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Sodium in PDB 1gvh: The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket

Enzymatic activity of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket

All present enzymatic activity of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket:
1.6.99.7;

Protein crystallography data

The structure of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket, PDB code: 1gvh was solved by A.Ilari, K.A.Johnson, A.Bonamore, A.Farina, A.Boffi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25 / 2.19
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 164.860, 164.860, 53.460, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 24.7

Other elements in 1gvh:

The structure of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket (pdb code 1gvh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket, PDB code: 1gvh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1gvh

Go back to Sodium Binding Sites List in 1gvh
Sodium binding site 1 out of 2 in the The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1399

b:11.8
occ:1.00
 O A:PHE43 2.4 20.8 1.0
O A:LYS40 2.4 14.5 1.0
O A:GLN201 2.4 12.2 1.0
OE1 A:GLU202 2.5 26.7 1.0
CD A:GLU202 2.9 24.5 1.0
OE2 A:GLU202 3.2 24.8 1.0
C A:LYS40 3.5 17.5 1.0
C A:PHE43 3.5 16.9 1.0
C A:GLN201 3.6 16.6 1.0
CG A:MET45 3.8 9.4 1.0
C A:GLU41 3.8 13.2 1.0
N A:MET45 3.9 14.1 1.0
CA A:GLU41 3.9 13.4 1.0
CB A:HIS200 4.0 15.1 1.0
O A:HOH2020 4.0 24.2 1.0
N A:ILE42 4.1 12.4 1.0
CA A:GLU202 4.1 17.7 1.0
CG A:GLU202 4.1 20.2 1.0
N A:GLU41 4.2 16.5 1.0
CA A:ASN44 4.2 16.3 1.0
O A:GLU41 4.2 12.4 1.0
N A:PHE43 4.2 17.3 1.0
CB A:MET45 4.3 10.5 1.0
N A:GLU202 4.3 18.2 1.0
N A:ASN44 4.3 17.1 1.0
C A:ILE42 4.3 14.2 1.0
C A:ASN44 4.4 13.5 1.0
N A:GLN201 4.4 17.1 1.0
CA A:PHE43 4.5 16.0 1.0
O A:ILE42 4.5 15.2 1.0
C A:HIS200 4.6 18.3 1.0
CA A:GLN201 4.7 16.5 1.0
CA A:ILE42 4.7 14.8 1.0
CA A:LYS40 4.7 15.6 1.0
CA A:MET45 4.7 17.0 1.0
CB A:GLU202 4.7 14.5 1.0
O A:HIS200 4.8 15.9 1.0
CG A:HIS200 4.9 15.7 1.0
CA A:HIS200 5.0 16.7 1.0

Sodium binding site 2 out of 2 in 1gvh

Go back to Sodium Binding Sites List in 1gvh
Sodium binding site 2 out of 2 in the The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unespected Geometry of the Distal Heme Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1400

b:2.0
occ:1.00
 O A:HOH2137 2.8 31.1 1.0
NE2 A:HIS294 3.1 18.3 1.0
N A:ALA303 3.2 14.5 1.0
OE1 A:GLN271 3.3 12.9 1.0
CA A:HIS302 3.6 13.6 1.0
CE1 A:HIS294 3.7 13.9 1.0
O A:GLY268 3.8 18.3 1.0
CA A:GLY268 3.9 15.6 1.0
CD2 A:HIS302 3.9 18.6 1.0
O A:VAL301 3.9 17.8 1.0
C A:HIS302 3.9 15.9 1.0
C A:GLY268 3.9 17.6 1.0
CB A:ALA296 4.1 16.6 1.0
O A:ALA303 4.2 15.4 1.0
CD2 A:HIS294 4.2 16.0 1.0
CA A:ALA303 4.3 12.3 1.0
CD1 A:ILE167 4.3 22.1 1.0
CB A:HIS302 4.4 13.9 1.0
CD A:GLN271 4.4 7.7 1.0
CB A:ALA303 4.4 11.0 1.0
N A:GLY268 4.5 12.1 1.0
C A:VAL301 4.5 19.1 1.0
N A:HIS302 4.5 17.0 1.0
CG A:HIS302 4.5 18.2 1.0
C A:ALA303 4.7 12.8 1.0
O A:HOH2136 4.7 11.1 1.0
CA A:ALA296 4.8 17.4 1.0
N A:VAL269 4.8 17.5 1.0
O A:ALA295 4.9 10.9 1.0

Reference:

A.Ilari, A.Bonamore, A.Farina, K.A.Johnson, A.Boffi. The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals An Unexpected Geometry of the Distal Heme Pocket J.Biol.Chem. V. 277 23725 2002.
ISSN: ISSN 0021-9258
PubMed: 11964402
DOI: 10.1074/JBC.M202228200
Page generated: Sun Aug 17 05:07:22 2025

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