Atomistry » Sodium » PDB 4iic-4j0n » 4iql
Atomistry »
  Sodium »
    PDB 4iic-4j0n »
      4iql »

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

Go back to Sodium Binding Sites List in 4iql
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

Go back to Sodium Binding Sites List in 4iql
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

Go back to Sodium Binding Sites List in 4iql
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

Go back to Sodium Binding Sites List in 4iql
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

Go back to Sodium Binding Sites List in 4iql
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

Go back to Sodium Binding Sites List in 4iql
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.
Page generated: Mon Oct 7 16:05:33 2024

Last articles

Cl in 5EAE
Cl in 5EAD
Cl in 5E9R
Cl in 5EAC
Cl in 5EAB
Cl in 5EA6
Cl in 5E9X
Cl in 5E8R
Cl in 5E9K
Cl in 5E9C
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy