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Zinc in PDB 1t8k: Crystal Structure of Apo Acyl Carrier Protein From E. Coli

Protein crystallography data

The structure of Crystal Structure of Apo Acyl Carrier Protein From E. Coli, PDB code: 1t8k was solved by X.Qiu, C.A.Janson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.510, 41.260, 62.480, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli (pdb code 1t8k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli, PDB code: 1t8k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1t8k

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Zinc binding site 1 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


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 Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:6.6
occ:1.00
N3 A:IMD301 2.0 6.8 1.0
OE2 A:GLU21 2.0 7.7 1.0
OE1 A:GLU21 2.4 8.4 1.0
CD A:GLU21 2.5 7.0 1.0
C2 A:IMD301 3.0 8.2 1.0
C4 A:IMD301 3.0 7.9 1.0
O A:HOH340 3.8 21.0 1.0
CG A:GLU21 4.0 7.6 1.0
N1 A:IMD301 4.1 9.9 1.0
C5 A:IMD301 4.2 9.4 1.0
NZ A:LYS18 4.3 9.2 1.0
CG A:LYS18 4.3 8.0 1.0
CG1 A:VAL17 4.5 8.4 1.0
N A:LYS18 4.6 6.8 1.0
CB A:VAL17 4.6 6.7 1.0
CA A:VAL17 4.8 6.5 1.0
CE A:LYS18 4.9 8.3 1.0
CB A:GLU21 5.0 7.4 1.0

Zinc binding site 2 out of 10 in 1t8k

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Zinc binding site 2 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


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 Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:7.5
occ:1.00
OE2 A:GLU58 1.9 10.6 1.0
N1 A:IMD304 2.0 10.2 1.0
NE2 A:HIS75 2.0 6.7 1.0
CD A:GLU58 2.7 9.6 1.0
OE1 A:GLU58 2.8 11.1 1.0
C2 A:IMD304 3.0 12.1 1.0
C5 A:IMD304 3.0 12.3 1.0
CE1 A:HIS75 3.0 6.5 1.0
CD2 A:HIS75 3.1 6.6 1.0
N3 A:IMD304 4.1 14.9 1.0
C4 A:IMD304 4.1 12.7 1.0
O A:HOH383 4.1 27.5 1.0
OH A:TYR71 4.1 9.8 1.0
CG A:GLU58 4.1 10.6 1.0
ND1 A:HIS75 4.1 6.2 1.0
CG A:HIS75 4.2 6.2 1.0
CE1 A:TYR71 4.2 9.0 1.0
CZ A:TYR71 4.5 8.1 1.0

Zinc binding site 3 out of 10 in 1t8k

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Zinc binding site 3 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


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 Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:10.7
occ:0.75
O A:HOH355 1.8 19.0 1.0
OE2 A:GLU5 2.0 11.9 1.0
CD A:GLU5 2.7 10.4 1.0
OE1 A:GLU5 2.7 12.2 1.0
CG A:GLU5 4.1 10.3 1.0
O A:HOH377 4.2 20.2 1.0

Zinc binding site 4 out of 10 in 1t8k

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Zinc binding site 4 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


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 Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:10.6
occ:0.75
OE2 A:GLU13 1.9 12.9 1.0
N3 A:IMD302 2.0 12.5 1.0
O A:HOH360 2.1 20.4 1.0
CD A:GLU13 2.6 10.6 1.0
OE1 A:GLU13 2.7 12.8 1.0
C2 A:IMD302 3.0 13.9 1.0
C4 A:IMD302 3.1 12.9 1.0
CG A:LYS9 3.9 14.1 1.0
CG A:GLU13 4.1 9.8 1.0
N1 A:IMD302 4.1 13.4 1.0
C5 A:IMD302 4.2 13.2 1.0
NZ A:LYS9 4.2 20.5 1.0
CE A:LYS9 4.5 20.7 1.0
O A:HOH373 4.6 24.0 1.0
O A:HOH371 4.7 21.0 1.0
CD A:LYS9 4.8 18.3 1.0
CB A:LYS9 4.9 9.3 1.0

Zinc binding site 5 out of 10 in 1t8k

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Zinc binding site 5 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:10.8
occ:0.70
OE1 A:GLU48 1.9 13.2 1.0
N3 A:IMD303 2.0 13.2 1.0
O A:HOH386 2.0 20.5 1.0
CD A:GLU48 2.9 11.0 1.0
C4 A:IMD303 3.0 13.9 1.0
C2 A:IMD303 3.0 14.4 1.0
OE2 A:GLU48 3.1 13.8 1.0
N1 A:IMD303 4.1 14.3 1.0
C5 A:IMD303 4.1 13.7 1.0
CG A:GLU48 4.2 9.8 1.0
O A:HOH352 4.8 26.3 1.0

Zinc binding site 6 out of 10 in 1t8k

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Zinc binding site 6 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:10.0
occ:0.40
O A:HOH343 1.9 20.7 1.0
OE1 A:GLU60 1.9 22.5 1.0
OD1 A:ASP56 2.0 11.0 0.6
O A:HOH328 2.2 17.4 1.0
O A:HOH361 2.7 16.4 0.5
CD A:GLU60 2.9 20.6 1.0
CG A:ASP56 3.0 10.1 0.6
OD2 A:ASP56 3.2 12.0 0.6
CG A:GLU60 3.3 16.0 1.0
OD1 A:ASP56 3.4 10.0 0.4
CG A:ASP56 3.5 8.4 0.4
CB A:ASP56 3.7 8.2 0.4
C2 A:IMD306 3.8 23.3 1.0
ZN A:ZN207 3.9 12.1 0.5
OD2 A:ASP56 4.0 9.4 0.4
OE2 A:GLU60 4.1 23.1 1.0
CB A:ASP56 4.3 9.8 0.6
N3 A:IMD306 4.3 22.6 1.0
O A:HOH389 4.4 19.1 1.0
O A:ASP56 4.5 9.2 0.4
O A:HOH405 4.6 12.4 0.5
O A:ASP56 4.7 8.6 0.6
CA A:ASP56 4.7 8.6 0.4
CB A:GLU60 4.7 13.6 1.0
CA A:ASP56 4.8 8.8 0.6
N1 A:IMD306 4.9 20.8 1.0
O A:HOH405 4.9 8.7 0.5

Zinc binding site 7 out of 10 in 1t8k

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Zinc binding site 7 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:12.1
occ:0.50
OD1 A:ASP56 1.9 10.0 0.4
N3 A:IMD305 2.0 16.9 1.0
N3 A:IMD306 2.0 22.6 1.0
O A:HOH389 2.1 19.1 1.0
CG A:ASP56 2.8 8.4 0.4
C2 A:IMD306 2.9 23.3 1.0
O A:HOH361 3.0 16.4 0.5
C2 A:IMD305 3.0 16.3 1.0
C4 A:IMD305 3.0 17.6 1.0
OD2 A:ASP56 3.0 9.4 0.4
C4 A:IMD306 3.1 19.9 1.0
OD1 A:ASP56 3.7 11.0 0.6
ZN A:ZN206 3.9 10.0 0.4
N1 A:IMD306 4.1 20.8 1.0
O A:HOH343 4.1 20.7 1.0
N1 A:IMD305 4.1 16.5 1.0
C5 A:IMD305 4.2 17.7 1.0
C5 A:IMD306 4.2 21.4 1.0
CB A:ASP56 4.2 8.2 0.4
CB A:ALA59 4.3 8.5 1.0
CA A:ASP56 4.8 8.6 0.4
CG A:ASP56 4.8 10.1 0.6
CG1 A:VAL40 4.8 13.3 1.0
CG1 A:VAL43 4.9 10.3 1.0
CA A:ASP56 4.9 8.8 0.6

Zinc binding site 8 out of 10 in 1t8k

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Zinc binding site 8 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:12.4
occ:0.35
O A:HOH406 1.5 11.2 0.5
O A:HOH380 1.8 11.8 1.0
O A:HOH390 1.9 24.9 1.0
O A:HOH406 2.1 14.2 0.5
O A:HOH392 2.3 20.8 1.0
OE1 A:GLU30 4.0 17.6 1.0
O A:HOH391 4.2 20.1 1.0
OE2 A:GLU30 4.3 11.8 1.0
CD A:GLU30 4.5 12.3 1.0

Zinc binding site 9 out of 10 in 1t8k

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Zinc binding site 9 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:15.2
occ:0.40
OE1 A:GLU41 1.8 16.2 1.0
O A:HOH378 2.4 21.5 1.0
CD A:GLU41 2.7 13.8 1.0
OE2 A:GLU41 2.9 15.3 1.0
O A:HOH395 2.9 15.2 1.0
CG A:GLU41 4.0 11.9 1.0
O A:HOH338 4.5 17.2 1.0
CD2 A:LEU37 5.0 10.4 1.0
CB A:LEU37 5.0 7.3 1.0

Zinc binding site 10 out of 10 in 1t8k

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Zinc binding site 10 out of 10 in the Crystal Structure of Apo Acyl Carrier Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Apo Acyl Carrier Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:14.6
occ:0.35
O A:HOH363 1.4 18.2 1.0
OE2 A:GLU20 2.1 16.0 1.0
O A:HOH370 2.1 23.0 1.0
CD A:GLU20 3.0 12.3 1.0
OE1 A:GLU20 3.4 14.2 1.0
O A:GLU20 4.2 10.1 1.0
CG A:GLU20 4.3 12.7 1.0
O A:HOH357 4.3 24.1 1.0
C A:GLU20 5.0 8.6 1.0

Reference:

X.Qiu, C.A.Janson. Structure of Apo Acyl Carrier Protein and A Proposal to Engineer Protein Crystallization Through Metal Ions. Acta Crystallogr.,Sect.D V. 60 1545 2004.
ISSN: ISSN 0907-4449
PubMed: 15333924
DOI: 10.1107/S0907444904015422
Page generated: Mon Jan 25 16:13:48 2021

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