Zinc in PDB 8rlk: Structure of the Apo Form of Pib-1 in An Orthorombic Space Group

Protein crystallography data

The structure of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group, PDB code: 8rlk was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.44 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.89, 101.452, 267.758, 90, 90, 90
R / Rfree (%) 19.1 / 23.5

Other elements in 8rlk:

The structure of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group (pdb code 8rlk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group, PDB code: 8rlk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8rlk

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Zinc binding site 1 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:51.8
occ:1.00
 OD2 A:ASP39 2.1 31.9 1.0
O A:HOH725 2.3 22.9 1.0
NE2 B:HIS243 2.3 33.5 1.0
O A:HOH721 2.3 19.2 1.0
CG A:ASP39 2.9 30.2 1.0
CD2 B:HIS243 3.2 25.8 1.0
CE1 B:HIS243 3.3 32.0 1.0
CB A:ASP39 3.4 27.7 1.0
O B:ARG247 3.8 28.3 1.0
O B:HOH631 3.8 32.8 1.0
OD1 A:ASP39 3.9 31.4 1.0
C B:ARG247 4.1 32.0 1.0
NE A:ARG36 4.1 28.0 1.0
ND1 B:HIS243 4.4 29.0 1.0
CG B:HIS243 4.4 28.2 1.0
CA B:ARG247 4.5 26.9 1.0
CG A:ARG36 4.6 26.4 1.0
N B:ILE248 4.7 26.5 1.0
CB A:ARG36 4.8 25.0 1.0
CD A:ARG36 4.8 26.5 1.0
NH2 A:ARG36 4.9 26.4 1.0
CZ A:ARG36 4.9 31.7 1.0
CA B:ILE248 4.9 26.7 1.0
CA A:ASP39 4.9 27.1 1.0
N A:ARG36 4.9 29.4 1.0

Zinc binding site 2 out of 7 in 8rlk

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Zinc binding site 2 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:54.1
occ:1.00
 OD2 C:ASP39 2.1 35.0 1.0
O C:HOH706 2.1 22.7 1.0
NE2 A:HIS243 2.3 30.8 1.0
O C:HOH710 2.3 25.5 1.0
CG C:ASP39 3.0 30.7 1.0
CE1 A:HIS243 3.2 32.1 1.0
CD2 A:HIS243 3.2 33.2 1.0
CB C:ASP39 3.4 28.6 1.0
O A:ARG247 3.8 35.2 1.0
O A:HOH677 3.9 32.5 1.0
C A:ARG247 4.1 32.0 1.0
OD1 C:ASP39 4.1 37.7 1.0
NE C:ARG36 4.1 36.2 1.0
ND1 A:HIS243 4.3 30.2 1.0
CG A:HIS243 4.4 31.6 1.0
CG C:ARG36 4.4 31.3 1.0
CA A:ARG247 4.5 31.9 1.0
N A:ILE248 4.6 32.6 1.0
CB C:ARG36 4.6 28.6 1.0
N C:ARG36 4.7 30.2 1.0
CA A:ILE248 4.7 28.6 1.0
CD C:ARG36 4.7 32.0 1.0
NH2 C:ARG36 4.9 35.3 1.0
C A:ILE248 4.9 33.3 1.0
CZ C:ARG36 4.9 33.5 1.0
CA C:ASP39 5.0 29.2 1.0
CD2 C:LEU43 5.0 24.9 1.0

Zinc binding site 3 out of 7 in 8rlk

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Zinc binding site 3 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:68.7
occ:1.00
 OD2 B:ASP157 2.2 45.4 1.0
O B:HOH725 2.3 35.6 1.0
O B:HOH724 2.5 37.0 1.0
CG B:ASP157 3.0 37.3 1.0
OD1 B:ASP157 3.1 39.7 1.0
CG B:GLN169 3.8 43.9 1.0
CD B:GLN169 4.3 42.5 1.0
CB B:ASP157 4.4 36.3 1.0
NE2 B:GLN169 4.6 39.0 1.0
N B:LYS158 4.7 37.7 1.0
N B:GLY170 4.7 35.5 1.0
CG B:PRO155 4.8 36.1 1.0
CB B:PRO155 4.8 36.5 1.0
OE1 B:GLN169 4.9 44.9 1.0
C B:ASP157 4.9 38.3 1.0
CB B:GLN169 4.9 41.2 1.0

Zinc binding site 4 out of 7 in 8rlk

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Zinc binding site 4 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:55.2
occ:1.00
 OD2 B:ASP39 1.9 36.1 1.0
O B:HOH714 2.2 22.2 1.0
O B:HOH722 2.3 18.9 1.0
NE2 C:HIS243 2.3 33.4 1.0
CG B:ASP39 2.9 30.0 1.0
CD2 C:HIS243 3.2 26.5 1.0
CE1 C:HIS243 3.3 31.6 1.0
CB B:ASP39 3.4 26.9 1.0
O C:ARG247 3.6 34.6 1.0
O C:HOH627 3.9 35.6 1.0
C C:ARG247 4.0 34.0 1.0
OD1 B:ASP39 4.0 30.4 1.0
NE B:ARG36 4.2 34.7 1.0
CG C:HIS243 4.4 32.7 1.0
ND1 C:HIS243 4.4 34.6 1.0
CA C:ARG247 4.4 31.2 1.0
CG B:ARG36 4.4 30.9 1.0
N C:ILE248 4.6 26.4 1.0
CB B:ARG36 4.7 30.0 1.0
N B:ARG36 4.7 28.5 1.0
CD B:ARG36 4.8 30.7 1.0
CA C:ILE248 4.8 30.2 1.0
CA B:ASP39 4.9 29.2 1.0
CD2 B:LEU43 4.9 30.6 1.0
CB C:ARG247 5.0 32.3 1.0

Zinc binding site 5 out of 7 in 8rlk

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Zinc binding site 5 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:62.4
occ:1.00
 OD2 D:ASP39 1.8 36.8 1.0
O D:HOH714 2.2 23.0 1.0
O D:HOH699 2.5 35.8 1.0
CG D:ASP39 2.9 31.6 1.0
CB D:ASP39 3.5 29.7 1.0
OD1 D:ASP39 4.0 34.0 1.0
NE D:ARG36 4.2 35.4 1.0
CG D:ARG36 4.4 31.1 1.0
CD D:ARG36 4.7 30.6 1.0
CB D:ARG36 4.8 29.4 1.0
N D:ARG36 4.8 31.6 1.0

Zinc binding site 6 out of 7 in 8rlk

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Zinc binding site 6 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:59.3
occ:1.00
 OD2 E:ASP39 2.0 41.3 1.0
O E:HOH694 2.2 26.5 1.0
O E:HOH691 2.2 32.4 1.0
CG E:ASP39 3.0 36.1 1.0
CB E:ASP39 3.5 38.2 1.0
OD1 E:ASP39 4.1 41.4 1.0
NE E:ARG36 4.2 41.2 1.0
CG E:ARG36 4.5 38.4 1.0
N E:ARG36 4.8 33.2 1.0
CD E:ARG36 4.8 40.6 1.0
CB E:ARG36 4.8 36.4 1.0
NH2 E:ARG36 4.9 38.1 1.0
CZ E:ARG36 4.9 42.4 1.0
CD2 E:LEU43 5.0 33.4 1.0
CA E:ASP39 5.0 37.8 1.0

Zinc binding site 7 out of 7 in 8rlk

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Zinc binding site 7 out of 7 in the Structure of the Apo Form of Pib-1 in An Orthorombic Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Apo Form of Pib-1 in An Orthorombic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:56.2
occ:1.00
 OD2 F:ASP39 2.0 35.2 1.0
O F:HOH646 2.2 19.2 1.0
O F:HOH647 2.4 27.4 1.0
CG F:ASP39 2.9 35.7 1.0
CB F:ASP39 3.4 30.2 1.0
OD1 F:ASP39 3.9 38.7 1.0
NE F:ARG36 4.2 34.2 1.0
CG F:ARG36 4.4 32.4 1.0
CD F:ARG36 4.7 32.1 1.0
N F:ARG36 4.7 34.9 1.0
CB F:ARG36 4.8 35.4 1.0
CD2 F:LEU43 4.9 31.9 1.0
CA F:ASP39 4.9 34.3 1.0

Reference:

F.J.Medrano, S.Hernando-Amado, J.L.Martinez, A.Romero. A New Type of Class C Beta-Lactamases Defined By Pib-1. A Metal-Dependent Carbapenem-Hydrolyzing Beta-Lactamase, From Pseudomonas Aeruginosa: Structural and Functional Analysis. Int.J.Biol.Macromol. 34298 2024.
ISSN: ISSN 0141-8130
PubMed: 39097051
DOI: 10.1016/J.IJBIOMAC.2024.134298
Page generated: Thu Oct 31 10:32:02 2024

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