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Sodium in PDB 4iqz: The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli

Enzymatic activity of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli

All present enzymatic activity of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli:
2.7.7.6;

Protein crystallography data

The structure of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli, PDB code: 4iqz was solved by V.Bhandari, S.N.Sugiman-Marangos, H.S.Naushad, R.S.Gupta, M.S.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.99 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 198.060, 65.630, 81.292, 90.00, 108.92, 90.00
R / Rfree (%) 20.3 / 24

Other elements in 4iqz:

The structure of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli also contains other interesting chemical elements:

Iodine (I) 56 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli (pdb code 4iqz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli, PDB code: 4iqz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4iqz

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Sodium binding site 1 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na316

b:21.8
occ:1.00
 O A:TRP109 2.2 14.9 1.0
O A:HOH451 2.2 33.2 1.0
OD1 A:ASN108 2.3 20.9 1.0
O A:SER37 2.3 15.8 1.0
OG A:SER37 2.5 23.2 1.0
O A:HOH455 2.7 17.6 1.0
CB A:SER37 3.1 21.4 1.0
C A:SER37 3.2 14.3 1.0
C A:TRP109 3.3 19.0 1.0
N A:TRP109 3.4 15.8 1.0
CG A:ASN108 3.4 19.6 1.0
CA A:SER37 3.8 17.8 1.0
O A:HOH520 3.9 42.4 1.0
CA A:TRP109 4.0 16.2 1.0
O A:HOH521 4.1 34.8 1.0
ND2 A:ASN108 4.1 20.6 1.0
CD A:PRO111 4.1 29.6 1.0
N A:SER38 4.2 16.5 1.0
C A:ASN108 4.3 16.2 1.0
O A:ALA34 4.3 24.9 1.0
CA A:ASN108 4.4 17.5 1.0
N A:ASP110 4.4 18.9 1.0
CB A:SER38 4.5 19.9 1.0
CB A:ASN108 4.5 19.6 1.0
CA A:ASP110 4.6 22.0 1.0
CA A:SER38 4.7 17.9 1.0
N A:PRO111 4.7 24.8 1.0
N A:SER37 4.7 22.1 1.0
C A:ASP110 4.9 19.4 1.0

Sodium binding site 2 out of 7 in 4iqz

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Sodium binding site 2 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na317

b:22.5
occ:1.00
 O A:HOH456 2.2 24.8 1.0
O A:VAL56 2.3 15.0 1.0
OG A:SER205 2.4 17.9 1.0
OG A:SER206 2.5 15.9 1.0
O A:SER206 2.6 12.1 1.0
N A:SER206 3.4 16.7 1.0
C A:SER206 3.4 11.6 1.0
C A:VAL56 3.5 14.3 1.0
CB A:SER206 3.6 16.2 1.0
CB A:SER205 3.7 16.5 1.0
CA A:SER206 3.7 14.7 1.0
CG2 A:VAL55 3.9 25.9 1.0
CA A:ASN57 3.9 14.2 1.0
C A:SER205 4.0 20.1 1.0
O A:HOH424 4.0 27.1 1.0
CB D:PRO191 4.2 31.1 1.0
N A:ASN57 4.2 13.9 1.0
OG A:SER121 4.3 19.4 1.0
CA A:SER205 4.4 19.2 1.0
C A:ASN57 4.5 16.8 1.0
O A:HOH438 4.5 42.5 1.0
O D:HOH406 4.5 42.9 1.0
N A:VAL56 4.6 19.9 1.0
CA A:VAL56 4.6 20.8 1.0
N A:GLY207 4.7 11.4 1.0
O A:SER205 4.7 19.7 1.0
CG D:PRO191 4.7 27.2 1.0
O A:HOH497 4.7 54.5 1.0
O A:ASN57 4.9 17.6 1.0
I A:IOD306 4.9 45.7 0.5
N A:SER58 5.0 17.9 1.0

Sodium binding site 3 out of 7 in 4iqz

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Sodium binding site 3 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na314

b:24.4
occ:1.00
 OG B:SER205 2.3 25.4 1.0
O B:VAL56 2.4 23.1 1.0
O B:SER206 2.4 23.1 1.0
OG B:SER206 2.5 25.4 1.0
O A:HOH406 2.5 29.6 1.0
N B:SER206 3.2 21.9 1.0
C B:SER206 3.3 22.2 1.0
CA B:SER206 3.5 22.1 1.0
CB B:SER206 3.5 23.9 1.0
C B:VAL56 3.6 22.2 1.0
CB B:SER205 3.6 26.8 1.0
C B:SER205 3.8 25.6 1.0
CB A:PRO191 3.9 23.3 1.0
CG2 B:VAL55 4.0 32.2 1.0
CA B:ASN57 4.2 17.7 1.0
CA B:SER205 4.2 27.4 1.0
N B:ASN57 4.3 17.4 1.0
OG B:SER121 4.4 25.9 1.0
O A:HOH449 4.4 33.2 1.0
N B:VAL56 4.5 25.8 1.0
O B:SER205 4.5 25.4 1.0
N B:GLY207 4.5 21.6 1.0
CA B:VAL56 4.6 21.9 1.0
C B:ASN57 4.6 18.6 1.0
CA A:PRO191 4.7 24.8 1.0
O B:HOH491 4.9 59.0 1.0

Sodium binding site 4 out of 7 in 4iqz

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Sodium binding site 4 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na312

b:35.9
occ:1.00
 O C:VAL86 2.4 20.3 1.0
OG1 C:THR69 2.6 25.7 1.0
O C:SER66 2.7 21.7 1.0
N C:THR69 2.9 15.9 1.0
CB C:THR69 3.0 22.2 1.0
C C:ARG67 3.4 26.0 1.0
N C:ASN68 3.4 27.0 1.0
OE1 D:GLU199 3.5 25.9 1.0
CA C:ARG67 3.5 25.5 1.0
CA C:THR69 3.5 21.2 1.0
C C:SER66 3.5 22.8 1.0
C C:VAL86 3.6 21.2 1.0
N C:TYR88 3.7 25.7 1.0
C C:PRO87 3.7 23.6 1.0
CG2 C:ILE64 3.7 24.1 1.0
N C:ARG67 3.9 24.7 1.0
C C:ASN68 4.0 30.9 1.0
O C:ARG67 4.0 26.3 1.0
CA C:PRO87 4.0 27.2 1.0
O C:PRO87 4.1 21.2 1.0
OG C:SER66 4.2 24.4 1.0
CA C:ASN68 4.2 30.3 1.0
N C:PRO87 4.2 23.3 1.0
CA C:TYR88 4.3 24.4 1.0
CD D:GLU199 4.4 24.2 1.0
I C:IOD310 4.4 24.7 1.0
CG2 C:THR69 4.4 19.6 1.0
O C:THR69 4.4 24.0 1.0
C C:THR69 4.5 21.7 1.0
CA C:VAL86 4.7 24.7 1.0
CA C:SER66 4.7 23.0 1.0
CB C:VAL86 4.8 24.1 1.0
CB C:ARG67 4.9 27.9 1.0
OE2 D:GLU199 4.9 23.6 1.0
CB C:SER66 4.9 26.0 1.0
N C:VAL86 5.0 26.8 1.0

Sodium binding site 5 out of 7 in 4iqz

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Sodium binding site 5 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na313

b:26.2
occ:1.00
 OG C:SER205 2.2 25.8 1.0
O C:VAL56 2.3 23.5 1.0
O C:SER206 2.3 24.4 1.0
OG C:SER206 2.5 23.6 1.0
O C:HOH464 2.7 23.0 1.0
N C:SER206 3.1 24.8 1.0
C C:SER206 3.2 23.1 1.0
CB C:SER205 3.4 26.7 1.0
CA C:SER206 3.4 22.7 1.0
C C:VAL56 3.4 18.8 1.0
CB C:SER206 3.5 22.7 1.0
C C:SER205 3.6 23.9 1.0
CA C:ASN57 4.0 21.9 1.0
CA C:SER205 4.0 24.8 1.0
CG2 C:VAL55 4.1 27.8 1.0
N C:ASN57 4.1 20.3 1.0
O C:SER205 4.3 23.5 1.0
O C:HOH405 4.3 27.3 1.0
N C:VAL56 4.4 20.5 1.0
N C:GLY207 4.4 22.6 1.0
CA C:VAL56 4.5 21.3 1.0
OG C:SER121 4.5 30.3 1.0
C C:ASN57 4.6 21.1 1.0
O C:HOH412 4.7 39.6 1.0
I C:IOD301 4.9 30.4 1.0

Sodium binding site 6 out of 7 in 4iqz

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Sodium binding site 6 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na314

b:30.3
occ:1.00
 O D:VAL56 2.3 27.7 1.0
O D:SER206 2.4 20.2 1.0
OG D:SER206 2.5 21.3 1.0
O D:HOH417 2.5 40.8 1.0
OG D:SER205 2.5 25.5 1.0
C D:SER206 3.2 21.8 1.0
N D:SER206 3.3 27.5 1.0
C D:VAL56 3.5 25.2 1.0
CB D:SER206 3.5 21.9 1.0
CA D:SER206 3.5 23.5 1.0
CB D:SER205 3.6 27.6 1.0
CG2 D:VAL55 3.7 30.4 1.0
C D:SER205 3.9 29.3 1.0
CB C:PRO191 4.1 29.0 1.0
CA D:ASN57 4.1 26.4 1.0
N D:ASN57 4.2 24.5 1.0
CA D:SER205 4.3 28.2 1.0
N D:VAL56 4.4 28.4 1.0
N D:GLY207 4.5 20.8 1.0
CA D:VAL56 4.5 27.7 1.0
O D:HOH416 4.6 36.8 1.0
OG D:SER121 4.6 29.8 1.0
C D:ASN57 4.7 28.7 1.0
O D:SER205 4.7 29.2 1.0
O C:HOH424 4.8 43.7 1.0
CG C:PRO191 4.9 25.8 1.0
CA D:GLY207 5.0 18.8 1.0

Sodium binding site 7 out of 7 in 4iqz

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Sodium binding site 7 out of 7 in the The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na305

b:55.6
occ:1.00
 OG E:SER206 2.3 34.7 1.0
O E:VAL56 2.4 27.2 1.0
OG E:SER205 2.4 46.9 1.0
O E:SER206 2.4 33.3 1.0
N E:SER206 2.9 31.9 1.0
C E:SER206 3.2 31.2 1.0
CA E:SER206 3.2 32.4 1.0
CB E:SER206 3.3 33.2 1.0
C E:VAL56 3.6 25.6 1.0
C E:SER205 3.6 35.2 1.0
CB E:SER205 3.6 44.5 1.0
CA E:ASN57 4.0 26.0 1.0
CA E:SER205 4.2 40.2 1.0
N E:ASN57 4.3 24.8 1.0
CG2 E:VAL55 4.3 38.2 1.0
O E:SER205 4.3 31.1 1.0
N E:GLY207 4.4 30.7 1.0
C E:ASN57 4.6 27.7 1.0
CA E:VAL56 4.7 25.1 1.0
N E:VAL56 4.7 26.9 1.0
N E:SER58 5.0 37.5 1.0

Reference:

V.Bhandari, S.N.Sugiman-Marangos, H.S.Naushad, R.S.Gupta, M.S.Junop. The Crystal Structure of A Large Insert in Rna Polymerase (Rpoc) Subunit From E. Coli To Be Published.
Page generated: Tue Dec 15 06:45:10 2020

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