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Sodium in PDB 1tqy: The Actinorhodin Ketosynthase/Chain Length Factor

Protein crystallography data

The structure of The Actinorhodin Ketosynthase/Chain Length Factor, PDB code: 1tqy was solved by A.T.Keatinge-Clay, D.A.Maltby, K.F.Medzihradszky, C.Khosla, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 262.700, 262.700, 224.030, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 25.3

Other elements in 1tqy:

The structure of The Actinorhodin Ketosynthase/Chain Length Factor also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Actinorhodin Ketosynthase/Chain Length Factor (pdb code 1tqy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Actinorhodin Ketosynthase/Chain Length Factor, PDB code: 1tqy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1tqy

Go back to Sodium Binding Sites List in 1tqy
Sodium binding site 1 out of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1091

b:39.1
occ:1.00
 O B:HOH1233 1.9 31.9 1.0
O B:PRO13 2.3 25.0 1.0
O B:GLN50 2.3 25.6 1.0
O B:HOH1112 2.3 31.7 1.0
O B:HOH1161 3.0 38.3 1.0
C B:PRO13 3.3 24.3 1.0
O B:GLY31 3.3 25.2 1.0
C B:GLN50 3.5 27.2 1.0
CA B:PRO13 3.8 24.7 1.0
CA B:GLY31 3.8 25.9 1.0
C B:GLY31 4.0 25.1 1.0
CB B:PRO13 4.1 23.8 1.0
OD2 B:ASP52 4.1 38.2 1.0
CA B:ILE51 4.3 28.7 1.0
O B:HOH1162 4.4 29.1 1.0
N B:ILE51 4.4 27.6 1.0
N B:ASP52 4.4 30.0 1.0
N B:ASN14 4.5 23.6 1.0
N B:GLN50 4.5 27.0 1.0
O B:HOH1205 4.5 45.0 1.0
CA B:GLN50 4.5 27.4 1.0
CG B:ASP52 4.8 35.2 1.0
C B:ILE51 4.8 29.0 1.0
CA B:ASN14 4.9 25.9 1.0
O B:HOH1123 4.9 31.5 1.0
CB B:GLN50 4.9 25.9 1.0

Sodium binding site 2 out of 4 in 1tqy

Go back to Sodium Binding Sites List in 1tqy
Sodium binding site 2 out of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1092

b:38.2
occ:1.00
 O D:HOH1104 2.0 25.7 1.0
O D:HOH1100 2.4 25.5 1.0
O D:PRO13 2.4 17.7 1.0
O D:GLN50 2.5 20.1 1.0
O D:HOH1192 2.5 38.7 1.0
O D:GLY31 3.2 18.4 1.0
C D:PRO13 3.4 18.0 1.0
C D:GLN50 3.7 21.7 1.0
CA D:GLY31 3.7 20.8 1.0
C D:GLY31 3.8 20.7 1.0
CA D:PRO13 3.9 19.0 1.0
CB D:PRO13 4.1 18.4 1.0
O D:HOH1260 4.2 43.8 1.0
OD2 D:ASP52 4.3 32.9 1.0
O D:HOH1153 4.5 30.8 1.0
O D:HOH1225 4.5 42.2 1.0
N D:GLN50 4.5 20.1 1.0
N D:ASP52 4.5 23.6 1.0
N D:ASN14 4.5 17.5 1.0
CA D:ILE51 4.6 21.8 1.0
CA D:GLN50 4.6 21.9 1.0
N D:ILE51 4.6 21.6 1.0
CG D:ASP52 4.9 28.2 1.0
O D:HOH1166 4.9 35.4 1.0
CA D:ASN14 4.9 19.3 1.0

Sodium binding site 3 out of 4 in 1tqy

Go back to Sodium Binding Sites List in 1tqy
Sodium binding site 3 out of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1093

b:45.5
occ:1.00
 O F:GLN50 2.3 27.1 1.0
O F:HOH1112 2.3 34.5 1.0
O F:PRO13 2.4 25.6 1.0
O F:HOH1135 2.4 31.6 1.0
O F:HOH1154 2.5 42.6 1.0
O F:GLY31 3.1 25.2 1.0
C F:PRO13 3.4 24.7 1.0
C F:GLN50 3.5 27.3 1.0
CA F:GLY31 3.6 24.6 1.0
C F:GLY31 3.7 24.6 1.0
CA F:PRO13 3.9 24.1 1.0
CB F:PRO13 4.1 23.3 1.0
OD2 F:ASP52 4.2 31.8 1.0
N F:GLN50 4.2 26.7 1.0
CA F:GLN50 4.4 27.4 1.0
N F:ILE51 4.4 27.6 1.0
CA F:ILE51 4.5 26.6 1.0
N F:ASP52 4.5 27.4 1.0
N F:ASN14 4.6 23.4 1.0
O F:HOH1155 4.7 40.0 1.0
CG F:ASP52 4.8 30.2 1.0
O F:HOH1142 4.8 33.4 1.0
CB F:GLN50 4.8 26.4 1.0
N F:LEU32 4.9 25.0 1.0
O F:HOH1241 4.9 39.0 1.0
C F:ILE51 5.0 26.3 1.0

Sodium binding site 4 out of 4 in 1tqy

Go back to Sodium Binding Sites List in 1tqy
Sodium binding site 4 out of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1094

b:36.6
occ:1.00
 O H:GLN50 2.3 26.8 1.0
O H:HOH1125 2.4 28.1 1.0
O H:PRO13 2.4 22.5 1.0
O H:HOH1176 2.5 25.1 1.0
O H:GLY31 3.1 19.4 1.0
C H:PRO13 3.4 19.4 1.0
C H:GLN50 3.6 24.6 1.0
CA H:GLY31 3.8 19.9 1.0
C H:GLY31 3.8 19.5 1.0
CA H:PRO13 3.8 18.6 1.0
OD2 H:ASP52 4.0 31.2 1.0
CB H:PRO13 4.0 16.0 1.0
N H:GLN50 4.4 21.8 1.0
N H:ASP52 4.4 24.3 1.0
CA H:ILE51 4.4 24.0 1.0
N H:ILE51 4.5 24.3 1.0
CA H:GLN50 4.5 24.2 1.0
N H:ASN14 4.5 19.7 1.0
O H:HOH1167 4.6 32.3 1.0
CG H:ASP52 4.7 28.3 1.0
O H:HOH1141 4.8 35.3 1.0
O H:HOH1219 4.9 33.6 1.0
C H:ILE51 4.9 24.5 1.0
O H:HOH1138 4.9 34.6 1.0
CA H:ASN14 4.9 22.5 1.0
CB H:GLN50 4.9 24.4 1.0

Reference:

A.T.Keatinge-Clay, D.A.Maltby, K.F.Medzihradszky, C.Khosla, R.M.Stroud. An Antibiotic Factory Caught in Action. Nat.Struct.Mol.Biol. V. 11 888 2004.
ISSN: ISSN 1545-9993
PubMed: 15286722
DOI: 10.1038/NSMB808
Page generated: Sun Oct 6 22:41:46 2024

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