Atomistry » Sodium » PDB 1t4b-1u8r » 1tqy
Atomistry »
  Sodium »
    PDB 1t4b-1u8r »
      1tqy »

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: Tue Dec 15 05:36:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy