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Sodium in PDB 4gcv: Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa, PDB code: 4gcv was solved by J.Choe, H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.897, 74.448, 230.492, 90.00, 90.03, 90.00
R / Rfree (%) 21.4 / 28.7

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa (pdb code 4gcv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa, PDB code: 4gcv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 4gcv

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Sodium binding site 1 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:34.6
occ:1.00
O A:HOH324 3.2 30.2 1.0
N A:TRP23 3.3 33.2 1.0
N A:TRP24 3.5 34.2 1.0
NH1 A:ARG56 3.5 64.2 1.0
CD1 A:TRP24 3.6 41.9 1.0
C A:GLY21 3.8 35.9 1.0
N A:GLU22 3.8 35.3 1.0
CB A:TRP23 3.8 34.0 1.0
CA A:TRP23 3.9 33.5 1.0
CA A:GLU18 3.9 41.0 1.0
C A:GLU22 4.0 33.7 1.0
CG A:GLU18 4.1 42.7 1.0
O A:GLY21 4.1 37.0 1.0
CA A:GLY21 4.1 36.6 1.0
CG A:TRP24 4.2 39.3 1.0
C A:TRP23 4.2 34.0 1.0
CB A:TRP24 4.3 37.5 1.0
O A:GLU18 4.3 42.6 1.0
CA A:GLU22 4.4 34.4 1.0
CB A:GLU18 4.4 41.6 1.0
NE1 A:TRP24 4.5 45.6 1.0
CA A:TRP24 4.5 36.3 1.0
O A:LEU17 4.6 37.2 1.0
C A:GLU18 4.7 41.4 1.0
N A:GLU18 4.7 39.4 1.0
CZ A:ARG56 4.8 64.8 1.0
N A:GLY21 4.9 37.2 1.0
CG A:TRP23 4.9 35.5 1.0
O A:GLU22 5.0 33.7 1.0

Sodium binding site 2 out of 11 in 4gcv

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Sodium binding site 2 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:31.1
occ:1.00
O B:HOH311 3.0 28.1 1.0
O B:HOH377 3.1 43.5 1.0
N B:TRP23 3.3 33.0 1.0
NH2 B:ARG56 3.6 59.6 1.0
N B:TRP24 3.6 32.3 1.0
CB B:TRP23 3.7 32.5 1.0
C B:GLY21 3.8 38.5 1.0
CD1 B:TRP24 3.8 45.5 1.0
N B:GLU22 3.9 36.0 1.0
CA B:TRP23 3.9 32.1 1.0
CA B:GLU18 3.9 40.0 1.0
O B:GLY21 4.1 38.8 1.0
C B:GLU22 4.1 33.7 1.0
CA B:GLY21 4.1 39.4 1.0
CG B:GLU18 4.1 43.9 1.0
C B:TRP23 4.3 30.8 1.0
O B:GLU18 4.3 40.5 1.0
NE B:ARG56 4.4 54.2 1.0
CA B:GLU22 4.4 35.4 1.0
CB B:GLU18 4.4 41.7 1.0
O B:LEU17 4.4 35.7 1.0
CZ B:ARG56 4.4 59.1 1.0
CB B:TRP24 4.4 36.8 1.0
CG B:TRP24 4.5 40.6 1.0
C B:GLU18 4.6 40.8 1.0
CA B:TRP24 4.6 34.4 1.0
NE1 B:TRP24 4.8 47.9 1.0
N B:GLU18 4.8 37.5 1.0
N B:GLY21 4.8 41.2 1.0
CG B:TRP23 4.8 33.3 1.0
C B:LEU17 5.0 35.0 1.0

Sodium binding site 3 out of 11 in 4gcv

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Sodium binding site 3 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:33.4
occ:1.00
N D:TRP23 3.2 41.8 1.0
O D:HOH306 3.3 30.4 1.0
N D:TRP24 3.7 41.6 1.0
NH1 D:ARG56 3.7 63.9 1.0
CB D:TRP23 3.7 40.7 1.0
CD1 D:TRP24 3.7 48.7 1.0
C D:GLY21 3.8 42.8 1.0
CA D:TRP23 3.8 40.5 1.0
N D:GLU22 3.9 41.7 1.0
CA D:GLU18 4.0 42.9 1.0
CA D:GLY21 4.0 42.7 1.0
O D:GLY21 4.1 44.0 1.0
C D:GLU22 4.2 41.6 1.0
CG D:GLU18 4.2 46.4 1.0
C D:TRP23 4.3 40.5 1.0
O D:GLU18 4.3 43.6 1.0
O D:LEU17 4.4 37.7 1.0
CA D:GLU22 4.5 42.3 1.0
CB D:GLU18 4.5 43.7 1.0
NE1 D:TRP24 4.5 52.3 1.0
CG D:TRP24 4.5 45.7 1.0
C D:GLU18 4.7 43.5 1.0
CB D:TRP24 4.7 43.5 1.0
CG D:TRP23 4.8 41.9 1.0
CA D:TRP24 4.8 41.7 1.0
N D:GLU18 4.8 41.0 1.0
N D:GLY21 4.8 42.6 1.0
CD1 D:TRP23 4.9 44.3 1.0
C D:LEU17 5.0 39.5 1.0
CZ D:ARG56 5.0 64.0 1.0

Sodium binding site 4 out of 11 in 4gcv

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Sodium binding site 4 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:31.5
occ:1.00
O E:HOH320 3.1 32.3 1.0
N E:TRP23 3.2 33.3 1.0
N E:TRP24 3.5 33.3 1.0
CD1 E:TRP24 3.6 40.6 1.0
NH1 E:ARG56 3.7 60.2 1.0
CB E:TRP23 3.7 34.1 1.0
C E:GLY21 3.8 36.5 1.0
N E:GLU22 3.8 35.4 1.0
CA E:GLU18 3.8 40.0 1.0
CA E:TRP23 3.9 33.2 1.0
CG E:GLU18 3.9 41.2 1.0
CA E:GLY21 4.0 37.3 1.0
C E:GLU22 4.1 33.4 1.0
O E:GLY21 4.1 37.4 1.0
C E:TRP23 4.2 33.2 1.0
O E:GLU18 4.2 41.8 1.0
CG E:TRP24 4.3 39.0 1.0
CB E:GLU18 4.3 40.3 1.0
CA E:GLU22 4.4 34.4 1.0
O E:LEU17 4.4 38.0 1.0
CB E:TRP24 4.4 36.6 1.0
NE1 E:TRP24 4.5 45.2 1.0
C E:GLU18 4.5 41.1 1.0
CA E:TRP24 4.6 35.2 1.0
N E:GLU18 4.7 38.8 1.0
N E:GLY21 4.7 38.6 1.0
C E:LEU17 4.9 38.0 1.0
CG E:TRP23 4.9 35.9 1.0
CZ E:ARG56 4.9 60.5 1.0
O E:GLU22 5.0 32.8 1.0

Sodium binding site 5 out of 11 in 4gcv

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Sodium binding site 5 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:31.9
occ:1.00
O F:HOH316 3.1 28.5 1.0
NH1 F:ARG56 3.3 60.3 1.0
N F:TRP23 3.3 35.9 1.0
N F:TRP24 3.7 35.0 1.0
C F:GLY21 3.7 38.7 1.0
CB F:TRP23 3.8 35.2 1.0
CD1 F:TRP24 3.8 46.4 1.0
NH2 F:ARG56 3.8 62.0 1.0
N F:GLU22 3.8 36.8 1.0
CA F:GLU18 3.9 36.7 1.0
CA F:TRP23 3.9 34.8 1.0
CZ F:ARG56 4.0 59.8 1.0
CA F:GLY21 4.0 39.2 1.0
O F:GLY21 4.1 39.2 1.0
C F:GLU22 4.1 36.1 1.0
CG F:GLU18 4.1 40.6 1.0
O F:GLU18 4.2 37.7 1.0
C F:TRP23 4.3 33.6 1.0
CB F:GLU18 4.4 38.4 1.0
O F:LEU17 4.4 32.9 1.0
CA F:GLU22 4.4 36.8 1.0
CG F:TRP24 4.5 41.0 1.0
CB F:TRP24 4.5 37.6 1.0
C F:GLU18 4.5 37.9 1.0
NE1 F:TRP24 4.7 49.1 1.0
CA F:TRP24 4.7 35.8 1.0
N F:GLU18 4.7 34.4 1.0
N F:GLY21 4.7 40.3 1.0
CG F:TRP23 4.9 35.0 1.0
C F:LEU17 4.9 32.8 1.0

Sodium binding site 6 out of 11 in 4gcv

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Sodium binding site 6 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:29.6
occ:1.00
O G:HOH306 3.1 28.3 1.0
N G:TRP23 3.3 41.1 1.0
N G:TRP24 3.6 42.0 1.0
CB G:TRP23 3.7 40.6 1.0
CD1 G:TRP24 3.7 49.5 1.0
C G:GLY21 3.8 42.1 1.0
N G:GLU22 3.8 40.9 1.0
CA G:TRP23 3.9 40.7 1.0
CA G:GLY21 4.0 42.6 1.0
O G:GLY21 4.1 42.4 1.0
CA G:GLU18 4.1 42.7 1.0
C G:GLU22 4.2 41.0 1.0
CG G:GLU18 4.2 46.9 1.0
C G:TRP23 4.2 40.6 1.0
O G:GLU18 4.3 43.5 1.0
O G:LEU17 4.4 38.0 1.0
CA G:GLU22 4.4 41.5 1.0
CG G:TRP24 4.4 46.3 1.0
CB G:TRP24 4.5 43.7 1.0
CA G:TRP24 4.6 42.3 1.0
NE1 G:TRP24 4.6 53.5 1.0
CB G:GLU18 4.7 43.5 1.0
C G:GLU18 4.8 43.7 1.0
N G:GLY21 4.8 43.6 1.0
CG G:TRP23 4.8 42.0 1.0
N G:GLU18 4.9 40.8 1.0

Sodium binding site 7 out of 11 in 4gcv

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Sodium binding site 7 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:31.2
occ:1.00
O H:HOH343 3.2 35.2 1.0
N H:TRP23 3.4 38.5 1.0
CD1 H:TRP24 3.5 43.3 1.0
N H:TRP24 3.6 40.1 1.0
NH1 H:ARG56 3.6 45.2 1.0
CB H:TRP23 3.6 39.9 1.0
N H:GLU22 3.8 39.7 1.0
C H:GLY21 3.9 41.6 1.0
CA H:GLU18 3.9 41.4 1.0
CA H:TRP23 3.9 39.5 1.0
CA H:GLY21 4.1 41.5 1.0
CG H:GLU18 4.1 44.0 1.0
C H:GLU22 4.2 39.1 1.0
C H:TRP23 4.2 39.9 1.0
CG H:TRP24 4.2 44.0 1.0
O H:GLU18 4.3 41.5 1.0
NE1 H:TRP24 4.4 45.7 1.0
CB H:TRP24 4.4 40.4 1.0
O H:GLY21 4.4 41.4 1.0
CB H:GLU18 4.5 41.4 1.0
CA H:GLU22 4.5 39.6 1.0
O H:LEU17 4.5 38.3 1.0
CA H:TRP24 4.6 40.4 1.0
N H:GLU18 4.6 39.8 1.0
C H:GLU18 4.6 41.7 1.0
CG H:TRP23 4.7 42.0 1.0
N H:GLY21 4.8 40.9 1.0
CZ H:ARG56 4.8 49.4 1.0
CD1 H:TRP23 4.9 44.3 1.0
C H:LEU17 4.9 39.7 1.0

Sodium binding site 8 out of 11 in 4gcv

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Sodium binding site 8 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:31.8
occ:1.00
O I:HOH358 2.9 24.8 1.0
N I:TRP23 3.4 39.0 1.0
NH1 I:ARG56 3.5 50.9 1.0
CD1 I:TRP24 3.5 45.9 1.0
N I:TRP24 3.5 40.2 1.0
N I:GLU22 3.7 41.0 1.0
C I:GLY21 3.7 42.2 1.0
CB I:TRP23 3.8 40.9 1.0
CA I:TRP23 3.9 39.9 1.0
CA I:GLU18 4.0 41.9 1.0
CA I:GLY21 4.1 41.8 1.0
O I:GLY21 4.1 41.6 1.0
CG I:GLU18 4.1 44.7 1.0
C I:GLU22 4.2 39.6 1.0
C I:TRP23 4.2 40.0 1.0
CG I:TRP24 4.2 45.0 1.0
NE1 I:TRP24 4.4 49.1 1.0
CB I:TRP24 4.4 41.5 1.0
CA I:GLU22 4.4 39.8 1.0
O I:GLU18 4.4 41.0 1.0
O I:LEU17 4.5 39.5 1.0
CB I:GLU18 4.5 42.5 1.0
CA I:TRP24 4.5 41.3 1.0
N I:GLU18 4.7 40.7 1.0
CZ I:ARG56 4.7 53.7 1.0
C I:GLU18 4.7 42.1 1.0
N I:GLY21 4.8 41.4 1.0
CG I:TRP23 4.8 43.0 1.0
C I:LEU17 4.9 40.2 1.0

Sodium binding site 9 out of 11 in 4gcv

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Sodium binding site 9 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:31.4
occ:1.00
O J:HOH305 3.0 27.8 1.0
N J:TRP23 3.1 41.6 1.0
CB J:TRP23 3.6 40.6 1.0
N J:TRP24 3.6 40.0 1.0
CD1 J:TRP24 3.7 47.1 1.0
CA J:TRP23 3.7 40.3 1.0
C J:GLY21 3.8 44.6 1.0
N J:GLU22 3.8 42.9 1.0
CA J:GLU18 4.0 43.7 1.0
CA J:GLY21 4.0 45.0 1.0
C J:GLU22 4.1 41.9 1.0
O J:GLY21 4.2 44.8 1.0
C J:TRP23 4.2 39.5 1.0
CG J:GLU18 4.2 46.1 1.0
O J:GLU18 4.3 45.5 1.0
CA J:GLU22 4.4 43.1 1.0
O J:LEU17 4.4 38.2 1.0
CG J:TRP24 4.5 44.1 1.0
NE1 J:TRP24 4.5 48.4 1.0
CB J:GLU18 4.6 43.9 1.0
CB J:TRP24 4.6 42.2 1.0
C J:GLU18 4.7 45.1 1.0
NH1 J:ARG56 4.7 62.6 1.0
CA J:TRP24 4.7 40.4 1.0
N J:GLU18 4.8 41.2 1.0
N J:GLY21 4.8 46.1 1.0
CG J:TRP23 4.8 41.6 1.0
C J:LEU17 4.9 39.8 1.0

Sodium binding site 10 out of 11 in 4gcv

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Sodium binding site 10 out of 11 in the Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of A Putative Transcription Factor (PA1374)From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na201

b:33.4
occ:1.00
O K:HOH321 3.2 26.9 1.0
NH2 K:ARG56 3.4 62.9 1.0
N K:TRP23 3.4 34.1 1.0
N K:TRP24 3.7 34.4 1.0
CD1 K:TRP24 3.8 45.8 1.0
CB K:TRP23 3.8 33.6 1.0
C K:GLY21 3.9 39.9 1.0
CA K:GLU18 3.9 38.6 1.0
N K:GLU22 3.9 37.5 1.0
CA K:TRP23 4.0 33.6 1.0
O K:GLY21 4.1 40.5 1.0
C K:GLU22 4.2 35.1 1.0
CA K:GLY21 4.2 41.1 1.0
CG K:GLU18 4.2 43.0 1.0
CZ K:ARG56 4.2 61.6 1.0
NE K:ARG56 4.3 56.3 1.0
O K:GLU18 4.3 39.4 1.0
C K:TRP23 4.4 32.8 1.0
CA K:GLU22 4.5 36.3 1.0
CB K:GLU18 4.5 40.2 1.0
CG K:TRP24 4.5 41.6 1.0
CB K:TRP24 4.5 37.7 1.0
O K:LEU17 4.5 33.0 1.0
C K:GLU18 4.6 39.8 1.0
NE1 K:TRP24 4.7 48.6 1.0
N K:GLU18 4.7 35.5 1.0
CA K:TRP24 4.7 35.6 1.0
N K:GLY21 4.8 42.3 1.0
CG K:TRP23 4.9 35.6 1.0

Reference:

H.Kim, J.Choe. The X-Ray Crystal Structure of PA1374 From Pseudomonas Aeruginosa, A Putative Oxidative-Stress Sensing Transcriptional Regulator. Biochem.Biophys.Res.Commun. V. 431 376 2013.
ISSN: ISSN 0006-291X
PubMed: 23337505
DOI: 10.1016/J.BBRC.2013.01.044
Page generated: Tue Dec 15 06:41:29 2020

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