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Sodium in PDB 4iql: Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn

Enzymatic activity of Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn

All present enzymatic activity of Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn:
1.3.1.9;

Protein crystallography data

The structure of Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn, PDB code: 4iql was solved by K.E.Hevener, B.D.Santarsiero, P.-C.Su, T.Boci, K.Truong, M.E.Johnson, S.Mehboob, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.652, 86.652, 150.505, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn (pdb code 4iql). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn, PDB code: 4iql:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4iql

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Sodium binding site 1 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


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 Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:13.9
occ:1.00
 O A:HOH648 2.3 27.4 1.0
O A:VAL159 2.3 8.7 1.0
O A:VAL162 2.4 7.8 1.0
O A:HOH647 2.4 26.5 1.0
O A:HOH578 2.4 22.5 1.0
O A:HOH531 2.5 11.9 1.0
C A:VAL159 3.4 9.5 1.0
C A:VAL162 3.6 10.2 1.0
CA A:VAL159 4.0 7.8 1.0
CA A:ASN163 4.1 11.4 1.0
CB A:VAL159 4.2 8.8 1.0
O A:HOH662 4.2 19.5 1.0
N A:ASN163 4.3 8.9 1.0
N A:VAL162 4.5 9.4 1.0
C A:ASN163 4.5 11.7 1.0
N A:ASP160 4.6 9.2 1.0
O A:HOH552 4.6 15.8 1.0
CA A:VAL162 4.6 10.1 1.0
O A:ASN163 4.7 14.0 1.0
CG2 A:VAL162 4.7 7.9 1.0
O A:ILE164 4.7 6.9 1.0
ND2 A:ASN163 4.8 21.8 1.0
CA A:ASP160 4.9 12.1 1.0
CG2 A:VAL159 5.0 12.3 1.0

Sodium binding site 2 out of 6 in 4iql

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Sodium binding site 2 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


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 Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:29.3
occ:1.00
 O A:HOH652 2.3 15.4 1.0
O A:ARG212 2.3 14.4 1.0
O A:HOH654 2.4 32.3 1.0
O A:HOH653 2.4 33.1 1.0
O A:HOH635 2.5 27.3 1.0
O A:ILE285 2.5 16.1 1.0
C A:ARG212 3.4 12.6 1.0
CA A:SER286 3.4 17.8 1.0
C A:ILE285 3.4 15.2 1.0
CB A:SER286 3.8 16.7 1.0
N A:SER286 3.9 15.5 1.0
O A:SER214 3.9 17.9 1.0
CA A:ARG212 4.1 12.6 1.0
O A:HOH582 4.1 21.4 1.0
O A:SER283 4.3 11.3 1.0
N A:ARG213 4.4 12.8 1.0
O A:VAL282 4.4 8.5 1.0
C A:SER286 4.6 17.5 1.0
N A:ILE285 4.6 12.7 1.0
CA A:ARG213 4.6 14.3 1.0
CA A:ILE285 4.6 12.7 1.0
C A:ARG213 4.7 15.9 1.0
CB A:ARG212 4.7 12.1 1.0
C A:SER283 4.8 11.7 1.0
O A:SER286 4.8 17.5 1.0
N A:SER214 4.8 15.4 1.0
O A:CYS211 4.9 12.9 1.0
C A:SER214 5.0 16.2 1.0

Sodium binding site 3 out of 6 in 4iql

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Sodium binding site 3 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


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 Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:14.7
occ:1.00
 O A:HOH649 2.3 26.7 1.0
OD1 A:ASN144 2.3 19.6 1.0
OE2 A:GLU136 2.4 12.7 1.0
O A:GLY141 2.5 8.0 1.0
O A:HIS143 2.7 12.2 1.0
CD A:GLU136 2.8 19.4 1.0
OE1 A:GLU136 2.8 25.3 1.0
C A:HIS143 3.4 11.1 1.0
CG A:ASN144 3.6 14.9 1.0
C A:GLY141 3.6 7.8 1.0
C A:GLY142 3.6 10.1 1.0
N A:HIS143 3.7 9.7 1.0
C1' A:FMN401 3.7 10.0 1.0
CB A:ALA140 3.8 6.4 1.0
O A:GLY142 3.9 11.0 1.0
CA A:GLY142 4.1 9.2 1.0
CG A:GLU136 4.1 9.5 1.0
N A:ASN144 4.2 10.1 1.0
CA A:HIS143 4.2 12.4 1.0
N A:GLY142 4.2 8.5 1.0
CA A:ASN144 4.3 10.6 1.0
ND2 A:ASN144 4.4 11.1 1.0
C A:ALA140 4.5 7.4 1.0
O A:ALA140 4.5 5.1 1.0
N10 A:FMN401 4.5 9.7 1.0
CB A:ASN144 4.6 10.8 1.0
N A:GLY141 4.6 7.5 1.0
O A:HOH631 4.6 22.0 1.0
O A:HOH591 4.7 23.0 1.0
O3' A:FMN401 4.7 7.4 1.0
C4' A:FMN401 4.7 6.8 1.0
CA A:GLY141 4.7 7.2 1.0
CA A:ALA140 4.8 6.1 1.0
O A:HOH572 4.9 22.2 1.0
C2' A:FMN401 5.0 7.8 1.0

Sodium binding site 4 out of 6 in 4iql

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Sodium binding site 4 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


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 Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:16.5
occ:1.00
 O B:VAL162 2.3 8.4 1.0
O B:HOH534 2.3 13.5 1.0
O B:HOH635 2.4 29.4 1.0
O B:VAL159 2.4 9.7 1.0
O B:HOH640 2.5 29.9 1.0
O B:HOH609 2.7 29.4 1.0
C B:VAL162 3.5 10.8 1.0
C B:VAL159 3.6 9.9 1.0
CG1 B:VAL159 4.1 11.8 1.0
CA B:ASN163 4.1 12.2 1.0
CA B:VAL159 4.2 7.2 1.0
N B:ASN163 4.2 11.6 1.0
O B:HOH606 4.3 27.3 1.0
N B:VAL162 4.5 9.7 1.0
C B:ASN163 4.5 13.0 1.0
CA B:VAL162 4.6 9.9 1.0
O B:ASN163 4.7 14.5 1.0
N B:ASP160 4.7 10.2 1.0
CG2 B:VAL162 4.7 10.6 1.0
O B:ILE164 4.7 8.9 1.0
NH2 B:ARG3 4.7 25.9 1.0
CB B:VAL159 4.7 10.0 1.0
O B:HOH541 4.7 13.6 1.0
OD1 B:ASN163 4.8 24.9 1.0
CA B:ASP160 4.9 11.4 1.0

Sodium binding site 5 out of 6 in 4iql

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Sodium binding site 5 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:26.9
occ:1.00
 O B:HOH607 2.3 21.7 1.0
O B:HOH646 2.3 15.2 1.0
O B:ARG212 2.3 14.8 1.0
O B:HOH622 2.4 24.6 1.0
O B:ILE285 2.6 15.8 1.0
O B:HOH611 2.7 25.6 1.0
C B:ARG212 3.5 14.8 1.0
C B:ILE285 3.5 15.5 1.0
CA B:SER286 3.6 18.9 1.0
O B:SER214 3.8 18.1 1.0
CB B:SER286 4.0 19.7 1.0
N B:SER286 4.1 16.5 1.0
O B:SER283 4.1 13.5 1.0
O B:HOH586 4.1 21.4 1.0
CA B:ARG212 4.2 13.9 1.0
N B:ARG213 4.5 14.8 0.5
N B:ARG213 4.5 14.9 0.5
O B:VAL282 4.5 11.4 1.0
N B:ILE285 4.6 11.8 1.0
C B:ARG213 4.6 16.6 0.5
CA B:ARG213 4.7 15.7 0.5
CA B:ARG213 4.7 15.6 0.5
CA B:ILE285 4.7 13.1 1.0
C B:SER283 4.7 13.4 1.0
C B:SER286 4.7 17.4 1.0
N B:SER214 4.8 16.9 1.0
O B:SER286 4.9 17.7 1.0
O B:CYS211 4.9 13.3 1.0
C B:ARG213 4.9 16.5 0.5
CB B:ARG212 4.9 12.7 1.0
C B:SER214 5.0 16.8 1.0

Sodium binding site 6 out of 6 in 4iql

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Sodium binding site 6 out of 6 in the Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) with Cofactors Nadph and Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:18.7
occ:1.00
 O B:HOH639 2.3 23.4 1.0
OE2 B:GLU136 2.3 16.3 1.0
OD1 B:ASN144 2.4 15.0 1.0
O B:GLY141 2.4 9.2 1.0
O B:HIS143 2.8 14.7 1.0
CD B:GLU136 2.8 16.0 1.0
OE1 B:GLU136 2.8 26.8 1.0
C B:HIS143 3.5 13.9 1.0
C B:GLY141 3.5 10.7 1.0
C B:GLY142 3.6 13.1 1.0
CG B:ASN144 3.6 15.2 1.0
N B:HIS143 3.7 11.7 1.0
C1' B:FMN401 3.7 11.2 1.0
CB B:ALA140 3.9 5.2 1.0
CA B:GLY142 4.0 12.1 1.0
O B:GLY142 4.0 12.5 1.0
O B:HOH643 4.0 27.1 1.0
CG B:GLU136 4.1 11.5 1.0
N B:GLY142 4.1 11.0 1.0
CA B:HIS143 4.2 13.4 1.0
N B:ASN144 4.3 12.3 1.0
ND2 B:ASN144 4.4 14.3 1.0
CA B:ASN144 4.4 12.6 1.0
O B:HOH608 4.4 22.6 1.0
C B:ALA140 4.5 7.4 1.0
N10 B:FMN401 4.5 9.0 1.0
N B:GLY141 4.5 7.5 1.0
O B:ALA140 4.6 7.3 1.0
CB B:ASN144 4.6 11.4 1.0
C4' B:FMN401 4.7 5.3 1.0
CA B:GLY141 4.7 9.9 1.0
O3' B:FMN401 4.7 8.1 1.0
CA B:ALA140 4.9 5.5 1.0
C2' B:FMN401 5.0 9.1 1.0

Reference:

K.E.Hevener, B.D.Santarsiero, P.-C.Su, T.Boci, K.Truong, M.E.Johnson, S.Mehboob. Structural and Biochemical Characterization of Porphyromonas Gingivalis Enoyl-Acp Reductase II (Fabk) To Be Published.
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