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Zinc in PDB 6bnc: Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex

Protein crystallography data

The structure of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex, PDB code: 6bnc was solved by P.J.Stogios, E.Evdokimova, Z.Wawrzak, A.Savchenko, W.F.Anderson, K.J.Satchell, A.Joachimiak, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.051, 154.246, 66.392, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 15.3

Other elements in 6bnc:

The structure of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex (pdb code 6bnc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex, PDB code: 6bnc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bnc

Go back to Zinc Binding Sites List in 6bnc
Zinc binding site 1 out of 4 in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:9.6
occ:1.00
 O A:HOH918 1.9 8.5 1.0
OD2 A:ASP498 1.9 9.8 1.0
OE2 A:GLU273 2.0 9.2 1.0
NE2 A:HIS499 2.0 8.6 1.0
OE1 A:GLU273 2.6 9.7 1.0
CD A:GLU273 2.6 9.6 1.0
CG A:ASP498 2.8 9.2 1.0
OD1 A:ASP498 3.0 9.7 1.0
CD2 A:HIS499 3.0 9.5 1.0
CE1 A:HIS499 3.0 7.6 1.0
N A:ALA315 3.3 9.3 1.0
ZN A:ZN602 3.4 11.2 1.0
CB A:ALA315 3.8 9.2 1.0
NE2 A:HIS511 3.9 9.4 1.0
CA A:ALA315 3.9 8.4 1.0
ND1 A:HIS499 4.0 8.8 1.0
C A:SER314 4.0 12.2 1.0
CG A:HIS499 4.0 8.6 1.0
CG A:GLU273 4.1 8.6 1.0
OG1 A:THR274 4.1 10.9 1.0
CB A:ASP498 4.2 8.9 1.0
CD2 A:HIS429 4.2 12.7 1.0
O A:HOH890 4.2 12.5 1.0
O A:HOH800 4.2 10.3 1.0
CA A:SER314 4.3 11.4 1.0
NE2 A:HIS429 4.4 14.7 1.0
CE1 A:HIS511 4.4 10.3 1.0
CD2 A:HIS511 4.5 10.2 1.0
N A:THR274 4.5 8.2 1.0
CA A:GLU273 4.7 9.6 1.0
OH B:TYR338 4.8 12.9 1.0
CB A:GLU273 4.9 9.3 1.0
O A:SER314 4.9 11.0 1.0

Zinc binding site 2 out of 4 in 6bnc

Go back to Zinc Binding Sites List in 6bnc
Zinc binding site 2 out of 4 in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:11.2
occ:1.00
 OH B:TYR338 1.9 12.9 1.0
O A:HOH918 2.0 8.5 1.0
NE2 A:HIS511 2.1 9.4 1.0
NE2 A:HIS429 2.1 14.7 1.0
CZ B:TYR338 2.9 15.8 1.0
CE1 A:HIS511 3.0 10.3 1.0
CE1 A:HIS429 3.0 14.9 1.0
CD2 A:HIS429 3.0 12.7 1.0
CD2 A:HIS511 3.1 10.2 1.0
CE1 B:TYR338 3.2 32.0 1.0
ZN A:ZN601 3.4 9.6 1.0
O A:HOH890 3.8 12.5 1.0
NE2 A:HIS499 4.0 8.6 1.0
OE2 A:GLU273 4.0 9.2 1.0
ND1 A:HIS429 4.1 13.3 1.0
CE2 B:TYR338 4.1 23.7 1.0
ND1 A:HIS511 4.1 11.7 1.0
CG A:HIS429 4.1 11.8 1.0
O B:HOH852 4.1 14.8 1.0
CG A:HIS511 4.2 10.0 1.0
N A:ALA315 4.3 9.3 1.0
CE1 A:HIS499 4.4 7.6 1.0
CD1 B:TYR338 4.6 30.4 1.0
CA A:SER314 4.6 11.4 1.0
CD A:GLU273 4.6 9.6 1.0
OE1 A:GLU273 4.7 9.7 1.0
CB A:SER314 4.7 11.3 1.0
O B:HOH730 4.9 35.1 1.0
OG1 A:THR274 4.9 10.9 1.0
O A:HOH1081 4.9 54.1 1.0
O A:HOH1084 5.0 21.6 1.0
C A:SER314 5.0 12.2 1.0

Zinc binding site 3 out of 4 in 6bnc

Go back to Zinc Binding Sites List in 6bnc
Zinc binding site 3 out of 4 in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:9.8
occ:1.00
 O B:HOH927 1.9 8.4 1.0
OD2 B:ASP498 2.0 8.9 1.0
OE2 B:GLU273 2.0 9.1 1.0
NE2 B:HIS499 2.0 8.4 1.0
OE1 B:GLU273 2.6 9.5 1.0
CD B:GLU273 2.6 9.0 1.0
CG B:ASP498 2.7 8.4 1.0
OD1 B:ASP498 2.9 8.8 1.0
CE1 B:HIS499 3.0 7.7 1.0
CD2 B:HIS499 3.0 9.1 1.0
N B:ALA315 3.4 9.5 1.0
ZN B:ZN602 3.4 10.6 1.0
CB B:ALA315 3.8 10.5 1.0
CA B:ALA315 3.9 8.0 1.0
NE2 B:HIS511 4.0 8.7 1.0
ND1 B:HIS499 4.0 8.5 1.0
CG B:HIS499 4.0 8.6 1.0
C B:SER314 4.1 11.2 1.0
OG1 B:THR274 4.1 11.1 1.0
CG B:GLU273 4.1 8.8 1.0
CB B:ASP498 4.2 8.6 1.0
CD2 B:HIS429 4.2 12.5 1.0
O B:HOH909 4.2 11.3 1.0
O B:HOH792 4.2 10.3 1.0
CA B:SER314 4.3 9.5 1.0
NE2 B:HIS429 4.4 10.3 1.0
N B:THR274 4.5 8.4 1.0
CE1 B:HIS511 4.5 10.1 1.0
CD2 B:HIS511 4.5 9.3 1.0
CA B:GLU273 4.7 7.6 1.0
OH A:TYR338 4.7 13.6 1.0
CB B:GLU273 4.9 8.8 1.0
O B:SER314 4.9 11.9 1.0

Zinc binding site 4 out of 4 in 6bnc

Go back to Zinc Binding Sites List in 6bnc
Zinc binding site 4 out of 4 in the Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Intrinsic Colistin Resistance Enzyme Icr(Mc) From Moraxella Catarrhalis, Catalytic Domain, THR315ALA Mutant Di- Zinc and Peg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:10.6
occ:1.00
 OH A:TYR338 1.9 13.6 1.0
O B:HOH927 2.0 8.4 1.0
NE2 B:HIS511 2.0 8.7 1.0
NE2 B:HIS429 2.1 10.3 1.0
CZ A:TYR338 2.8 14.8 1.0
CE1 B:HIS429 3.0 11.8 1.0
CE1 B:HIS511 3.0 10.1 1.0
CD2 B:HIS429 3.0 12.5 1.0
CE2 A:TYR338 3.1 32.5 1.0
CD2 B:HIS511 3.1 9.3 1.0
ZN B:ZN601 3.4 9.8 1.0
O B:HOH909 3.8 11.3 1.0
NE2 B:HIS499 4.0 8.4 1.0
OE2 B:GLU273 4.0 9.1 1.0
ND1 B:HIS429 4.1 12.2 1.0
CG B:HIS429 4.1 9.8 1.0
O A:HOH867 4.1 13.6 1.0
CE1 A:TYR338 4.1 24.9 1.0
ND1 B:HIS511 4.1 11.0 1.0
CG B:HIS511 4.2 9.0 1.0
N B:ALA315 4.3 9.5 1.0
CE1 B:HIS499 4.4 7.7 1.0
CD2 A:TYR338 4.5 33.8 1.0
CA B:SER314 4.6 9.5 1.0
CD B:GLU273 4.6 9.0 1.0
OE1 B:GLU273 4.6 9.5 1.0
CB B:SER314 4.6 11.0 1.0
OG1 B:THR274 4.9 11.1 1.0
O A:HOH731 4.9 31.3 1.0
C B:SER314 5.0 11.2 1.0

Reference:

P.J.Stogios, G.Cox, H.L.Zubyk, E.Evdokimova, Z.Wawrzak, G.D.Wright, A.Savchenko. Substrate Recognition By A Colistin Resistance Enzyme From Moraxella Catarrhalis. Acs Chem. Biol. V. 13 1322 2018.
ISSN: ESSN 1554-8937
PubMed: 29631403
DOI: 10.1021/ACSCHEMBIO.8B00116
Page generated: Mon Oct 28 18:09:36 2024

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