Atomistry » Cadmium » PDB 4evc-4l1l » 4j6y
Atomistry »
  Cadmium »
    PDB 4evc-4l1l »
      4j6y »

Cadmium in PDB 4j6y: Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence

Protein crystallography data

The structure of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence, PDB code: 4j6y was solved by A.D.Nikulin, V.Murina, N.Lekontseva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.60 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.562, 72.863, 107.275, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.9

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence (pdb code 4j6y). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence, PDB code: 4j6y:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 1 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:32.3
occ:0.49
ND1 A:HIS57 2.5 13.5 1.0
O B:HOH208 2.6 27.3 1.0
O A:HOH210 2.8 16.6 1.0
O A:HOH213 2.8 41.6 1.0
O B:HOH213 3.0 38.0 1.0
CG A:HIS57 3.4 15.6 1.0
CE1 A:HIS57 3.4 13.9 1.0
CB A:HIS57 3.6 16.1 1.0
CD1 A:PHE42 4.4 37.3 1.0
NE2 A:HIS57 4.6 17.5 1.0
CD2 A:HIS57 4.6 14.2 1.0
N A:HIS57 4.6 16.1 1.0
CA A:HIS57 4.7 16.8 1.0
CD1 A:TYR55 4.7 15.2 1.0
O A:HOH214 4.8 35.7 1.0
O B:HOH220 4.8 36.5 1.0

Cadmium binding site 2 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 2 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:55.5
occ:0.43
OD2 A:ASP9 2.6 53.5 1.0
O A:HOH208 2.8 39.6 1.0
OD1 A:ASP9 2.9 41.8 1.0
CG A:ASP9 3.0 40.5 1.0
O A:HOH209 4.1 33.5 1.0
CB A:ASP9 4.4 37.2 1.0
O A:HOH215 4.4 44.1 1.0

Cadmium binding site 3 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 3 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd101

b:37.2
occ:0.52
ND1 B:HIS57 2.5 17.7 1.0
O C:HOH210 2.6 31.3 1.0
O B:HOH215 2.8 33.8 1.0
O B:HOH207 2.9 19.8 1.0
O C:HOH204 3.0 33.5 1.0
CE1 B:HIS57 3.5 16.2 1.0
CG B:HIS57 3.5 16.9 1.0
CB B:HIS57 3.7 18.3 1.0
CD1 B:PHE42 4.4 32.5 1.0
O B:HOH213 4.6 38.0 1.0
NE2 B:HIS57 4.6 15.6 1.0
CD2 B:HIS57 4.6 16.8 1.0
O C:HOH213 4.7 39.9 1.0
CD1 B:TYR55 4.7 15.9 1.0
O C:HOH206 4.7 34.0 1.0
N B:HIS57 4.8 17.7 1.0
CA B:HIS57 4.8 16.0 1.0

Cadmium binding site 4 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 4 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd102

b:58.8
occ:0.57
OD2 B:ASP9 2.6 50.4 1.0
O B:HOH217 2.7 38.5 1.0
ND1 B:HIS5 2.7 43.6 0.7
OD1 B:ASP9 2.9 42.1 1.0
CG B:ASP9 3.1 39.3 1.0
CG B:HIS5 3.1 44.2 0.7
CE1 B:HIS5 3.3 41.2 0.7
CB B:HIS5 3.6 39.0 0.7
CD2 B:HIS5 3.8 42.5 0.7
NE2 B:HIS5 3.8 42.5 0.7
CG B:GLN41 4.2 46.6 1.0
CB B:ASP9 4.5 35.2 1.0
NE2 B:GLN41 4.9 56.8 1.0
CD B:GLN41 5.0 56.9 1.0

Cadmium binding site 5 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 5 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd101

b:30.3
occ:0.41
ND1 C:HIS57 2.6 14.8 1.0
O D:HOH212 2.6 35.5 1.0
O D:HOH211 2.7 30.6 1.0
O C:HOH211 2.7 33.8 1.0
O C:HOH201 2.9 20.5 1.0
O D:HOH214 3.2 38.7 1.0
CG C:HIS57 3.5 18.3 1.0
CE1 C:HIS57 3.6 15.7 1.0
CB C:HIS57 3.7 15.4 1.0
O C:HOH213 4.1 39.9 1.0
CD1 C:PHE42 4.4 36.0 1.0
O D:HOH213 4.5 35.2 1.0
NE2 C:HIS57 4.7 18.5 1.0
CD2 C:HIS57 4.7 14.9 1.0
CD1 C:TYR55 4.7 15.8 1.0
N C:HIS57 4.8 18.3 1.0
O C:HOH204 4.8 33.5 1.0
CA C:HIS57 4.9 16.1 1.0

Cadmium binding site 6 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 6 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd102

b:45.6
occ:0.70
OD2 C:ASP9 2.6 43.3 1.0
OD1 C:ASP9 2.7 36.8 1.0
O C:HOH212 2.7 40.4 1.0
ND1 C:HIS5 2.7 52.3 1.0
CG C:ASP9 3.0 35.3 1.0
CG C:HIS5 3.0 46.6 1.0
O C:HOH214 3.0 41.2 1.0
CE1 C:HIS5 3.3 45.3 1.0
CB C:HIS5 3.4 43.5 1.0
CD2 C:HIS5 3.7 51.4 1.0
NE2 C:HIS5 3.8 49.6 1.0
CB C:ASP9 4.4 28.9 1.0
CA C:HIS5 5.0 44.2 1.0

Cadmium binding site 7 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 7 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd101

b:29.8
occ:0.48
ND1 D:HIS57 2.5 14.2 1.0
O E:HOH209 2.6 28.6 1.0
O D:HOH201 2.7 15.8 1.0
O D:HOH216 2.8 34.3 1.0
O D:HOH217 2.8 39.3 1.0
CG D:HIS57 3.4 14.1 1.0
CE1 D:HIS57 3.5 13.2 1.0
CB D:HIS57 3.5 13.7 1.0
CD1 D:PHE42 4.5 37.5 1.0
CD2 D:HIS57 4.6 13.7 1.0
NE2 D:HIS57 4.6 11.4 1.0
N D:HIS57 4.6 16.5 1.0
CA D:HIS57 4.7 17.5 1.0
CD1 D:TYR55 4.7 14.6 1.0
O E:HOH210 4.8 33.6 1.0

Cadmium binding site 8 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 8 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd102

b:55.6
occ:0.41
OD1 D:ASP9 2.6 43.7 1.0
O D:HOH215 2.8 38.6 1.0
OD2 D:ASP9 2.8 46.5 1.0
CG D:ASP9 3.0 38.0 1.0
CB D:ASP9 4.5 30.4 1.0
OE1 D:GLN41 4.7 59.0 1.0
CA D:GLN41 4.8 25.0 1.0
CB D:GLN41 5.0 29.6 1.0

Cadmium binding site 9 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 9 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd101

b:29.5
occ:0.45
ND1 E:HIS57 2.5 18.7 1.0
O F:HOH209 2.6 30.2 1.0
O F:HOH208 2.6 35.1 1.0
O E:HOH211 2.9 15.5 1.0
CG E:HIS57 3.4 15.9 1.0
CE1 E:HIS57 3.5 12.0 1.0
CB E:HIS57 3.6 13.3 1.0
O F:HOH216 4.0 37.5 1.0
CD1 E:PHE42 4.6 33.3 1.0
NE2 E:HIS57 4.6 15.0 1.0
CD2 E:HIS57 4.6 14.9 1.0
CD2 E:TYR55 4.7 15.5 1.0
N E:HIS57 4.8 12.7 1.0
CA E:HIS57 4.8 14.9 1.0

Cadmium binding site 10 out of 12 in 4j6y

Go back to Cadmium Binding Sites List in 4j6y
Cadmium binding site 10 out of 12 in the Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Hfq From Pseudomonas Aeruginosa Crystallized in Gtp Presence within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd102

b:62.7
occ:0.60
OD2 E:ASP9 2.5 48.7 1.0
ND1 E:HIS5 2.8 47.7 1.0
O E:HOH215 2.8 38.5 1.0
OD1 E:ASP9 2.9 40.6 1.0
CG E:ASP9 3.1 38.8 1.0
O E:HOH205 3.1 33.4 1.0
CG E:HIS5 3.4 48.4 1.0
CE1 E:HIS5 3.5 48.4 1.0
CB E:HIS5 3.6 42.7 1.0
CD2 E:HIS5 4.3 46.8 1.0
NE2 E:HIS5 4.3 52.3 1.0
CB E:ASP9 4.5 30.5 1.0

Reference:

V.Murina, N.Lekontseva, A.Nikulin. Hfq Binds Ribonucleotides in Three Different Rna-Binding Sites. Acta Crystallogr.,Sect.D V. 69 1504 2013.
ISSN: ISSN 0907-4449
PubMed: 23897473
DOI: 10.1107/S090744491301010X
Page generated: Sat Dec 12 08:24:55 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy