8 25.0 1.0
C A:VAL109 4.9 24.8 1.0

Calcium binding site 2 out of 8 in 3fl9

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Calcium binding site 2 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca300

b:23.4
occ:1.00
 O B:TYR108 2.6 25.8 1.0
OD1 B:ASP110 2.7 26.2 1.0
OE2 D:GLU147 2.8 25.7 1.0
OD2 B:ASP110 2.9 25.8 1.0
O B:HOH175 3.1 24.6 1.0
CG B:ASP110 3.1 25.8 1.0
CD D:GLU147 3.4 25.4 1.0
C B:TYR108 3.7 25.8 1.0
OE1 D:GLU147 4.0 25.4 1.0
O B:MET1 4.1 26.8 1.0
CG D:GLU147 4.2 25.4 1.0
CG2 B:VAL3 4.3 26.0 1.0
CA B:TYR108 4.3 25.7 1.0
CB B:ASP110 4.5 25.6 1.0
O B:VAL109 4.5 25.6 1.0
O B:HOH362 4.6 25.4 1.0
C B:VAL109 4.6 25.7 1.0
CB B:VAL3 4.6 26.1 1.0
CB B:TYR108 4.7 26.1 1.0
O B:HOH187 4.7 25.7 1.0
N B:VAL109 4.8 26.4 1.0
N B:VAL3 4.8 26.8 1.0
N B:ASP110 4.9 25.7 1.0

Calcium binding site 3 out of 8 in 3fl9

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Calcium binding site 3 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca300

b:29.9
occ:1.00
 O C:TYR108 2.9 28.3 1.0
OE2 A:GLU147 2.9 29.1 1.0
OD1 C:ASP110 3.2 26.6 1.0
C C:TYR108 3.4 28.2 1.0
CA C:TYR108 3.7 28.9 1.0
CG C:ASP110 3.8 27.0 1.0
OD2 C:ASP110 3.8 27.7 1.0
CD A:GLU147 4.1 29.1 1.0
NZ C:LYS160 4.1 25.9 1.0
O C:VAL109 4.2 26.9 1.0
N C:VAL109 4.4 28.0 1.0
O C:PRO107 4.4 28.9 1.0
O C:HOH177 4.5 25.0 1.0
C C:VAL109 4.5 26.9 1.0
CB C:TYR108 4.6 29.1 1.0
OE1 A:GLU147 4.6 29.1 1.0
N C:TYR108 4.8 29.2 1.0
CA C:VAL109 5.0 27.5 1.0
N C:ASP110 5.0 26.8 1.0

Calcium binding site 4 out of 8 in 3fl9

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Calcium binding site 4 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca300

b:32.4
occ:1.00
 OD1 D:ASP110 3.1 28.2 1.0
C D:TYR108 3.3 28.4 1.0
CA D:TYR108 3.4 28.4 1.0
O D:TYR108 3.4 28.3 1.0
O D:PRO107 3.8 29.4 1.0
N D:VAL109 3.9 28.2 1.0
CG D:ASP110 4.0 27.1 1.0
NZ D:LYS160 4.0 29.3 1.0
O D:VAL109 4.2 27.3 1.0
CB D:TYR108 4.3 28.5 1.0
OD2 D:ASP110 4.3 26.9 1.0
N D:TYR108 4.4 28.7 1.0
C D:VAL109 4.4 27.5 1.0
C D:PRO107 4.5 28.9 1.0
CA D:VAL109 4.8 27.8 1.0
N D:ASP110 4.9 27.2 1.0

Calcium binding site 5 out of 8 in 3fl9

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Calcium binding site 5 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca300

b:34.1
occ:1.00
 OD1 E:ASP110 3.4 30.6 1.0
OE2 G:GLU147 3.8 30.2 1.0
OD2 E:ASP110 3.8 30.5 1.0
CG E:ASP110 4.0 30.1 1.0
OE1 G:GLU147 4.2 30.5 1.0
CD G:GLU147 4.4 30.2 1.0
O G:HOH186 4.6 27.7 1.0
O E:TYR108 4.7 29.9 1.0
O E:MET1 4.9 30.6 1.0

Calcium binding site 6 out of 8 in 3fl9

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Calcium binding site 6 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca300

b:26.1
occ:1.00
 OD1 F:ASP110 2.7 26.4 1.0
O F:HOH268 2.9 26.2 1.0
O F:TYR108 2.9 27.5 1.0
OD2 F:ASP110 2.9 26.7 1.0
CG F:ASP110 3.2 26.4 1.0
C F:TYR108 3.8 27.3 1.0
CA F:TYR108 4.1 27.3 1.0
CG2 F:VAL3 4.3 27.2 1.0
CB F:TYR108 4.4 27.9 1.0
O F:MET1 4.5 26.9 1.0
CB F:ASP110 4.7 26.4 1.0
O F:HOH173 4.8 26.1 1.0
O F:VAL109 4.8 27.1 1.0
CB F:VAL3 4.9 26.8 1.0
C F:VAL109 4.9 26.8 1.0
N F:VAL109 4.9 27.2 1.0

Calcium binding site 7 out of 8 in 3fl9

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Calcium binding site 7 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca300

b:29.4
occ:1.00
 OD1 G:ASP110 3.1 29.5 1.0
OD2 G:ASP110 3.2 29.1 1.0
CG G:ASP110 3.5 29.2 1.0
O G:TYR108 3.8 29.8 1.0
C G:TYR108 4.4 29.6 1.0
CA G:TYR108 4.7 29.8 1.0
CB G:ASP110 5.0 28.7 1.0

Calcium binding site 8 out of 8 in 3fl9

Go back to Calcium Binding Sites List in 3fl9
Calcium binding site 8 out of 8 in the Crystal Structure of B. Anthracis Dihydrofolate Reductase (Dhfr) with Trimethoprim


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 Trimethoprim within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca300

b:24.4
occ:1.00
 OE2 F:GLU147 2.7 25.8 1.0
OD1 H:ASP110 2.9 26.8 1.0
O H:TYR108 3.0 25.6 1.0
CG H:ASP110 3.6 25.9 1.0
CD F:GLU147 3.6 25.9 1.0
C H:TYR108 3.6 25.6 1.0
OD2 H:ASP110 3.7 26.2 1.0
OE1 F:GLU147 3.7 26.0 1.0
CA H:TYR108 3.9 25.7 1.0
NZ H:LYS160 4.4 26.6 1.0
O H:VAL109 4.4 25.5 1.0
CB H:TYR108 4.5 25.6 1.0
C H:VAL109 4.6 25.6 1.0
N H:VAL109 4.6 25.7 1.0
CB H:ASP110 4.8 25.8 1.0
O H:PRO107 4.9 25.6 1.0
N H:ASP110 4.9 25.6 1.0
CA H:ASP110 5.0 25.9 1.0
CG F:GLU147 5.0 26.1 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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