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Nickel in PDB 4r8z: Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center

Enzymatic activity of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center

All present enzymatic activity of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center:
3.1.4.1;

Protein crystallography data

The structure of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center, PDB code: 4r8z was solved by G.Giardina, F.Cutruzzolaa, S.Rinaldo, V.Stelitano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 93.984, 93.984, 78.469, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.3

Other elements in 4r8z:

The structure of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center (pdb code 4r8z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center, PDB code: 4r8z:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4r8z

Go back to Nickel Binding Sites List in 4r8z
Nickel binding site 1 out of 4 in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:23.9
occ:1.00
 O A:HOH516 2.0 23.1 1.0
O A:HOH501 2.0 20.7 1.0
NE2 A:HIS220 2.0 22.1 1.0
O A:HOH508 2.0 21.4 1.0
OD2 A:ASP221 2.1 20.8 1.0
NE2 A:HIS180 2.1 26.3 1.0
CE1 A:HIS220 2.9 21.3 1.0
CD2 A:HIS180 3.0 23.3 1.0
CD2 A:HIS220 3.1 20.3 1.0
CE1 A:HIS180 3.2 24.8 1.0
CG A:ASP221 3.2 18.1 1.0
CB A:ASP221 3.7 18.3 1.0
ND1 A:HIS220 4.0 20.2 1.0
OD1 A:ASP310 4.1 28.1 1.0
O A:HOH510 4.1 18.1 1.0
CG A:HIS220 4.2 19.3 1.0
O A:HOH597 4.2 43.4 1.0
CG A:HIS180 4.2 23.2 1.0
ND1 A:HIS180 4.2 23.2 1.0
OD1 A:ASP221 4.3 17.2 1.0
O A:HOH502 4.4 36.5 1.0
O A:HOH580 4.4 43.8 1.0
OD1 A:ASP171 4.5 42.1 1.0
O A:HOH514 4.5 21.2 1.0
NZ A:LYS224 4.6 34.8 1.0
OD2 A:ASP171 4.8 40.0 1.0

Nickel binding site 2 out of 4 in 4r8z

Go back to Nickel Binding Sites List in 4r8z
Nickel binding site 2 out of 4 in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:20.3
occ:1.00
 O A:HOH509 1.9 18.8 1.0
OD1 A:ASP221 2.0 17.2 1.0
NE2 A:HIS281 2.0 18.1 1.0
NE2 A:HIS282 2.1 20.9 1.0
O A:HOH510 2.1 18.1 1.0
NE2 A:HIS249 2.1 21.7 1.0
CE1 A:HIS281 2.9 18.4 1.0
CE1 A:HIS249 3.0 23.0 1.0
CE1 A:HIS282 3.0 22.3 1.0
CD2 A:HIS282 3.0 19.5 1.0
CD2 A:HIS281 3.1 19.6 1.0
CD2 A:HIS249 3.1 23.6 1.0
CG A:ASP221 3.1 18.1 1.0
OD2 A:ASP221 3.7 20.8 1.0
ND1 A:HIS281 4.1 18.9 1.0
ND1 A:HIS249 4.1 24.4 1.0
ND1 A:HIS282 4.1 23.1 1.0
CG A:HIS282 4.2 20.6 1.0
CG A:HIS281 4.2 17.1 1.0
CG A:HIS249 4.2 22.3 1.0
CD2 A:HIS220 4.4 20.3 1.0
CB A:ASP221 4.5 18.3 1.0
O A:HOH580 4.5 43.8 1.0
CE A:LYS224 4.6 31.4 1.0
OD2 A:ASP310 4.6 33.0 1.0
NZ A:LYS224 4.7 34.8 1.0
CA A:ASP221 4.8 18.4 1.0
O A:HOH531 4.9 36.9 1.0
O A:HIS220 4.9 18.9 1.0

Nickel binding site 3 out of 4 in 4r8z

Go back to Nickel Binding Sites List in 4r8z
Nickel binding site 3 out of 4 in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:20.3
occ:1.00
 O B:HOH502 1.9 15.0 1.0
O B:HOH501 2.0 19.6 1.0
OD1 B:ASP221 2.0 17.9 1.0
NE2 B:HIS281 2.0 16.8 1.0
NE2 B:HIS282 2.0 23.5 1.0
NE2 B:HIS249 2.1 23.0 1.0
CE1 B:HIS281 2.9 17.3 1.0
CE1 B:HIS249 2.9 25.6 1.0
CE1 B:HIS282 3.0 23.4 1.0
CD2 B:HIS282 3.0 20.3 1.0
CG B:ASP221 3.1 17.9 1.0
CD2 B:HIS281 3.1 19.1 1.0
CD2 B:HIS249 3.1 24.2 1.0
OD2 B:ASP221 3.6 16.8 1.0
ND1 B:HIS281 4.1 16.8 1.0
ND1 B:HIS249 4.1 25.3 1.0
ND1 B:HIS282 4.1 23.7 1.0
CG B:HIS282 4.1 21.3 1.0
CG B:HIS281 4.2 17.0 1.0
CG B:HIS249 4.2 22.9 1.0
CD2 B:HIS220 4.5 18.8 1.0
CB B:ASP221 4.5 18.0 1.0
OD2 B:ASP310 4.7 33.9 1.0
CE B:LYS224 4.7 39.6 1.0
NZ B:LYS224 4.7 43.3 1.0
CA B:ASP221 4.8 16.7 1.0
O B:HIS220 4.9 17.4 1.0
O B:HOH505 4.9 18.2 1.0

Nickel binding site 4 out of 4 in 4r8z

Go back to Nickel Binding Sites List in 4r8z
Nickel binding site 4 out of 4 in the Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of PA4781 Hd-Gyp Domain From Pseudomonas Aeruginosa at 2.2A Resolution Showing A Bi-Metallic Ni Ion Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:22.1
occ:1.00
 O B:HOH503 2.0 22.0 1.0
O B:HOH505 2.0 18.2 1.0
O B:HOH504 2.0 21.1 1.0
NE2 B:HIS220 2.0 17.9 1.0
OD2 B:ASP221 2.1 16.8 1.0
NE2 B:HIS180 2.1 23.5 1.0
CE1 B:HIS220 2.9 17.8 1.0
CD2 B:HIS180 3.0 22.3 1.0
CD2 B:HIS220 3.1 18.8 1.0
CE1 B:HIS180 3.1 21.4 1.0
CG B:ASP221 3.2 17.9 1.0
CB B:ASP221 3.8 18.0 1.0
O B:HOH501 4.0 19.6 1.0
ND1 B:HIS220 4.0 17.4 1.0
OD1 B:ASP310 4.1 27.3 1.0
CG B:HIS220 4.1 16.7 1.0
CG B:HIS180 4.1 23.4 1.0
ND1 B:HIS180 4.2 22.6 1.0
O B:HOH557 4.2 39.9 1.0
OD1 B:ASP221 4.3 17.9 1.0
O B:HOH522 4.3 37.2 1.0
OD1 B:ASP171 4.5 43.2 1.0
O B:HOH506 4.5 18.6 1.0
NZ B:LYS224 4.6 43.3 1.0
OD2 B:ASP171 4.8 46.2 1.0

Reference:

S.Rinaldo, A.Paiardini, V.Stelitano, P.Brunotti, L.Cervoni, S.Fernicola, C.Protano, M.Vitali, F.Cutruzzola, G.Giardina. The Structural Basis of Functional Diversification of Hd-Gyp Domain Revealed By the Pseudomonas Aeruginosa PA4781 Protein Displaying An Unselective Bi-Metallic Binding Site. J.Bacteriol. 2015.
ISSN: ESSN 1098-5530
PubMed: 25691523
DOI: 10.1128/JB.02606-14
Page generated: Wed Dec 16 01:34:44 2020

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