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Calcium in PDB 2z6i: Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)

Enzymatic activity of Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)

All present enzymatic activity of Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk):
1.3.1.9;

Protein crystallography data

The structure of Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk), PDB code: 2z6i was solved by J.Saito, M.Yamada, T.Watanabe, Y.Takeuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.386, 126.895, 53.335, 90.00, 111.54, 90.00
R / Rfree (%) 20.2 / 23.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) (pdb code 2z6i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk), PDB code: 2z6i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2z6i

Go back to Calcium Binding Sites List in 2z6i
Calcium binding site 1 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:17.1
occ:1.00
 OD1 A:ASN201 2.3 14.1 1.0
O A:HOH727 2.3 24.7 1.0
O A:HOH644 2.4 16.7 1.0
O A:HOH667 2.4 19.7 1.0
CG A:ASN201 3.5 14.2 1.0
ND2 A:ASN201 4.1 14.9 1.0
O A:GLU199 4.4 14.1 1.0
OD2 A:ASP27 4.6 20.9 1.0
CB A:ASN201 4.7 12.8 1.0
O A:SER200 4.7 12.2 1.0
CA A:ASN201 4.8 12.4 1.0
O A:LYS198 4.8 14.2 1.0
C A:GLU199 4.9 13.2 1.0

Calcium binding site 2 out of 6 in 2z6i

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Calcium binding site 2 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:15.5
occ:1.00
 O A:ALA158 2.3 13.6 1.0
O A:ILE161 2.3 16.5 1.0
O A:HOH633 2.4 13.7 1.0
O A:HOH750 2.4 23.9 1.0
O A:HOH736 2.5 22.4 1.0
C A:ALA158 3.5 14.5 1.0
C A:ILE161 3.6 16.3 1.0
CA A:SER162 4.2 16.3 1.0
CA A:ALA158 4.2 13.6 1.0
O A:HOH681 4.3 28.3 1.0
N A:SER162 4.3 16.2 1.0
N A:THR159 4.5 15.1 1.0
N A:ILE161 4.6 17.0 1.0
C A:SER162 4.6 15.6 1.0
CA A:ILE161 4.7 16.7 1.0
O A:SER162 4.7 16.1 1.0
O A:ILE163 4.7 13.1 1.0
O A:HOH659 4.7 17.8 1.0
CB A:ALA158 4.8 14.0 1.0
C A:THR159 4.8 16.6 1.0
CA A:THR159 4.8 16.6 1.0
O A:THR159 4.8 17.5 1.0

Calcium binding site 3 out of 6 in 2z6i

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Calcium binding site 3 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:12.6
occ:0.70
 O A:HOH631 2.2 13.3 1.0
O A:HIS144 2.3 11.6 1.0
O A:HOH664 2.4 19.5 1.0
O A:HOH636 2.4 18.8 1.0
OE1 A:GLU137 2.5 15.9 1.0
CD A:GLU137 3.4 15.3 1.0
C A:HIS144 3.5 12.3 1.0
OE2 A:GLU137 3.6 15.5 1.0
CA A:HIS144 4.2 12.4 1.0
CB A:HIS144 4.3 13.2 1.0
N A:HIS144 4.3 12.4 1.0
N1 A:FMN401 4.4 12.4 1.0
O A:HOH640 4.4 17.5 1.0
O A:HOH605 4.4 9.9 1.0
N A:ILE145 4.5 11.8 1.0
O A:HOH694 4.6 25.8 1.0
CA A:ILE145 4.7 11.8 1.0
CG A:GLU137 4.8 13.1 1.0
C1' A:FMN401 4.8 10.6 1.0
O2 A:FMN401 4.8 13.4 1.0
C2 A:FMN401 4.9 14.1 1.0
CG1 A:VAL116 4.9 13.1 1.0
C10 A:FMN401 4.9 11.9 1.0
O A:GLY142 5.0 11.9 1.0

Calcium binding site 4 out of 6 in 2z6i

Go back to Calcium Binding Sites List in 2z6i
Calcium binding site 4 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:15.0
occ:1.00
 OD1 B:ASN201 2.2 14.9 1.0
O B:HOH557 2.3 18.7 1.0
O B:HOH600 2.4 20.8 1.0
O B:HOH611 2.4 28.4 1.0
O B:HOH610 2.5 28.9 1.0
CG B:ASN201 3.4 14.4 1.0
ND2 B:ASN201 4.1 14.5 1.0
O B:GLU199 4.4 13.8 1.0
CB B:ASN201 4.6 13.3 1.0
O B:SER200 4.7 13.9 1.0
O B:LYS198 4.7 14.7 1.0
CA B:ASN201 4.8 13.4 1.0
OD2 B:ASP27 4.8 22.7 1.0
C B:GLU199 4.8 13.9 1.0
C B:SER200 5.0 13.1 1.0

Calcium binding site 5 out of 6 in 2z6i

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Calcium binding site 5 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:15.1
occ:1.00
 O B:ALA158 2.3 14.5 1.0
O B:HOH589 2.4 21.8 1.0
O B:HOH563 2.4 18.3 1.0
O B:ILE161 2.4 15.6 1.0
O B:HOH638 2.6 25.1 1.0
O B:HOH576 2.6 20.5 1.0
O B:HOH575 2.6 24.8 1.0
C B:ALA158 3.5 14.2 1.0
C B:ILE161 3.7 16.1 1.0
CA B:ALA158 4.2 12.8 1.0
CA B:SER162 4.3 16.1 1.0
N B:SER162 4.5 15.7 1.0
N B:THR159 4.6 15.2 1.0
O B:HOH524 4.6 18.9 1.0
N B:ILE161 4.6 15.9 1.0
CB B:ALA158 4.7 12.8 1.0
C B:SER162 4.7 15.7 1.0
O B:SER162 4.7 15.4 1.0
O B:ILE163 4.7 14.7 1.0
CA B:ILE161 4.7 15.7 1.0
O B:HOH515 4.7 13.9 1.0
CA B:THR159 4.8 16.6 1.0
C B:THR159 4.8 16.6 1.0
CD1 B:ILE161 4.9 19.6 1.0
O B:THR159 4.9 17.4 1.0

Calcium binding site 6 out of 6 in 2z6i

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Calcium binding site 6 out of 6 in the Crystal Structure of S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk)


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 S. Pneumoniae Enoyl-Acyl Carrier Protein Reductase (Fabk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:14.1
occ:0.70
 O B:HOH545 2.2 13.2 1.0
O B:HIS144 2.4 12.4 1.0
O B:HOH567 2.4 19.6 1.0
O B:HOH594 2.4 23.5 1.0
OE1 B:GLU137 2.4 15.7 1.0
O B:HOH578 3.0 26.8 1.0
CD B:GLU137 3.3 14.9 1.0
OE2 B:GLU137 3.5 16.2 1.0
C B:HIS144 3.6 12.6 1.0
N1 B:FMN402 4.3 13.7 1.0
CA B:HIS144 4.3 12.9 1.0
N B:HIS144 4.4 12.4 1.0
CB B:HIS144 4.4 13.6 1.0
O B:HOH546 4.4 18.5 1.0
O B:HOH507 4.5 10.3 1.0
N B:ILE145 4.6 12.0 1.0
O2 B:FMN402 4.7 14.2 1.0
CG B:GLU137 4.7 10.5 1.0
C2 B:FMN402 4.7 13.9 1.0
CA B:ILE145 4.8 12.0 1.0
C1' B:FMN402 4.9 12.0 1.0
O B:GLY142 4.9 11.3 1.0
CG1 B:VAL116 4.9 15.5 1.0
C10 B:FMN402 4.9 13.6 1.0

Reference:

J.Saito, M.Yamada, T.Watanabe, M.Iida, H.Kitagawa, S.Takahata, T.Ozawa, Y.Takeuchi, F.Ohsawa. Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (Fabk) From Streptococcus Pneumoniae Reveals the Binding Mode of An Inhibitor. Protein Sci. V. 17 691 2008.
ISSN: ISSN 0961-8368
PubMed: 18305197
DOI: 10.1110/PS.073288808
Page generated: Fri Jul 12 19:49:04 2024

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