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Zinc in PDB 4mmk: Q8A Hfq From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Q8A Hfq From Pseudomonas Aeruginosa, PDB code: 4mmk was solved by V.N.Murina, V.V.Filimonov, B.S.Melnik, M.Uhlein, U.Mueller, M.Weiss, A.D.Nikulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.31 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.590, 116.540, 66.620, 90.00, 119.98, 90.00
R / Rfree (%) 21.6 / 25.6

Other elements in 4mmk:

The structure of Q8A Hfq From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium (K) 8 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Q8A Hfq From Pseudomonas Aeruginosa (pdb code 4mmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Q8A Hfq From Pseudomonas Aeruginosa, PDB code: 4mmk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in 4mmk

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Zinc binding site 1 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:27.9
occ:1.00
ND1 A:HIS57 2.0 8.5 1.0
O B:HOH206 2.5 7.3 1.0
CE1 A:HIS57 2.8 11.6 1.0
O A:HOH212 3.0 11.9 1.0
CG A:HIS57 3.2 11.0 1.0
CB A:HIS57 3.7 9.2 1.0
NE2 A:HIS57 4.0 9.4 1.0
CD2 A:HIS57 4.2 12.4 1.0
O B:HOH223 4.3 16.9 1.0
CD1 A:TYR55 4.5 10.2 1.0
N A:HIS57 4.6 11.7 1.0
CA A:HIS57 4.8 9.3 1.0
O E:HOH229 5.0 16.1 1.0

Zinc binding site 2 out of 23 in 4mmk

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Zinc binding site 2 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:45.9
occ:1.00
OD1 A:ASP9 2.7 26.4 1.0
CD2 A:HIS5 2.8 34.2 1.0
CG A:HIS5 3.1 34.0 1.0
CB A:HIS5 3.4 31.8 1.0
OD2 A:ASP9 3.4 25.4 1.0
CG A:ASP9 3.4 24.3 1.0
NE2 A:HIS5 3.6 33.7 1.0
ND1 A:HIS5 4.0 37.9 1.0
CE1 A:HIS5 4.3 35.5 1.0
O A:HOH225 4.3 19.9 1.0
NZ A:LYS56 4.4 19.1 1.0
CA A:GLN41 4.4 18.1 1.0
CG A:GLN41 4.6 17.2 1.0
O B:SER2 4.7 24.7 1.0
CB A:GLN41 4.8 17.2 1.0
CB A:ASP9 4.9 30.2 1.0
O A:HIS5 4.9 27.4 1.0
CA A:HIS5 4.9 30.9 1.0

Zinc binding site 3 out of 23 in 4mmk

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Zinc binding site 3 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:28.5
occ:1.00
ND1 B:HIS57 2.0 10.6 1.0
O B:HOH204 2.2 18.4 1.0
O B:HOH219 2.5 14.8 1.0
CG B:HIS57 3.0 11.9 1.0
CE1 B:HIS57 3.0 12.7 1.0
O B:HOH222 3.1 7.4 1.0
CB B:HIS57 3.3 13.4 1.0
O B:HOH223 3.8 16.9 1.0
NE2 B:HIS57 4.1 8.9 1.0
CD2 B:HIS57 4.1 10.0 1.0
O E:HOH228 4.3 13.0 1.0
N B:HIS57 4.5 13.2 1.0
CA B:HIS57 4.5 12.6 1.0
CD1 B:TYR55 4.6 13.6 1.0
O E:HOH221 4.6 19.5 1.0
O C:HOH206 4.9 16.7 1.0

Zinc binding site 4 out of 23 in 4mmk

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Zinc binding site 4 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:32.5
occ:1.00
O B:HOH218 2.2 13.3 1.0
O B:HOH228 2.2 14.8 1.0
CG B:HIS5 3.3 22.6 1.0
CB B:HIS5 3.3 21.1 1.0
O C:SER2 3.4 28.1 1.0
CD2 B:HIS5 3.5 26.3 1.0
NZ B:LYS56 3.5 17.1 1.0
CE1 B:PHE39 3.7 25.4 1.0
ND1 B:HIS5 3.9 22.2 1.0
NE2 B:HIS5 4.2 24.7 1.0
CE1 B:HIS5 4.4 24.4 1.0
O B:HOH203 4.4 9.4 1.0
CD1 B:PHE39 4.5 23.7 1.0
CZ B:PHE39 4.5 23.4 1.0
CB B:ASP9 4.5 21.4 1.0
C C:SER2 4.6 30.4 1.0
CA B:GLN41 4.6 19.4 1.0
CA B:HIS5 4.8 23.4 1.0
CA B:ASP9 4.9 18.6 1.0
N B:ASP9 4.9 18.2 1.0
N B:GLN41 5.0 20.1 1.0
O B:ASP40 5.0 20.2 1.0

Zinc binding site 5 out of 23 in 4mmk

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Zinc binding site 5 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:25.8
occ:1.00
O C:HOH228 2.0 8.9 1.0
O C:HOH229 2.1 15.4 1.0
ND1 C:HIS57 2.2 11.3 1.0
O C:HOH230 2.7 16.0 1.0
CE1 C:HIS57 3.1 10.7 1.0
CG C:HIS57 3.2 13.8 1.0
CB C:HIS57 3.6 10.5 1.0
O C:HOH206 3.7 16.7 1.0
NE2 C:HIS57 4.2 8.8 1.0
CD1 C:TYR55 4.3 14.2 1.0
CD2 C:HIS57 4.3 11.2 1.0
N C:HIS57 4.4 13.4 1.0
O C:HOH215 4.6 6.8 1.0
CA C:HIS57 4.6 12.2 1.0
O C:PHE42 4.9 14.1 1.0
CB C:PHE42 4.9 17.1 1.0
CB C:TYR55 5.0 15.3 1.0

Zinc binding site 6 out of 23 in 4mmk

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Zinc binding site 6 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:36.0
occ:1.00
O C:HOH216 2.4 14.3 1.0
O C:HOH227 2.9 13.2 1.0
CD2 C:HIS5 3.4 28.1 1.0
CB C:HIS5 3.5 25.1 1.0
CG C:HIS5 3.6 27.2 1.0
NZ C:LYS56 3.7 15.4 1.0
OD1 C:ASP9 3.9 31.0 1.0
CB C:ASP9 3.9 26.9 1.0
CG C:ASP9 4.0 24.2 1.0
CE2 C:PHE39 4.3 21.0 1.0
CA C:ASP9 4.4 21.0 1.0
O B:HOH202 4.4 13.4 1.0
NE2 C:HIS5 4.5 28.2 1.0
N C:ASP9 4.5 21.6 1.0
OD2 C:ASP9 4.6 25.5 1.0
ND1 C:HIS5 4.7 32.4 1.0
CA C:GLN41 4.8 17.7 1.0
CD2 C:PHE39 4.8 21.7 1.0
O C:ASP40 4.9 20.8 1.0
CA C:HIS5 5.0 23.6 1.0
CB C:ALA8 5.0 21.6 1.0

Zinc binding site 7 out of 23 in 4mmk

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Zinc binding site 7 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:30.5
occ:1.00
O D:HOH225 1.9 13.3 1.0
O D:HOH203 2.0 10.2 1.0
O D:HOH209 2.0 14.1 1.0
ND1 D:HIS57 2.6 12.1 1.0
CG D:HIS57 3.4 14.8 1.0
CB D:HIS57 3.5 11.6 1.0
CE1 D:HIS57 3.6 11.6 1.0
O E:HOH201 4.0 12.8 1.0
CD1 D:PHE42 4.2 21.6 1.0
N D:HIS57 4.3 13.2 1.0
CA D:HIS57 4.5 12.8 1.0
CD2 D:HIS57 4.6 10.3 1.0
CD1 D:TYR55 4.6 16.5 1.0
NE2 D:HIS57 4.6 10.4 1.0
CE1 D:PHE42 4.7 20.8 1.0
O E:HOH204 4.9 19.9 1.0

Zinc binding site 8 out of 23 in 4mmk

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Zinc binding site 8 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:41.6
occ:1.00
O E:HOH209 2.2 22.3 1.0
O D:HOH217 2.4 19.2 1.0
O D:HOH221 2.8 13.3 1.0
ND1 D:HIS5 3.2 32.3 1.0
CE1 D:HIS5 3.7 29.5 1.0
CG D:HIS5 3.9 34.2 1.0
NZ D:LYS56 3.9 19.5 1.0
OD1 D:ASP9 4.1 32.7 1.0
CB D:ASP9 4.1 27.8 1.0
CB D:HIS5 4.3 27.1 1.0
CE2 D:PHE39 4.4 22.6 1.0
CA D:GLN41 4.4 17.5 1.0
CG D:ASP9 4.5 29.1 1.0
O E:SER2 4.5 26.9 1.0
NE2 D:HIS5 4.5 37.4 1.0
CA D:ASP9 4.6 23.5 1.0
CD2 D:HIS5 4.7 39.6 1.0
N D:ASP9 4.8 23.9 1.0
N D:GLN41 4.9 17.7 1.0
O D:ASP40 4.9 17.8 1.0
CD2 D:PHE39 4.9 22.1 1.0

Zinc binding site 9 out of 23 in 4mmk

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Zinc binding site 9 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:26.8
occ:1.00
O E:HOH233 1.8 19.4 1.0
O E:HOH232 1.9 11.2 1.0
ND1 E:HIS57 2.0 12.4 1.0
O E:HOH231 2.4 11.4 1.0
CE1 E:HIS57 2.7 10.8 1.0
CG E:HIS57 3.2 13.6 1.0
CB E:HIS57 3.8 12.4 1.0
NE2 E:HIS57 3.9 9.7 1.0
O E:HOH204 3.9 19.9 1.0
CD1 E:TYR55 4.0 11.6 1.0
CD2 E:HIS57 4.2 10.0 1.0
CD1 E:PHE42 4.3 21.4 1.0
O E:HOH202 4.5 10.9 1.0
CE1 E:TYR55 4.6 10.2 1.0
O F:HOH233 4.7 15.8 1.0
N E:HIS57 4.7 14.3 1.0
CB E:PHE42 4.8 21.4 1.0
O E:PHE42 4.9 13.3 1.0
CA E:HIS57 4.9 11.6 1.0
CG E:TYR55 5.0 10.9 1.0

Zinc binding site 10 out of 23 in 4mmk

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Zinc binding site 10 out of 23 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:38.3
occ:1.00
O E:HOH212 2.1 30.2 1.0
OD1 E:ASP9 2.1 29.5 1.0
O F:HOH213 2.3 20.3 1.0
O E:HOH230 2.7 20.6 1.0
CG E:ASP9 2.7 28.9 1.0
OD2 E:ASP9 2.8 26.9 1.0
CD2 E:HIS5 3.3 31.4 1.0
CB E:HIS5 3.4 25.9 1.0
CG E:HIS5 3.4 29.6 1.0
CB E:ASP9 4.1 23.8 1.0
NE2 E:HIS5 4.3 30.9 1.0
ND1 E:HIS5 4.4 27.5 1.0
O F:SER2 4.5 32.2 1.0
NZ E:LYS56 4.6 21.5 1.0
CA E:ASP9 4.7 22.9 1.0
CB F:SER2 4.8 27.7 1.0
CE1 E:HIS5 4.8 28.0 1.0
N E:ASP9 4.8 24.4 1.0
CA E:HIS5 4.8 24.1 1.0
CA E:GLN41 4.8 25.7 1.0

Reference:

V.N.Murina, B.S.Melnik, V.V.Filimonov, M.Uhlein, M.S.Weiss, U.Muller, A.D.Nikulin. Effect of Conserved Intersubunit Amino Acid Substitutions on Hfq Protein Structure and Stability. Biochemistry Mosc. V. 79 469 2014.
ISSN: ISSN 0006-2979
PubMed: 24954598
DOI: 10.1134/S0006297914050113
Page generated: Wed Dec 16 05:35:34 2020

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