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Chlorine 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:

Nickel (Ni) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4r8z

Go back to Chlorine Binding Sites List in 4r8z
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl403

b:40.2
occ:1.00
 CD A:ARG363 3.4 49.7 1.0
CG2 A:VAL360 3.9 23.6 1.0
CZ A:ARG186 4.1 72.6 1.0
CA A:VAL360 4.1 20.2 1.0
NE A:ARG186 4.2 67.0 1.0
CE1 A:TYR364 4.2 47.3 1.0
NH2 A:ARG186 4.3 89.6 1.0
NE A:ARG363 4.4 62.4 1.0
NH1 A:ARG186 4.4 71.6 1.0
CG A:GLU359 4.4 31.5 1.0
CB A:ARG363 4.5 34.1 1.0
CG A:ARG363 4.5 41.8 1.0
N A:VAL360 4.5 20.4 1.0
CD1 A:TYR364 4.6 38.9 1.0
O A:GLU359 4.6 21.1 1.0
CB A:VAL360 4.6 22.2 1.0
CD A:ARG186 4.6 58.7 1.0
C A:GLU359 4.7 21.7 1.0

Chlorine binding site 2 out of 2 in 4r8z

Go back to Chlorine Binding Sites List in 4r8z
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
B:Cl403

b:41.8
occ:1.00
 NE B:ARG363 3.4 53.9 1.0
CD B:ARG363 3.6 43.5 1.0
CG2 B:VAL360 4.1 23.7 1.0
CA B:VAL360 4.1 20.1 1.0
CE2 B:TYR364 4.1 28.2 1.0
CB B:ARG363 4.2 31.4 1.0
CG B:GLU359 4.3 39.7 1.0
O B:GLU359 4.4 23.7 1.0
N B:VAL360 4.4 22.5 1.0
CG B:ARG363 4.4 40.6 1.0
CD2 B:TYR364 4.5 25.9 1.0
C B:GLU359 4.5 25.5 1.0
CZ B:ARG363 4.6 63.5 1.0
CB B:VAL360 4.7 21.5 1.0
CD B:ARG186 4.8 35.5 1.0
NH2 B:ARG363 5.0 59.0 1.0
OE2 B:GLU359 5.0 46.0 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: Sat Dec 12 11:11:05 2020

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